Genomics I

Genomics is the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. It is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes. Genomics I - Humans, Animals and Plants is the first volume of our Genomics series. There are totally three volumes in this series.

Chapter 1 describes the development of a unique nascent DNA enrichment peak detection algorithm which utilizes Savitzky-Golay convolution kernel smoothing at different base-pair resolutions. Chapter 2 summarizes disease-causing mutations in the human genome which affect RNA splicing. Chapter 3 discusses Reactive oxygen species (ROS), which are reactive ions and free radicals generated by oxidative reactions. ROS can damage cells by reacting with cellular macromolecules including DNA. Chapter 4 proposes a methodological approach to analyze telomeric chromatin structure independently of Interstitial Telomeric Sequences (ITSs). The method is based on the use of the frequently cutting enzyme Tru9I.

In Chapter 5, the authors detail recent advances in understanding mechanisms of gene regulation in Drosophila. A combination of molecular genetics and mathematical modeling approaches reveals the emerging evidence for an underlying architecture of transcription factor binding sites in cis-regulatory modules. Chapter 6 provides a systematic evaluation and general summary of the gene expression spectra of drug metabolizing enzymes and transporters (DMETs). Chapter 7 addresses the problem of determination of absolute copy numbers in the tumor genomic profile measured by a single nucleotide polymorphism array. Chapter 8 describes bioinformatics of computer-based reconstruction of the mitochondrial DNA sequences of extinct hominin lineages and demonstrates how to identify evolutionary important information that these ancestral DNA sequences provide.

Chapter 9 proposes a phylogenetic identity of human and monkeys chlamydial strains and role of plasmids and causative agents genotypes in chlamydiosis pathogenesis. Defined the relationship between plasmid presence and IncA protein activity. In Chapter 10, based on a comparison of seven different inbred mouse strains in a model of chemical-induced asthma, it demonstrates the genetic background of the different mouse strains has a large impact on the phenotypical outcome of TDI-induced asthma and suggests caution has to be taken when comparing results from different mouse strains. Chapter 11 reviews the phylogenetic study of rabies virus emergence in wild carnivores in Turkey using viral genomic sequence analysis. It also considers options for control rabies using oral vaccination and how phylogenic information can support attempts to control the disease. Chapter 12 reveals global transcriptomic changes that occur during germination in plants. The methods of analyzing high-throughput data in plants are described and the biological significance of these transcriptomic changes are discussed.

Chapter 13 discusses the different covalent histone modifications in plants and their role in regulating gene expression and focuses on the SET-domain containing proteins belonging to the Polycomb-Group (PcG) and trithorax-Group (trxG) protein complexes and their targets in plants. Chapter 14 describes a genome-wide strategy to identify high-identity segmental duplications, combine molecular cytogenetics assays.. In Chapter 15, the authors introduce a map-based cloning and functional identification of a rice gene that plays an important role for the substance storage in the endosperm. In Chapter 16, three deep-sequencing studies are presented, which were included in a project develop of a specific biocontrol strategy for sustainable agriculture in desert ecosystems.