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15th international conference on dna computing and molecular programming

作者： Garzon, Max H. Wong, Tit-Yee Phan, Vinhthuy Univ Memphis Memphis TN 38152 USA

ISBN: (纸本)9783642106033

the codeword design problem is an important problem in dna computing and its applications. Several theoretical analyses as well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. these solutions have, in turn, suggested new applications to dna-based indexing and natural language processing, in addition to the obvious applications to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of dna-based indexing for biological applications and show that dna noncrosshybridizing (nxh) sets can be successfully applied to infer ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. these phylogenies are solidly established and well accepted in biology. the new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it can be scaled up to newly available universal dna chips readily available both in vitro and in silica. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in dna spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform reference system, a veritable and comprehensive "Atlas of Life", as it is or as it could be on earth.

关键词： dna codeword design noncrosshybridizing oligonucleotide bases phylogenetic analysis genomic signatures dna chips 16S rRNA tree of life

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EWOD based microfluidic system with coplanar electrodes for parallel dna ligation of ultramicro volume

EWOD based microfluidic system with coplanar electrodes for ...

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TRANSDUCERS 2009 - 15th international conference on Solid-State Sensors, Actuators and Microsystems

作者： Lin, H.C. Liu, Y.J. Yao, D.J. Chang, H.Y. Institute of NanoEngineering and MicroSystems National Tsing Hua University Hsinchu Taiwan Institute of Molecular Medicine National Tsing Hua University Hsinchu Taiwan

ISBN: (纸本)9781424441938

this paper reports the completion of a parallel ultramicro-volume dna ligation processes using a coplanar electrode type of electrowetting-on- dielectric (EWOD) microfluidic system. the droplets, containing dna, a ligation enzyme and a multi-salt reaction buffer, served to complete the ligation using a developed EWOD system. In order to reduce the effect from environment, so the concept of core-shell droplet was used in this study. Droplets of ultramicro volume (0.3L) were successfully generated from reservoirs between one plate with coplanar electrodes and another plate with a hydrophobic surface free of electrodes. In one successful cloning, the total usage of reagents in an ultramicro-volume EWOD chip was 2.1L;no volume was wasted, in comparison with 85% waste with the standard protocol (15L). the results also show that the four parallel dna ligation processes were accomplished without damage to the chip surface and without biomaterial annulment. ©2009 IEEE.

关键词： Drops

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dna computing and molecular programming: Preface

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2009年 5877 LNCS卷

作者： Deaton, Russell Suyama, Akira Dept. of Computer Science and Computer Engineering JBHT - CSCE 504 1 University of Arkansas Fayetteville AR 72701 United States Department of Life Science Graduate School of Arts and Sciences University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan

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dna computing Hardware Design and Application to Multiclass Cancer Data

DNA Computing Hardware Design and Application to Multiclass ...

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15th international conference on Neuro-Information Processing

作者： Choi, Sun-Wook Lee, Chong Ho Inha Univ Sch Informat & Commun Engn Inchon 402751 South Korea

ISBN: (纸本)9783642030390

dna computing-inspired pattern classification based on the hypernetwork model is a novel approach to pattern classification problems. the hypernetwork model has been shown to be a powerful tool for analysis of gene expression data. However, the ordinary hypernetwork model has limitations, such as using only binary data and operating sequentially. In this paper, we propose an improved method to process four-level data and to implement a hardware circuit for dna computing-inspired pattern classifier. We show simulation results of multi-class cancer classification from the dna microarray data for performance evaluation. Experiments show competitive diagnosis results over other conventional machine learning algorithms. Our four-level data approach also results stable and improved performance over the ordinary hypernetwork model.

关键词： Diseases

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Rapid detection of bacterial cell from whole blood: Integration of dna sample preparation into single micro-PCR chip

Rapid detection of bacterial cell from whole blood: Integrat...

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TRANSDUCERS 2009 - 15th international conference on Solid-State Sensors, Actuators and Microsystems

作者： Hwang, K.Y. Jung, S.Y. Han, J.I. Kim, Y.R. Kim, J.H. Samsung Electronics Co. Ltd. Yongin-Si Gyeonggi-Do Korea Republic of College of Life Sciences and Biotechnology KyungHee University Yongin-Si Gyeonggi-Do Korea Republic of

ISBN: (纸本)9781424441938

A novel bacterial cell detection method from whole blood has been developed for molecular diagnostics. Functional integration of dna sample preparation into polymerase chain reaction (PCR) chip enabled detection of pathogenic bacterial cells in a single microchip. Surface-modified micropillars possessing affinity for bacterial cells were fabricated inside a PCR chip, and reaction conditions were optimized to render the microchip with high surface-to-volume ratio PCR-compatible. After bacterial cells were captured on the micropillars from whole blood and PCR inhibitors were washed out, PCR mixture was injected to allow real-time amplification of dna extracted from the isolated cells. Cell enrichment effect produced by volume reduction from large initial sample to small micro-PCR chip chamber led to increased detection sensitivity. Moreover, the developed method from sample preparation to detection of bacterial cells took less than one hour. these results demonstrated that the surface-modified pillar-packed microchip would be a practical approach for integration into Lab-on-a-chip (LOC) to enable point-of-care genetic analysis. ©2009 IEEE.

关键词： dna

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Dynamics of total, linear nonintegrated, and integrated HIV-1 dna in vivo and in vitro

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JOURNAL OF INFECTIOUS DISEASES 2008年第3期197卷 411-419页

作者： Koelsch, Kersten K. Liu, Lin Haubrich, Richard May, Susanne Havlir, Diane Guenthard, Huldrych F. Ignacio, Caroline C. Campos-Soto, Paula Little, Susan J. Shafer, Robert Robbins, Gregory K. D'Aquila, Richard T. Kawano, Yuji Young, Karen Dao, Phillip Spina, Celsa A. Richman, Douglas D. Wong, Joseph K. Univ Calif San Diego San Diego CA 92103 USA Vet Affairs Med Ctr La Jolla CA USA Univ Calif San Francisco San Francisco CA 94143 USA Stanford Univ Stanford CA 94305 USA Roche Mol Diagnost Alameda CA USA Harvard Univ Sch Med Boston MA 02115 USA Vanderbilt Univ Nashville TN USA Univ Zurich Hosp Div Infect Dis & Hosp Epidemiol Zurich Switzerland

Background. In patients infected with human immunodeficiency virus type 1 (HIV-1), HIV-1 dna persists during highly active antiretroviral treatment, reflecting long-lived cellular reservoirs of HIV-1. Recent studies report an association between HIV-1 dna levels, disease progression, and treatment outcome. However, HIV-1 dna exists as distinct molecular forms that are not distinguished by conventional assays. Methods. We analyzed HIV-1 RNA levels in plasma, CD4 cell counts, and levels of integrated and nonintegrated HIV-1 dna in peripheral blood mononuclear cells (PBMCs) from patients with early or chronic infection before and during antiretroviral treatment. We also studied HIV-1 dna decay in primary CD4 T cells infected in vitro. HIV-1 dna was analyzed using an assay that is unaffected by the location of HIV-1 integration sites. Results. HIV-1 RNA levels and total HIV-1 dna levels decayed rapidly in patients during receipt of suppressive antiretroviral therapy. Ratios of total HIV-1 dna levels to integrated HIV-1 dna levels were high before initiation of therapy but diminished during therapy. Levels of linear nonintegrated HIV-1 dna decayed rapidly in vitro (t(1/2) = 1-4.8 days). Conclusion. Total HIV-1 dna decays rapidly with suppression of virus replication in vivo. Clearance of HIV-1 dna during the first 6 months of therapy reflects a disproportionate loss of nonintegrated HIV-1 dna genomes, suggesting that levels of total HIV-1 dna in PBMCs after prolonged virus suppression largely represent integrated HIV-1 genomes.

关键词： HIV infections RESEARCH COMMUNICABLE diseases EPIDEMIOLOGY -- Research IMMUNOGENETICS DISEASES -- Causes & theories of causation

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GENETIC VARIATION AND POPULATION STRUCTURE IN BIG BROWN BATS (EPTESICUS FUSCUS): IS FEMALE DISPERSAL IMPORTANT?

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JOURNAL OF MAMMALOGY 2008年第6期89卷 1411-1420页

作者： Vonhof, Maarten J. Strobeck, Curtis Fenton, M. Brock Western Michigan Univ Dept Biol Sci Kalamazoo MI 49008 USA Univ Alberta Dept Biol Sci Edmonton AB T6G 2E9 Canada Univ Western Ontario Dept Biol London ON N6A 5B7 Canada

the prevailing view of the social organization of temperate bats is that maternity colonies represent aggregations of philopatric females connected to other maternity colonies via male-mediated gene flow. However, few studies have examined fine-scale patterns of matrilineal diversity within and between colonies, and clear evidence of strict philopatry generally is lacking. Here we examine patterns of genetic diversity within and among maternity colonies of big brown bats (Eptesicus fuscus) using both microsatellites and mitochondrial sequences. As in other temperate bats, we observed no differentiation among colonies using nuclear microsatellite markers (F-ST: -0.0001-0.012;99.5% of variation within populations). Overall, there was significant mitochondrial structure among colonies, but the pattern was complex, With low (DST values among some populations and high values among others (range: -0.007-0.491). three groups of colonies were identified in nested analyses of molecular variance, among which variation was high (21.2% of the variation), but within which variation was low (1.4%), and significant matrilineal isolation by distance (r = 0.56, P = 0.012) was observed. Maternity colonies were characterized by high haplotype diversity (h (X) over bar = 0.83) and a large number of matrilines (5-15) per colony. Furthermore, we observed a small number of maternities within colonies, and only 5-17% ((X) over bar = 9%) of the sampled females were found roosting with a mother or daughter. Our results are inconsistent with strict female philopatry, and suggest that female-mediated gene flow may occur among some maternity colonies. the potential for female dispersal in temperate bats prompts new and exciting questions about social and dispersal dynamics.

关键词： bats dispersal Eptesicus fuscus genetic population structure microsatellites mitochondrial dna parentage philopatry

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Exploring dna translocation through a nanopore via a multiscale Lattice-Boltzmann molecular-Dynamics methodology

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international JOURNAL OF MODERN PHYSICS C 2007年第4期18卷 685-692页

作者： Melchionna, Simone Fyta, Marla G. Kaxiras, Efthimios Succi, Sauro Univ Roma La Sapienza Dept Phys I-00185 Rome Italy Harvard Univ Dept Phys Cambridge MA 02138 USA Harvard Univ Dept Phys Div Engn & Appl Sci Cambridge MA 02138 USA CNR Ist Applicaz Calcolo I-00161 Rome Italy

A multiscale approach is used to simulate the translocation of dna through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of various initial configurations and lengths we map the probability distibutions of the passage times of the dna through the nanopore. A scaling law behavior for the most probable of these times with respect to length is derived, and shown to exhibit an exponent that is in a good agreement with the experimental findings. the essential features of the dna dynamics as it passes through the pore are explored.

关键词： multiscale modeling translocation hydrodynamics dna

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Solving Planted-Motif Problem A New Approach

Solving Planted-Motif Problem A New Approach

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international conference on Advanced computing and Communications (ADCOM)

作者： Pankaj Agarwal Sanjeev K. Yadav A.P. Shukla Department of Computer Science & Engineering Krishna Institute of Engineering and Technology Ghaziabad Uttar Pradesh India

this paper presents a new method for solving planted-motif problem, which is a well-known motif-finding problem in the field of computational molecular biology. Motif-finding problem is considered to be a NP-complete problem and constant research is being carried out to solve the stated problem using some deterministic algorithm in polynomial time. this paper is an attempt to solve the plated-motif problem using a deterministic method in polynomial time. the method presented is not an exact algorithm but the probability of success is quite high. Significance of the technique is its simplicity and time efficiency. the presented technique is implemented as one of the modules in our general-purpose tool by the name "Sequence Comparison and Analysis Tool" for solving a number of sequence comparison problems encountered in the field of bioinformatics.

关键词： Sequences Proteins dna RNA Polynomials Gene expression Pulse width modulation Greedy algorithms Sampling methods Computer science

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Biclustering Expression Data Using Node Addition Algorithm

Biclustering Expression Data Using Node Addition Algorithm

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international conference on Advanced computing and Communications (ADCOM)

作者： B. Borah D.K. Bhattacharyya Department of Computer Science and Engineering Tezpur University Tezpur India

Biclustering algorithms simultaneously cluster both rows and columns. this type of algorithms are applied to gene expression data analysis to find a subset of genes that exhibit similar expression pattern under a subset of conditions. Cheng and Church introduced the mean squared residue measure to capture the coherence of a subset of genes over a subset of conditions. they provided a set of heuristic algorithms based primarily on node deletion to find one bicluster or a set of biclusters after masking discovered biclusters with random values. Masking of discovered biclusters with random values interferes with discovery of high quality biclusters. We provide an efficient node addition algorithm to find a set of biclusters without the need of masking discovered biclusters. Initialized with a gene and a subset of conditions, a bicluster is extended by adding more genes and conditions. thus it provides facility to study individual genes, besides generating a large number of biclusters with different initializations. Biclusters with lower or higher scores within a specified limit can be generated by parameter setting. Use of incremental method of computing score makes the algorithm faster.

关键词： Gene expression Clustering algorithms Data analysis Heuristic algorithms Biology computing Fluctuations Computer science Data engineering Coherence dna

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