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检索条件"任意字段=15th International Conference on DNA Computing and Molecular Programming, DNA 15"

共 143 条记录，以下是91-100 订阅

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Agarose droplet microfluidic approach for molecular evolution of aptamers

Agarose droplet microfluidic approach for molecular evolutio...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Zhang, Wenhua Zhang, Weiyun Liu, Zhiyuan Li, Cong Jenkins, Gareth Yang, Chaoyong James Department of Chemical Biology Xiamen University Xiamen 361005 China

ISBN: (纸本)9781618395955

We have developed a novel method for efficient screening of affinity ligands (aptamers) from a complex single-stranded dna (ssdna) library by employing single molecule emulsion PCR based on agarose droplet microfluidic technology . Statistically diluted ssdna of a pre-enriched library was encapsulated into individual uniform agarose droplets for highly efficient single molecule emulsion PCR to generate clonal agarose beads. the binding affinity of amplified ssdna from each clonal agarose bead was tested via high-throughput flow cytometry. dna clones with high binding affinity and low dissociation constant (Kd) were chosen as potential aptamers and can be directly used for downstream biomedical applications. Copyright © (2011) by the Chemical and Biological Microsystems Society.

关键词： dna

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dna sequence visualization and feature extraction

DNA sequence visualization and feature extraction

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15th World Multi-conference on Systemics, Cybernetics and Informatics, WMSCI 2011

作者： Trifas, Monica Francia III, Guillermo Murdock, Chris Mann, Crystal Mayo, Quention Wiggins, Ashley Department of Mathematical Computing and Information Sciences Jacksonville State University 700 Pelham Road N. Jacksonville AL 36265 United States Department of Biology Jacksonville State University 700 Pelham Road N. Jacksonville AL 36265 United States

ISBN: (纸本)9781936338306

the 2010-2011 Jacksonville State University (JSU)-CREU project's focus is on problems in the area of dna sequence visualization. Specialized software (BLAST, FASTA, etc) are utilized for identifying and aligning nucleotide sequences obtained from sample data provided by the Biology department at JSU. the project team designed and implemented a visualization system that takes, as input, the output of the specialized dna-analysis software. the output of the visualization system is a visual display of the text-formatted input data. To complete the JSU-CREU project, biology students will be asked to complete a survey on the usability of this and other visualization systems. the results of the survey will be statistically analyzed and an analysis report will be written.

关键词： dna sequences

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molecular screening on a chip by dna-displayed protein microarray

Molecular screening on a chip by DNA-displayed protein micro...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Biyani, M. Kobayashi, R. Sato, S. Ichiki, T. School of Engineering University of Tokyo Tokyo Japan Core Research of Evolutional Science and Technology JST Japan

ISBN: (纸本)9781618395955

Self-assembled and spatially addressable protein microarrays are poised to become a central proteomics technology. However, it has been burdened with issues of reproducibility and standardization mainly due to the less availability of functionalized surface chemistry. Here, a microintaglio printing-based system is described that relies on coupling cdna display technique with scaffolded dna origami to print in situ-synthesized protein microarray on gold surface. A microarray of genotypes encoding the green fluorescent protein variants was patterned on gold-thiol surface using a three-way junctions (TWJs) formed from two single-stranded oligonucleotides with self-complementary sticky ends and a PDMS micromold comprising an array of uniformly arranged 4 μm-diameter holes at a density of 10,000 per mm 2.

关键词： Oligonucleotides

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Point-mutation detection of mitochondrial dna by using microfluidic systems

Point-mutation detection of mitochondrial DNA by using micro...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Chang, Chen-Min Chiou, Li-Fang Shieh, Dar-Bin Lee, Gwo-Bin Department of Engineering Science Taiwan Institute of Oral Medicine National Cheng Kung University Tainan 701 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu 300 Taiwan

ISBN: (纸本)9781618395955

Mitochondrial disorders are a group of complex and heterogeneous diseases that may be caused by molecular defects in mitochondrial genomes. Pathogenic mitochondrial dna (mtdna) mutations are usually present in the heteroplasmic form. the degree of mtdna mutation heteroplasmy varies among different tissues. thus, it is important to detect and quantify the degree of mutation heteroplasmy of mtdna. Currently, more than 100 pathogenic mtdna point-mutations have been documented and new ones are still being extensively explored. Among them, A3243G mutation, which causes the myopathy encephalopathy lactic acidosis and stroke (MELAS) syndrome and diabetes, attracts considerable interest recently. In this study, a new microfluidic system capable of point-mutation detection of mtdna has been demonstrated. the entire process including cell lysis, enzyme digestion, amplification of target fragment of mtdna and optical detection can be automatically performed. Experimental results showed that the point-mutation of mtdna can be successfully detected. Copyright © (2011) by the Chemical and Biological Microsystems Society.

关键词： Microfluidics

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Design of molecular-based network robots-Toward the environmental control

Design of molecular-based network robots-Toward the environm...

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2011 11th IEEE international conference on Nanotechnology, NANO 2011

作者： Hirabayashi, Miki Nishikawa, Akio Tanaka, Fumiaki Hagiya, Masami Kojima, Hiroaki Oiwa, Kazuhiro Advanced ICT Research Institute National Institute of Information and Communications Technology Hyogo Japan Hosei University Tokyo Japan Department of Computer Science Grad School of Information Science and Technology University of Tokyo Tokyo Japan

ISBN: (纸本)9781457715143

Toward the intelligent control of internal and external environments, we present an idea of the sequence design for the network formation of dna-based nanorobots. We already developed a dna nanomachine that has the potential ability of producing a functional molecule called aptamer when bacterial two-component signal transduction systems are detected. Here we have succeeded in demonstrating the network formation based on the sticky-end programming of dna modules. By combining the aptamer transcription function with the network formation ability, we can implement various missions in dna nanomacines. the network design is essential to keep the appropriate density, configurations and functions to carry out target missions. We expect that the network of dna nanorobots make a contribution to realize the effective regulation of microorganisms to promote environmental preservation and health maintenance. © 2011 IEEE.

关键词： dna

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A three-Dimensional Model of the Yeast Genome 15th

A Three-Dimensional Model of the Yeast Genome

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15th Annual international conference on Research in Computational molecular Biology

作者： Noble, William Duan, Zhi-jun Andronescu, Mirela Schutz, Kevin McIlwain, Sean Kim, Yoo Jung Lee, Choli Shendure, Jay Fields, Stanley Blau, C. Anthony Univ Washington Seattle WA 98195 USA

ISBN: (纸本)9783642200359

Layered on top of information conveyed by dna sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate dna elements co-localize into functionally defined aggregates or factories for transcription and dna replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. the map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between dna sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early dna replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

关键词： dna sequences

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Spiking dna neural trees with applications to conceptual design

Spiking DNA neural trees with applications to conceptual des...

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international conference on Computer Supported Cooperative Work in Design

作者： Xiyu Liu Hongyan Zhang School of Management and Economics Shandong Normal University Jinan Shandong China

this paper presents a design evaluation technique by dna neural trees. We propose a new dna tree computing model to represent a neural tree. the optimization of the neural tree is performed by the dna operations. this is a new technique different with other evolutionary optimization methods and scale well for large optimizations. Finally, we present an application framework in conceptual architectural design.

关键词： Vegetation dna Optimization Educational institutions Connectors Electron tubes Biochemistry

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Optimally Orienting Physical Networks 15th

Optimally Orienting Physical Networks

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RECOMB - 15th Annual international conference on Research in Computational molecular Biology

作者： Silverbush, Dana Elberfeld, Michael Sharan, Roded Tel Aviv Univ Blavatnik Sch Comp Sci IL-69978 Tel Aviv Israel Univ Lubeck Inst Theoret Comp Sci Lubeck Germany

ISBN: (纸本)9783642200359

In a network orientation problem, one is given a mixed graph, consisting of directed and undirected edges, and a set of source-target vertex pairs. the goal is to orient the undirected edges so that a maximum number of pairs admit a directed path from the source to the target. this NP-complete problem arises in the context of analyzing physical networks of protein-protein and protein-dna interactions. While the latter are naturally directed from a transcription factor to a gene, the direction of signal flow in protein-protein interactions is often unknown or cannot be measured en masse. One then tries to infer this information by using causality data on pairs of genes such that the perturbation of one gene changes the expression level of the other gene. Here we provide a first polynomial-size ILP formulation for this problem, which can be efficiently solved on current networks. We apply our algorithm to orient protein-protein interactions in yeast and measure our performance using edges with known orientations. We find that our algorithm achieves high accuracy and coverage in the orientation, outperforming simplified algorithmic variants that do not use information on edge directions. the obtained orientations can lead to a better understanding of the structure and function of the network.

关键词： integer linear program mixed graph network orientation protein-dna interaction protein-protein interaction

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Experiment Specific Expression Patterns 15th

Experiment Specific Expression Patterns

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RECOMB - 15th Annual international conference on Research in Computational molecular Biology

作者： Petri, Tobias Kueffner, Robert Zimmer, Ralf Ludwig Maximilians Univ Munchen Dept Informat D-80333 Munich Germany

ISBN: (纸本)9783642200359

the differential analysis of genes between microarrays from several experimental conditions or treatments routinely estimates which genes change significantly between groups. As genes are never regulated individually, observed behavior may be a consequence of changes in other genes. Existing approaches like co-expression analysis aim to resolve such patterns from a wide range of experiments. the knowledge of such a background set of experiments can be used to compute expected gene behavior based on known links. It is particularly interesting to detect previously unseen specific effects in other experiments. Here, a new method to spot genes deviating from expected behavior (PAttern DEviation SCOring Padesco) is devised. It uses linear regression models learned from a background set to arrive at gene specific prediction accuracy distributions. For a given experiment, it is then decided whether each gene is predicted better or worse than expected. this provides a novel way to estimate the experiment specificity of each gene. We propose a validation procedure to estimate the detection of such specific candidates and show that these can be identified with an average accuracy of about 85%.

关键词： algorithms biochemical networks cancer genomics dna arrays

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computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data 15th

Computing Fragmentation Trees from Metabolite Multiple Mass ...

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RECOMB - 15th Annual international conference on Research in Computational molecular Biology

作者： Scheubert, Kerstin Hufsky, Franziska Rasche, Florian Boecker, Sebastian Univ Jena Lehrstuhl Bioinformat D-07743 Jena Germany Max Planck Inst Chem Ecol Jena Germany

ISBN: (纸本)9783642200359

Since metabolites cannot be predicted from the genome sequence, high-throughput de novo identification of small molecules is highly sought. Mass spectrometry (MS) in combination with a fragmentation technique is commonly used for this task. Unfortunately, automated analysis of such data is in its infancy. Recently, fragmentation trees have been proposed as an analysis tool for such data. Additional fragmentation steps (MSn) reveal more information about the molecule. We propose to use MSn data for the computation of fragmentation trees, and present the COLORFUL SUBTREE CLOSURE problem to formalize this task: there, we search for a colorful subtree inside a vertex-colored graph, such that the weight of the transitive closure of the subtree is maximal. We give several negative results regarding the tractability and approximability of this and related problems. We then present an exact dynamic programming algorithm, which is parameterized by the number of colors in the graph and is swift in practice. Evaluation of our method on a dataset of 45 reference compounds showed that the quality of constructed fragmentation trees is improved by using MSn instead of MS2 measurements.

关键词： computational mass spectrometry hardness results metabolomics multiple-stage mass spectrometry parameterized algorithms

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