eChapters

Introduction

Zymomonas mobilis, a gram negative, anaerobic, micro aerotolerant, ethanologenic bacterium metabolizes glucose, fructose, and sucrose. One of the major factor that limits the usage of Z. mobilis is the narrow substrate range. Moreover, there are no obvious genes reported for using lactose, maltose or cellobiose. Our preliminary sequence analysis of the Zymomonas mobilis ZM4 genome indicated the presence of a putative beta-galactosidase (bga) gene. However, the mechanism of beta-galactosidase (Bga) function is still unknown. Hence, Bioinformatics analysis was made to predict the physicochemical, biochemical and biophysical properties, domains, secondary and tertiary structures of the putative beta-galactosidase. These studies suggested that the putative beta-galactosidase gene was poorly expressed from its native promoter in Z. mobilis. The absence of beta-galactoside transacetylase and permease genes in Z. mobilis led to its inability to metabolize lactose. Hence, function predictions of Bga are performed because of the fact that it has a homologous partner.

Significant advancement in high throughput technologies (microarrays, automated sequencing and mass spectrometry), transcriptomics, the global study of transcription, together with genomics and proteomics, has undoubtedly contributed to a systems biology approach. These technologies have generated vast amount of sequence data from plants, animals and microorganisms. Fortunately, efficient computational tools (intelligent data networks, query, retrieval, analysis and visualization tools) have now optimized data mining, accelerating the process of discovery. The analysis of sequence variation is of major importance in genetic studies. In this context, molecular markers represent one of the most powerful tools for the analysis of variations in the genome and the association of heritable traits with underlying genetic variation. The development of high-throughput methods for the detection of simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) has led to a revolution in their use as molecular markers. The availability of large sequence data sets permits mining for these molecular markers, which may then be used for numerous applications such as genetic mapping, association mapping, evolutionary and phylogenic studies.

Introduction

The proteome is often described as the set of all expressed proteins in a cell, tissue or organism. It is the systematic analysis of cellular proteins, that is, their identity, quantity and function. One advantage of proteomics over transcriptome is that mRNA represents an early stage of gene expression whereas the study at the proteome level describes the state of protein which is the final functional molecule of the cell. Thus, it gives a clear picture of the cell function that may not be concluded from mRNA study. In fact we can say that proteins are more than just information carriers so it gives more information with respect to only nucleic acid based studies.  Proteomics covers two-dimensional gel electrophoresis (2-DE), image analysis, mass spectrometry, amino acid sequencing, and bio-informatics to resolve comprehensively, to quantify, and to characterize proteins. Biomarker discovery as an important aspect of proteomics technology is highly appreciable when it comes to diseases. Today,  a better understanding of the disease mechanisms leading to discovery of new disease specific biomarkers are very much possible due to the sequencing of the human genome. It has accelerated the proteomic technologies for accepting the challenges so as to meet the diseased related investigations.

1. Introduction
The era of genome sequencing was exploded by the upcoming of Human Genome Project (1989), coordinated by the U.S. Department of Energy and the National Institute of Health to identify all the approximately 20,000-25,000 genes, 3 billion chemical base pairs, store this information in databases, improve the tools for data analysis, transfer related technologies to the private sector, and address the ethical, legal, and social issues (ELSI) that may arise from the project. The dawn of genome sequencing began with Fredric Sanger’s sequencing almost twenty-five years ago. The time consuming and labor intensive gel preparation and their running, as well as the cost of such experiments replaced the conventional sequencing by “shotgun” sequencing.

Abstract
In-silico analysis of nucleic acids and proteins from fishes has enriched our understanding to several fundamental problems of classical fish biology and genetics. Mining of data which is analogous to information discovery is the process of automating knowledge discovery. Analysis of data in all possible manner and recognition of a pattern which has a scientific basis by an efficient algorithm is the fundamental principle of Bioinformatics. Ever increasing number of Bioinformatics tools as computational packages are now a days used in tandem to analyze sequence of a loci and to model a novel gene product. High efficiency algorithms with excellent homology searching functions have lead to this advancement. Cat fishes, a group of diverse bony fishes have been studied with respect to genetic analysis in several species and several peptides. Tracking of the evolutionary foot prints using genomic libraries and between expressed sequences has been generating much interest.

Introduction

Saffron is a naturally derived plant product from the dried stigma of the Crocus sativus flower  (Gresta et al., 2009).The saffron (Crocus sativus L.) is an Iridaceae family member, herbal perennial, sterile (2n=3x=24) geophyte, traditionally propagated by vegetative corms. Its cultivation dates back to late Bronze Age in the Mediterranean region (Negbi, 1999) in Anatolia since the ancient times (Arslan et al., 2007) and for at least 3500 years in Egypt and Middle East. Saffron contains more than 150 volatile and aroma yielding compounds. The chemical components mainly include carotenoids, crocin, picrocrocin, safranal etc (Abdullaev, 1993, Tarantalis et al., 1995, Karaoglu 
et al., 2007). Saffron is mostly used as spice, food colorant, dye or perfume. The dried stigmas introduce unique color, taste and fragrance and thus making it the world’s most expensive spice (Baghlian et al., 2010). Saffron has been used in folklore herbal medicines for centuries (Basker and Negbi, 1983).

The analysis of chromosome behaviour at meiosis can provide valuable information about the genomic composition of both species and hybrids. The basis for this analysis is the idea that chromosomes that pair and undergo chiasma formation are homologous. Where two genomes are present, as in diploids, the expectation is that only bivalents will be observed and where there are multiple genomes, as in polyploids, two general patterns of pairing are possible. In autopolyploids, configurations of multiple chromosomes are to be expected since all the component genomes are homologous and have the possibility of pairing with each other, whereas in allopolyploids, with different genomes, bivalent formation is the expectation. Thus, meiotic analysis can provide an oversight for genome analysis to investigate genetic relationships between the species. Further, chromosomal rearrangements are correlated with pollen fertility in species and F₁ hybrids.  Observations on pollen formation, size and viability can provide useful information, as low pollen viability is often indicative of meiotic irregularities and large sized pollen can indicate the formation of unreduced gametes. In addition, the occurrence of nucleolar dominance has been recorded in many interspecific hybrids.

Introduction

The recent revolution in genomics and bioinformatics has caught the world by storm. The issues surrounding the human genome, including the analysis of genetic variation, access to genetic information and the privacy of the individual have fuelled public debate and extended way beyond the scientific and technical literature. During the past few years, bioinformatics, defined as the computational handling and processing of genetic information, has become one of the most highly visible fields of modern science. A flood of data means that many of the challenges in biology are now challenges in computing. Bioinformatics, the application of computational techniques to analyse the information associated with bio-molecules on a large-scale, has now firmly established itself as a discipline in molecular biology, and encompasses a wide range of subject areas from structural biology, genomics to gene expression studies. In this chapter we provide an introduction and overview of the current state of the field.

Biology is in the middle of a major paradigm shift driven by computing technology. Due to the impact of information technology, biological sciences have been rapidly becoming much more computational and analytical. Rapid progress in research in the field of genetics and related field combined with the tools provided by modern biotechnology has generated massive volumes of genetic and protein sequence data over last two decades. Compilation, storage, analysis for extraction of information and knowledge from this data becomes a challenging task as usual analytical procedures are not directly applicable to these data sets.
 
Bioinformatics has been defined as a means for analysing, comparing, graphically displaying, modeling, storing, systemising, searching, and ultimately distributing biological information, which includes sequences, structures, functions, and phylogeny. Thus, bioinformatics may be defined as a discipline that generates computational tools, databases, and methods to support genomic and post-genomic research. It comprises the study of DNA structure and function, gene and protein expression, protein production, structure and function, genetic regulatory systems, and clinical applications. Bioinformatics applications need knowledge from computer science, mathematics, statistics, medicine, chemistry and biology.

Introduction

Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein) functions and interactions. Unlike genomics and proteomics, functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein-protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics includes function-related aspects of the genome itself such as mutation and polymorphism (such as SNP) analysis, as well as measurement of molecular activities. The latter comprise a number of “-omics” such as transcriptomics (gene expression), proteomics (protein expression), phosphoproteomics and metabolomics. Together these measurement modalities quantifies the various biological processes and powers the understanding of gene and protein functions and interactions. Functional genomics uses mostly high-throughput techniques to characterize the abundance gene products such as mRNA and proteins.

A microarray, as the name suggests, is a two dimensional array of microscopic probes which captures certain molecules in an environment by a process known as hybridization, and are used to detect quantities of these molecules in the environment. The probes can vary according to requirement of experiment, and so can the environment, which in technical terms is an extract of tissue under study.

Appendix A: Diagrammatic Presentation of Processes Involved in Obtaining an Indian Patent

6.1    Copyrights
    
6.2    Trademarks
    
6.3    Geographical Indications
    
6.4    Trade Secrets

5.1    TRIPS
    
5.2    WTO
    
5.3    WIPO
    
5.4    Paris Convention
    
5.5    Berne Convention
    
5.6    Budapest Treaty
    
5.7    Madrid Agreement Marks (MAM)
    
5.8    The Patent Law Treaty (PLT)

4.1    Provisional and Complete Specifications
    
4.2    Publication
    
4.3    Request of Examination
    
4.4    PCT Application: Gateway to Foreign Patents

3.1    Competitive and Collaborative Research
    
3.2    The Strategy to Protecting Plants : Plant Variety Protection Act
    
3.3    IPR Issues in Biotechnological Patents Haldi, Neem and Basmati Rice
    
3.4    Patent Litigation

2.1    Specification Drafting
    
2.2    Methods and Precautions in Drafting Patent Specification
    
2.3    Disclosure Requirements
    
2.4    Patent Claims
    
2.5    Filing of A Patent Application

1.1    General Introduction, History, Ownership of Tangible and Intellectual Property
    
1.2    Patentable Subject Matter
    
1.3    Basic Requirements of Patentability
    
1.4    Novelty, Public Domain, Obviousness and Non Obviousness
    
1.5    Inventive Step (Non-Obviousness) and Industrial Application

Bulls are considered as the half of the herd as the genetic contribution of a male almost commensurate with that of a female. The male gamete, following deposition in the female reproductive tract, traverses a long path before it could effect a successful fertilization process. It is the beauty of the nature’s creation that in spite of encountering much of this physical and chemical stress, the male chromatin remains stable until it forms the male pronucleus following fertilization. This amazing feature is endowed by the high level of compaction of the sperm nuclear DNA which in turn is due to the replacement of the sperm nuclear histones by protamines.