Structural model of DNA

Ebook "Topology in molecular biology: DNA and proteins" presents a class of new results in molecular biology for which topological methods and ideas are important. These include: the large-scale conformation properties of DNA; computational methods (Monte Carlo) allowing the simulation of large-scale properties of DNA; the tangle model of DNA recombination and other applications of Knot theory; dynamics of supercoiled DNA and biocatalitic properties of DNA; the structure of proteins; and other very recent problems in molecular biology.

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Circulating tumor DNA (ctDNA) offers minimally invasive means to repeatedly interrogate tumor genomes, providing opportunities to monitor clonal dynamics induced by metastasis and therapeutic selective pressures. In metastatic cancers, ctDNA profiling allows for simultaneous analysis of both local and distant sites of recurrence. Despite the promise of ctDNA sampling, its utility in real-time genetic monitoring remains largely unexplored.

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Part 2 book "Biomedical tissue culture" includes content: Placental structure and biological aspects of fetal membranes cultured in vitro; tissue development and mechanical property in the regenerated cartilage tissue; the art of animal cell culture for virus isolation; tissue based model of HCV replication as a replacement for animal models in drug testing; tissue culture to assess bacterial enteropathogenicity; viral DNA and CDNA array in the diagnosis of respiratory tract infections.

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Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs).

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The structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constraints and a small number of structural parameters can explain diverse experimental data on nuclear architecture.

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A series of sulfonamide derivatives were synthesized by reactions with various functional groups containing benzenesulfonyl chlorides and aniline derivatives under different substitution reaction conditions. The structures of SMZ derivatives were confirmed with melting point, FT-IR, 1 H NMR, 13 C NMR, and LC-MS/MS techniques. In order to investigate the cytotoxic effects of these derivatives, we used a model plant species. The synthesized compounds (S1–S5) and sulfamethazine (SMZ) as a positive control were applied to Arabidopsis thaliana seeds.

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With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies.

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The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles

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The honeybee (Apis mellifera) represents a model organism for social insects displaying behavioral plasticity. This is reflected by an age-dependent task allocation. The most protruding tasks are performed by young nurse bees and older forager bees that take care of the brood inside the hive and collect food from outside the hive, respectively.

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Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research.

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In some recently experiments with virus, Abstract their core part are DNA tightly packed with very high charge density. The contribution of this highly charged part to the electrical field outside virus now cannot be easily neglected in general case. In this work we propose a simple core-shell model for this type of soft particles and virus.

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Chapter 16 - The molecular basis of inheritance. This chapter presents the following content: The search for genetic material led to DNA, Watson and Crick discovered the double helix by building models to conform to X-ray data.

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Chapter 19 - The organization and control of eukaryotic genomes. After reading this chapter and attending lecture, the student should be able to: Compare the organization of prokaryotic and eukaryotic genomes, describe the current model for progressive levels of DNA packing, explain how histones influence folding in eukaryotic DNA,...

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The chapter describe the contributions of the following people: Griffith; Avery, McCary, and MacLeod; Hershey and Chase; Chargaff; Watson and Crick; Franklin; Meselson and Stahl; describe the structure of DNA; describe the process of DNA replication; include the following terms: antiparallel structure, DNA polymerase, leading strand, lagging strand, Okazaki fragments, DNA ligase, primer, primase, helicase, topoisomerase, single-strand binding proteins.

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Meiotic recombination between homologous chromosomes provides natural combinations of genetic variations and is a main driving force of evolution. It is initiated via programmed DNA double-strand breaks (DSB) and involves a specific axial chromosomal structure.

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Topic models are statistical algorithms which try to discover the structure of a set of documents according to the abstract topics contained in them. Here we try to apply this approach to the discovery of the structure of the transcription factor binding sites (TFBS) contained in a set of biological sequences, which is a fundamental problem in molecular biology research for the understanding of transcriptional regulation.

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Chromosome structure is a very limited model of the genome including the information about its chromosomes such as their linear or circular organization, the order of genes on them, and the DNA strand encoding a gene. Gene lengths, nucleotide composition, and intergenic regions are ignored.

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DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how the DNA will fold given a distribution of bound factors, here viewed as a type of sequence, is currently an unsolved problem and several heterogeneous polymer models have shown that many features of the measured structure can be reproduced from simulations.

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Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data.

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Chromosomal rearrangements are the typical phenomena in cancer genomes causing gene disruptions and fusions, corruption of regulatory elements, damage to chromosome integrity.

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