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international conference on Tools for Artificial Intelligence (ICTAI)

作者： P.C.H. Ma K.C.C. Chan Department of Computing Hong Kong Polytechnic University Hung Hom Kowloon Hong Kong China

the combined interpretation of gene expression data and gene sequences offers a valuable approach to investigate the intricate relationships involving gene transcriptional regulation. the highly interactive expression data produced by microarray hybridization experiments allow us to find the clusters of coexpressed genes. By analyzing the upstream regions of the identified coexpressed genes, we can discover the regulatory patterns characterized by transcription factor binding sites, which govern the process of transcriptional regulation. this paper presents a generic clustering algorithm that uses a Hybrid GA approach to discover clusters in gene expression data. the advantage of this method is that large search space can be effectively explored by utilizing the evolutionary algorithm techniques. Moreover, it is able to discover underlying patterns in noisy gene expression data for meaningful data groupings, and also statistically significant patterns hidden in each cluster can be extracted at the same time. Since the proposed method can handle both continuous-and discrete-valued data, it can be used with different microarray and biomedical data. To test its effectiveness, we have used it on real expression data. the experimental results reveal meaningful groupings and uncover many known transcription factor binding sites.

关键词： Gene expression Clustering algorithms dna Partitioning algorithms Data mining Genetics Working environment noise Sequences Pattern analysis Evolutionary computation

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Electrical molecular focusing for laser induced fluorescence based single dna detection

Electrical molecular focusing for laser induced fluorescence...

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15th IEEE international conference on Micro Electro Mechanical Systems MEMS 2002

作者： Wang, Tza-Huei Wong, Pak Kin Ho, Chih-Ming Mechanical and Aerospace Engineering Univ. of California Los Angeles Los Angeles CA United States

this paper details an electrokinetic focusing technique that significantly enhances the detection efficiency for laser induced fluorescence (LIF) based molecular sensing by concentrating fluorescence labeled molecules in a tiny probe region. 3-D electrodes were fabricated to generate wider and denser electric fields toward the probe region in the microchannel. the generated electric field is able to focus flowing dna molecules to widths as narrow as 3 μm in a 120 μm wide channel. A single molecule detection technique is developed and the enhancement of detection efficiency by using the focusing method is demonstrated.

关键词： Microelectrodes

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Processing dna tokens in parallel computing 15

Processing DNA tokens in parallel computing

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15th international Parallel and Distributed Processing Symposium, IPDPS 2001

作者： Nowak, R. WĄsiewicz, P. Plucienniczak, A. Mulawka, J.J. Institute of Electronic Systems Warsaw University of Technology Nowowiejska 15/19 Warsaw00-665 Poland Institute of Biotechnology and Antibiotics Starościńska 5 Warsaw02-516 Poland

ISBN: (纸本)0769509908

In this paper a new technique of sending data between molecular processors is presented. the molecular processor is a processing data unit. Its computation results have to be sent to other units in the form of addressed messages - tokens. Necessary experiments were performed. All operations were implemented in dna. dna processors and tokens were specially designed dna strings. Results of experiments prove our assumptions. © 2001 IEEE.

关键词： dna

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Solving computational learning problems of boolean formulae on dna computers 1

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6th international Workshop on dna-Based Computers, dna 2000

作者： Sakakibara, Yasubumi Department of Information Sciences Tokyo Denki University Hiki-gunSaitama350-0394 Japan

ISBN: (数字)9783540449928

ISBN: (纸本)3540420762

We apply a dna-based massively parallel exhaustive search to solving the computational learning problems of DNF (disjunctive normal form) Boolean formulae. Learning DNF formulae from examples is one of the most important open problems in computational learning theory and the problem of learning 3-term DNF formulae is known as intractable if RP 6 ≠ NP. We propose new methods to encode any k-term DNF formula to a dna strand, evaluate the encoded DNF formula for a truth-value assignment by using hybridization and PCR, and find a consistent DNF formula with the given examples. By employing these methods, we show that the class of k-term DNF formulae (for any constant k) and the class of general DNF formulae are eficiently learnable on dna computer. © Springer-Verlag Berlin Heidelberg 2001.

关键词： dna

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Primary structure of guinea pig plasma prekallikrein

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IMMUNOPHARMACOLOGY 1999年第1-3期45卷 127-134页

作者： Shibuya, Y Semba, U Nishino, N Khan, MMH Tanase, S Okabe, H Yamamoto, T Kumamoto Univ Grad Sch Med Sci Div Mol Pathol Kumamoto 8600811 Japan Kumamoto Univ Sch Med Dept Biochem Kumamoto 8600811 Japan Kumamoto Univ Sch Med Dept Lab Med Kumamoto 8600811 Japan Kyushu Inst Technol Dept Appl Chem Kitakyushu Fukuoka 8040015 Japan

A full length guinea pig plasma prekallikrein (PK) cdna was cloned from a liver cdna library. the nucleotide sequence with 2242 bp was analyzed and the amino acid sequence with 618 residues was deduced. Kallikrein was purified from guinea pig plasma and cleavage site in the activation was determined. the amino acid sequence around the cleavage site -(368)Ile-Asp-Ala-Arg-Ile-Val-Gly-(375)Gly- differed from that of the human PK -(368)thr-Ser-thr-Arg-Ile-Val-Gly-(375)Gly-. Protease substrates containing penta-peptides which mimicked the sequence of the cleavage sites from P-3 to P-2' of guinea pig Hageman factor (HF) and PK were synthesized, and kinetic analyses of the hydrolysis by guinea pig activated HF (HFa) and kallikrein were carried out. the combination between HFa and the PK mimicking peptide provided the best kinetics. these results in part explain why the cascade activation of PK by HFa is predominant in the guinea pig system. (C) 1999 Elsevier Science B.V. All rights reserved.

关键词： plasma prekallikrein amino acid sequence cdna guinea pig

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Bradykinin-potentiating peptides and C-type natriuretic peptides from snake venom

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IMMUNOPHARMACOLOGY 1999年第1-2期44卷 129-135页

作者： Higuchi, S Murayama, N Saguchi, K Ohi, H Fujita, Y Camargo, ACM Ogawa, T Deshimaru, M Ohno, M Showa Univ Sch Pharmaceut Sci Shinagawa Ku Tokyo 1428555 Japan Inst Butantan Biochem & Biophys Lab Sao Paulo Brazil Kyushu Univ Fac Sci Fukuoka 812 Japan

Cloning of cdnas encoding bradykinin-potentiating peptides (BPPs)-C-type natriuretic peptide (CNP) precursor or its homologue was performed for cdna libraries of Bothrops jararaca (South American snake), Trimeresurus flavoviridis, Trimeresurus gramineus and Agkistrodon halys blomhoffi (Asian snakes), all belonging to Crotalinae subfamily. Each cdna library was constructed from the venom glands of a single snake to preclude ambiguity by intraspecies variation in venom components. thirteen positive clones derived from B. jararaca were divided into two types depending on restriction sites. Differences in the nucleotide sequence arise at three locations and two of them accompanied amino acid conversions. Despite the differences, both types of cdna clones encode the BPP-CNP precursor of 256 amino acid residues. Sequence analysis demonstrated that cdna clones from three Asian snakes encode homologues of the BPP-CNP precursor from B. jararaca. In a precursor polypeptide, a signal sequence (similar to 25 aa) at the N-terminus is followed by sequences of BPP or the analogue (5-13 aa) with flanking spacer sequences (indefinite number of aa), an intervening linker sequence (similar to 144 aa) with unidentified function, and a CNP sequence (22 aa) with a preceding processing signal sequence (10 aa), cdna clones from A. halys blomhoffi encode two distinct peptides in place of BPP, and T. flavoviridis and T, gramineus were shown to have considerably different sequences in the BPP domain from those known as BPP sequences. the present results provide evidence for a wide distribution of the orthologous gene expressing a series of bioactive peptides among Crotalinae subfamily. (C) 1999 Elsevier Science B.V. All nights reserved.

关键词： snake venom dna sequence analysis bradykinin potentiating peptide natriuretic peptide

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Configuration-level optimization of RPC-based distributed programs

Configuration-level optimization of RPC-based distributed pr...

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international conference on Distributed computing Systems

作者： Tae-Hyung Kim J.M. Purtilo Computer Science Department University of Maryland College Park MD USA

Many strategies for improving performance of distributed programs can be described abstractly in terms of an application's overall configuration. But previously those techniques would need to be implemented manually, and the resulting programs, though yielding good performance, are more expensive to build and much less easy to reuse. this paper describes research towards an automatic system for introducing performance improvement techniques based upon an application's configuration description.

关键词： programming profession Sequences Writing Computer languages Computer science Educational institutions Functional programming Costs Employment dna

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PRESIDENTIAL-ADDRESS AT thE 15th international PIGMENT CELL conference - molecular-CONTROL AND BIOLOGICAL-CONTROL OF MELANOGENESIS thROUGH TYROSINASE GENES AND INTRINSIC AND EXTRINSIC REGULATORY FACTORS

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PIGMENT CELL RESEARCH 1994年第6期7卷 376-387页

作者： MISHIMA, Y Department of Dermatology Kobe Kaisei Hospital and Mishima Institute for Dermatological Research Kobe Japan

Non-premelanosomal melanogenic compartments and their melanogenesis-controlling functions have been further elucidated. In addition to enzymatic and nonenzymatic controlling factors, we have also been exploring the role of melanogenesis-related genes. Naturally occurring intrinsic melanogenic inhibitors, MW <6,000(alpha), 6,000-30,000(beta), and >30,000(gamma), having different modes of action, have been identified within melanoma cells. One of the alpha-type melanogenic inhibitors of isolated tyrosinase(Ty) nonsuppressive types, later identified as lactic acid, induces depigmentation of cultured B-16 cells by the reduction in Ty activity level due to the inhibition of its mRNA expression. the transfection of Ty cdna, rather than nuclear dna-binding master regulatory gene, can induce, within both Ty-deficient amelanotic melanoma cells and also within fibroblasts, melanin polymer formation. this multisequential step occurs not only by the induction of Ty synthesis but also by the induction of other regulatory proteins and factors such as dopachrome tautomerase, DHICA-oxidase, catalase, Ty-glycosylation in GERL, and Ty-transfer by coated vesicles to newly assigned melanogenic vacuoles in which not only eumelanin but also rather pronounced concomitant pheomelanin formation is seen. Investigation of melanin-producing vacuoles in transfected fibroblasts and reexamination of premelanosomes in pigment cells has revealed the following: 1) Melanosomes possess phagocytic ability;2) melanosomes receive tyrosinase and hydrolases via coated vesicles from GERL;3) melanosomes possess lysosome-associated membrane protein 1 (LAMP-1);4) amelanotic melanoma contains lysosome-like vacuoles with myelin figures that acquire typical premelanosome structure after Ty-cdna transfection. thus it is proposed that melanosomes are specialized lysosomes in pigment cells. Coated vesicles synthesize melanin monomers such as DHICA and some DHI, and have a monomer-stabilizing system. thus they can tr

关键词： TY MESSENGER-RNA INHIBITOR TY Cdna TRANSFECTED FIBROBLASTS MELANOSOME AS LYSOSOME COATED VESICAL MELANOMA NEUTRON CAPTURE thERAPY

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Solid state dna polymer based molecular electronic/photonic structures

Solid state DNA polymer based molecular electronic/photonic ...

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Proceedings of the 15th Annual international conference of the IEEE Engineering in Medicine and Biology Society. Part 3 (of 3)

作者： Heller, Michael J. Tu, Eugene Nanotronics Inc San Diego United States

ISBN: (纸本)0780313771

Synthetic dna polymers have unique attributes which may make them the ideal material for organic based molecular electronic and photonic device fabrication. they represent a programmable self-organizing polymeric material which is easily synthesized and derivated with functional properties. this work demonstrates the ability to use dna polymers to selforganize into predictable molecular arrangements with solid state photonic energy transfer properties.

关键词： Polymers

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dna sequencing: suggested principles for the design of an automated system

Dna sequencing: suggested principles for the design of an au...

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Annual international conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： M.V. Olson Department of Molecular Biotechnology University of Washington Seattle DC USA

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