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METAL-ION ASSISTED, RADIATION-INDUCED CONVERSION OF B-dna TO Z-dna IN POLY (DGDC) AND 2 NATURAL dnaS

international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 479-483页

作者： TRUMBORE, CN MYERS, YN HYDE, CK HUDSON, RD RHODES, CN MASSELINK, JK Department of Chemistry and Biochemistry University of Delaware Newark 19716.

Metal-ion assisted, gamma-radiation-induced B-Z conformation changes have been observed with UV and circular dichroism spectroscopy for poly (dGdC), calf thymus and herring testis dna. these conformational changes are similar to those induced by increasing multivalent metal ion concentrations in dna containing alternating purine and pyrimidine base sequences. In both the metal-ion-induced and the metal-ion-assisted, radiation-induced conformation changes, the conversions were from the right-handed B-dna to the left-handed Z-dna conformation. It is proposed that radiation-induced dna strand breaks markedly reduce the high activation energy barrier in the metal ion-driven B-Z conformation conversion and allow much smaller metal ion concentrations to induce this conversion than in the absence of strand breaks. the biological importance of such radiation-induced conformational changes is discussed in terms of the potential significance of the Z-dna conformation in the control of the dna transcription process.

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COMBINATION IS thE DOMINANT FREE-RADICAL PROCESS INITIATED IN dna BY IONIZING-RADIATION - AN OVERVIEW BASED ON SOLID-STATE EPR STUDIES

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 491-497页

作者： BERNHARD, WA MROCZKA, N BARNES, J Department of Biophysics University of Rochester NY 14642.

An overview of the early processes initiated in dna by ionizing radiation is given from the perspective of studies done by solid-state EPR with the focus on radical combination. Comparisons with free radical formation and trapping in crystalline pyrimidines (1-methylcytosine, thymine, 1-methylthymine, 1-methyluracil, and cytosine monohydrate) provide insight into the processes occurring in dna. Between 25 and 50% of low LET ionizations in fully hydrated dna at 4K lead to trapped free radicals, the remaining unobserved radicals are assumed to have combined. the majority of the radicals trapped in dna at 4K (G similar to 0.3 mu mol/J) are believed to be in clusters. Based on the value of G, it is argued that the range of holes and bound electrons in dna at 4K are, in the main, limited to within the cluster diameter, similar to 4 nm. Proton transfer across hydrogen bonds promotes radical trapping and inhibits combination but is thermally reversible. Warming to room temperature mobilizes the reversibly trapped radicals and gives additional combination (50-80% of those trapped at 4K). the yield of free radicals, after anneal, is sufficient to account for the yield of single-strand breaks produced by direct effects.

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ON thE LINEARITY OF thE DOSE-EFFECT RELATIONSHIP OF dna DOUBLE-STRAND BREAKS

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 549-552页

作者： CHADWICK, KH LEENHOUTS, HP RIVM LSO3720 BA BILTHOVENNETHERLANDS

Most radiation biologists believe that dna double-strand breaks are induced linearly with radiation dose for all. types of radiation. Since 1985, with the advent of elution and gel electrophoresis techniques which permit the measurement of dna double-strand breaks induced in mammalian cells at doses having radiobiological relevance, the true nature of the dose-effect relationship has been brought into some doubt. Many investigators measured curvilinear dose-effect relationships and a few found good correlations between the induction of the dna double-strand breaks and cell survival. We approach the problem pragmatically by assuming that the induction of dna double-strand breaks by I-125 Auger electron emitters incorporated into the dna of the cells is a linear function of the number of I-125 decays, and by comparing the dose-effect relationship for sparsely ionizing radiation against this standard. the conclusion drawn in that the curvilinear dose-effect relationships and the correlations with survival are real. the problem of why the dose-effect relationship is curvilinear when microdosimetric considerations predict that even for sparsely ionizing radiation energy deposition in and close to the Watson-Crick double helix should give a linear dose-effect relationship remains.

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CLONING HUMAN dna-REPAIR GENES

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 573-577页

作者： JEGGO, PA CARR, AM LEHMANN, AR UNIV SUSSEX MRCCELL MUTAT UNITBRIGHTON BN1 9RRE SUSSEXENGLAND

Many human genes involved in the repair of UV damage have been cloned using different procedures and they have been of great value in assisting the understanding of the mechanism of nucleotide excision-repair. Genes involved in repair of ionizing- radiation damage have proved more difficult to isolate. Positional cloning has localized the XRCC5 gene to a small region of chromosome 2q33-35, and a series of yeast artificial chromosomes covering this region have been isolated. Very recent work has shown that the XRCC5 gene encodes the 80 kDa subunit of the Ku dna-binding protein. the Ku80 gene also maps to this region. Studies with fission yeast have shown that radiation sensitivity can result not only from defective dna repair but also from abnormal cell cycle control following dna damage. Several genes involved in this 'checkpoint' control in fission yeast have been isolated and characterized in detail. It is likely that a similar checkpoint control mechanism exists in human cells.

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thE COMPLEXITY OF dna-DAMAGE - RELEVANCE TO BIOLOGICAL CONSEQUENCES

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 427-432页

作者： WARD, JF Department of Radiology School of Medicine UCSD La Jolla 92093.

Ionizing radiation causes both singly and multiply damaged sites in dna when the range of radical migration is limited by the presence pf hydroxyl radical scavengers (e.g. within cells). Multiply damaged sites are considered to be more biologically relevant because of the challenges they present to cellular repair mechanisms. these sites occur in the form of dna double-strand breaks (dsb) but also as other multiple damages that can be converted to dsb during attempted repair. the presence of a dsb can lead to loss of base sequence information and/or can permit the two ends of a break to separate and rejoin with the wrong partner. (Multiply damaged sites may also be the biologically relevant type of damage caused by other agents, such as UVA, B and/or C light, and some antitumour antibiotics.) the quantitative data available from radiation studies of dna are shown to support the proposed mechanisms for the production of complex damage in cellular dna, i.e. via scavengable and non-scavengable mechanisms. the yields of complex damages can in turn be used to support the conclusion that cellular mutations are a consequence of the presence of these damages within a gene. Literature data are used to support these statements and to develop overall mechanisms connecting the production of primary species to the production of biologically relevant damages. the consequences of the LET of the radiation on multiplicity of damage are discussed and suggestions made for the cause of the decrease of the oxygen enhancement ratio as the LET increases.

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Advancements in Modern Steganography Techniques for Enhanced Data Security: A Comprehensive Review 18

Advancements in Modern Steganography Techniques for Enhanced...

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18th INDIAcom;11th international conference on computing for Sustainable Global Development, INDIACom 2024

作者： Bohra, Shresty Naik, Charmi Batra, Rashi Popat, Kinshu Kaur, Hargeet Pandit Deendayal Energy University Computer Science Engineering Gandhinagar India

ISBN: (纸本)9789380544519

Information security has become a major concern in today's digital world with the rapid growth of the internet. To confront this challenge, various techniques like cryptography and steganography have developed in the fields of computer security for protecting sensitive data from unauthorized access. the review paper explores modern steganography techniques, providing valuable information about their applications in data security. It analyzes the emerging field of dna-based steganography. the paper also examines the dynamic domain of audio steganography, focusing on the challenge of developing strong, high-capacity systems for secure communication. Additionally, it focuses on evaluation of digital image steganography methods. © 2024 Bharati Vidyapeeth, New Delhi.

关键词： Audio steganography Cracking probability Discrete Cosine Transform dna steganography Image steganography LSB Prisoners'problem RGB SNR Stego-Image Temporal Domain Transform Domain

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Evaluating Graphene and Molybdenum Disulfide Nanopores for dna Sequencing 18

Evaluating Graphene and Molybdenum Disulfide Nanopores for D...

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18th international conference on Nano/Micro Engineered and molecular Systems, NEMS 2023

作者： Li, Lei Qi, Han Xu, Wei Wang, Yujuan Bi, Kedong Southeast University School of Mechanical Engineering Mechanical Design and Theory Major Nanjing China

ISBN: (纸本)9798350333480

Graphene and molybdenum disulfide (MoS2) nanopores, with their superior characteristics and subnanometer thickness, are expected to be the next generation of rapid and low-cost methods of dna sequencing. In this paper, focused ion beam (FIB) is employed to fabricate nanopores with similar sizes on these two-dimensional (2D) materials to compare their performance in sequencing dna. According to our experimental results, graphene nanopores have a stronger interaction with dna than MoS2, which contributes to a better temporal resolution. However, in the low-frequency region, the 1/f noise level of MoS2 is obviously lower than that of graphene. Furthermore, the nanopore was fabricated on graphene and MoS2 heterostructure for dna sequencing, and the translocation events were successfully captured. It is demonstrated that the new heterostructure reduces the high noise level in the low-frequency region of graphene nanopores in dna sequencing. It is expected that graphene and MoS2 can complement each other and facilitate the realization of single-base detection resolution in the future. © 2023 IEEE.

关键词： Molybdenum disulfide

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dna/RNA computing with biological nanopore in droplets system: And operation using RNA polymerization 18

DNA/RNA computing with biological nanopore in droplets syste...

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18th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014

作者： Ohara, M. Takinoue, M. Kawano, R. Tokyo University of Agriculture and Technology Japan Tokyo Institute of Technology Japan

ISBN: (纸本)9780979806476

this paper describes AND operation using RNA translocation through an alpha-hemolysin (αHL) nanopore in two droplets system. We define the output of the binary signals "1" or "0" as "RNA transfers droplet through the nanopore" or "no translocation". the phenomena can be electrically monitored as the channel currents at the single molecule level. Although we have already proposed logic operation using dna and the nanopore, the next calculation cannot work due to the low concentration of output molecule. In this study, we used RNA polymerization in order to increase the concentration of the output molecule. © 14CBMS.

关键词： Drops

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A High-Performance Sequence Analysis Engine for Shotgun Metagenomics through GPU Acceleration 18

A High-Performance Sequence Analysis Engine for Shotgun Meta...

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18th IEEE international conference on Bioinformatics and Bioengineering

作者： Hsu, Ying-Feng Matsuoka, Morito Jung, Nicolas Matsumoto, Yuki Motooka, Daisuke Nakamura, Shota Osaka Univ Cybermedia Ctr Osaka Japan Osaka Univ Res Inst Microbial Dis Genome Informat Res Ctr Osaka Japan

ISBN: (纸本)9781538662175

With the continual growth of low-cost and high-throughput dna sequence technology, the scale and amount of next-generation sequencing (NGS) datasets are continually increasing in many genomics research areas. Shotgun metagenomics sequencing provides comprehensive information on microorganisms, based on complex samples of the ecosystem. Due to challenges of its scale and computational complexity, efficient sequence processing and analyzing tools are needed. In this paper, we propose a novel high-performance shotgun metagenomics sequence analysis engine for the task of sequence comparison. It includes two major components. First, a customized shifting database, which is optimized from any existing dna sequence dataset. Second, a high-performance sequence computation algorithm that utilizes the customized shifting reference database and accelerates GPU parallel computing. We elaborated upon the efficiency and computational complexity of our proposed approach in an HPC server, which has eight Nvidia Tesla P100 GPUs. We also conducted a case study to detect viral sequences from patients' blood samples. Our experimental result shows that we obtain similar accuracy to the conventional BLAST method, but with a computational speed that is about twenty times faster.

关键词： component shotgun metagenomics sequencing sequence comparison GPU acceleration parallel computing

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Repeat analysis in dna sequences with parallel computing method on Grid

Repeat analysis in dna sequences with parallel computing met...

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18th IASTED international conference on Parallel and Distributed computing and Systems, PDCS 2006

作者： Arefin, Md. Ahsan Anwar, Abdullah Ibney Wasif, Abu Computer Science and Engineering Bangladesh University of Engineering and Technology Dhaka Bangladesh

the development of Grid environment provides an efficient way for implementing the parallel algorithm. Here we focus on the discovery of short recurring patterns in dna sequences that represent binding sites for certain proteins in the process of gene regulation. We develop parallel computing algorithm for solving this problem by partitioning the overall dna sequences. this provides us an option to implement the algorithm on Grid and to evaluate its performance. We use the open source software "Alchemi" for building the Grid environment. Also by using a merging repeat approach to find these patterns, we address other related problems, including finding of repetition with insertion and deletion.

关键词： dna sequences

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