eChapters

Neisseria meningitidis, also simply known as meningococcus, is a gram-negative bacterium best known for its role in meningitis. It only infects humans; there is no animal reservoir. It is the only form of bacterial meningitis known to cause epidemics. The carbohydrate capsule of N. meningitidis determines its virulence and is targeted by the immune system. Approximately 12 strains of N. meningitidis exist and are characterized by the polysaccharide expressed on its capsule: A, B, C, 29-E, H, I, K, L, W-135, X, Y and Z. Inhibition of Pencillin Binding proteins (PBPs) leads to irregularities in cell wall structure such as elongation, lesions, loss of selective permeability and eventual cell death and lysis. 3-D structure of PBP was studied using Bioinformatics tool. Using Homology modelling, converted protein sequence of penicillin binding protein, extracted from NCBI server, in FASTA format and performed PDB-BLAST to search a desired template. Selection of template was based on lower E-value, bit score and identity. Using MSA with the help of CLUSTAL W software conserved region was found between the target and template sequence, 1K25. The 3-D structure of penicillin binding protein was found with the help of Modeller 9v2 and molecular dynamics was performed using GROMACS software. The docking was performed (Autodock 3.0 software) using 3 ligands viz. Cefuroxime, Chloramphenicol, Cefalotoxime with standard Bioinformatics tools.

Among several respiratory diseases affecting man, bronchial asthma is the most common disabling syndrome, nearly 7 to 10 per cent of the world population suffer from bronchial asthma, which is a chronic illness involving the respiratory system in which the airway occasionally constricts, becomes inflamed, and is lined with excessive amounts of mucus, often in response to one or more triggers. These episodes may be triggered by such things as exposure to an environmental stimulant (or allergen), cold air, warm air, moist air, exercise or exertion, or emotional stress. In children, the most common triggers are viral illnesses such as those that cause the common cold. A variety of exogenous determinants of asthma were also been, some of which are air pollution, tobacco smoking, diet, occupation and respiratory infection, these pollutants may serve as inciters or triggers of asthmatic reaction in airways that are already hyper responsive, they may exert direct toxic influence on the respiratory epithelium or may augment or modify immune responses to inhaled antigens. During an asthma episode, inflamed airways react to environmental triggers such as smoke, dust, or pollen. The airways narrow and produce excess mucus, making it difficult to breathe. In essence, asthma is the result of an immune response in the bronchial airways. As according to the World Health Organization over 80% of the people in developing countries depend upon traditional medicine for their primary health care. Medicinal plants are considered as source of various alkaloids and other chemical substances essential for mankind.

Biodiversity conservation and sustainable use has, for many people, become associated mainly with issues related to plants and wild animals. Although much less discussed, the loss of farm animal genetic resources may well be much more serious than in crops because the gene pool is smaller and very few wild relatives remain. The fact that 32% of livestock breeds worldwide are at risk of becoming extinct and that the rate of extinction continues to accelerate (FAO, 2000) is thus a serious cause for concern. Animals of different characteristics and hence outputs suit differing local community needs.

The union territory of A & N Islands constitutes the farthest and the remotest part of Indian union. The islands are situated in the Bay of Bengal surrounded by sea. The neighboring countries are Burma in north east and Singapore, Malaysia and Indonesia in south east. The Union territory of A & N Islands is situated between 60 and 140 north latitude and 920 and 940 east longitude forming a broken row of continuous islands from. North to South direction. They can be divided into two groups namely Andaman and Nicobar groups. The dreaded 100 channel which is about 145 Kms wide and 400 fathoms deep, separates the two groups

Bioinformatics can be defined as “the collection, archiving, organization and interpretation of biological data” (Orengo et al., 2003). By extension, structural bioinformatics deals with the collection, archiving, organization and interpretation of 3-D structural data of bio macromolecules. Structural bioinformatics emerged with the first crystal structures of haemoglobin and myoglobin. These structures were analyzed and contributed significantly to our understanding of the principles of life at a molecular level. A repository of all publicly accessible protein crystal structures, the Protein Data Bank (PDB) was established by Walter Hamilton et al., at Brookhaven National Laboratory in 1971. Until the late 1980s, structural biologists often knew all the available structures of bio macromolecules and much of the analysis, such as structure comparison and hydrogen-bonding analysis was done manually without much computer intervention. As the number of available structures increased, so did the need for software tools for structure analysis. Structural bioinformatics encompasses a wide variety of applications, including structure visualization, validation, classification, structure-based function prediction, identification of targets for structural genomics projects and prediction of the structures of individual bio macromolecules and complexes as well the binding modes of small molecules inside proteins of pharmaceutical or biotechnological interestStructural and theoretical analyses of proteins are central to the understanding of complex molecular mechanisms and are fundamental to the drug discovery process.

Bioinformatics can be defined as the application of computer technology for the management and analysis of biological data using computer to gather, store, analyze and merge the biological data. It consists of the organization of many kinds of large-scale biological data, particularly that based on DNA and protein sequence, into web-accessible databases and the methods required analyzing these data. Bioinformatics is a fast growing field within the biological sciences that was developed because of the need to handle large amounts of genetic and biochemical data. The goal of bioinformatics is to uncover the wealth of biological information hidden in the mass of data and to obtain a clearer insight into the fundamental biology of organism. This knowledge can have profound impact on various fields such as human health, agriculture, environment, energy and biotechnology. Bioinformatics involves use of various biological databases, which are archives of consistent data that are stored in a uniform and efficient manner. Biological databases are large collections of data that are relatively different to maintain outside the centers and institutions that produce them. These data are traditionally accessed and analysed using browser-based World Wide Web (www) interfaces. There are two types of databases i.e. Primary database and Secondary database. Primary databases contain information and annotations of DNA and Protein sequences, DNA and Protein structure and DNA and Protein expression profiles catalogued for the end users.

A genome is an organism’s complete genetic signature and the collection of information that an organism can pass on to its offspring. Genomics, the study of the structure, function, and evolution of entire genomes is principally dealing with genetic information which helps us to understand how organisms and ecosystems work, how theymalfunction, or how they might be melded to human needs. The model organisms used in genomics have, in general, small genomes and short generation times. To meaningfully analyze the gene-to-phenotype relationships, a large amount of sequencing information is necessary. Progress in DNA sequencing technologies leads to accumulate Information about structures of genomes (Mohan Kumar, 2007).

HISTORY OF INSECT GENOMICS

Commencing from the publication of the entire nucleotide sequence of the genome of Haemophilus influenzae in 1995, a complete genome sequence of many organisms, including lower and higher eukaryotes, have been reported. The cost-effective way to get sufficient sequence information to address the questions is to sequence a high-quality reference genome and then map sequences from other genomes onto the reference sequence. Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. Hence, a study of Insect genomics is imperative to elucidate information to other organisms.

ANALYSIS OF CODON USAGE VARIATION

Multivariate analysis methods such as Correspondence Analysis and Principle Component Analysis have often been used to identify major trends of variation in synonymous codon usage among inter or intra specific genes. Genetic codes are degenerate meaning most of amino acids can be encoded by more than one codon (triplet of nucleotides); such codons are synonymous and usually differ by one nucleotide in the third position. The alternative synonymous codons are not used with similar frequency and their usage varies among different genes. Hence there is the presence of Relative Synonymous Codon Usage values. 

SEQUENCE DATA

The gene sequences downloaded from Genbank of National Center for Biotechnology Information that is the nucleotide sequence repository known worldwide, serves as the secondary data used for analysis. Relative synonymous codon usage value of each gene is extracted separately using the Codon Usage software of Sequence Manipulation Suite. These are the raw data which needs to be normalized to be used before application of various multivariate analysis.

In the context of molecular biology, a consensus sequence is the minimum nucleotide sequence that shows the characteristics common to most members of the family among a set of related genetic sequences.It serves in representing the results of a multiple sequence alignment, where related sequences are compared to each other, and similar functional sequence motifs are found. It also shows conserved/variable residues. It is found several times in the genome and is thought to play the same role in its different locations. For example, many transcription factors recognize particular consensus sequences in the promoters of the genes they regulate. In the same way restriction enzymes usually have palindromic consensus sequences, usually corresponding to the site where they cut the DNA. Transposons act in much the same manner in their identification of target sequences for transposition. Splice sites, i.e. those sequences immediately surrounding the exon-intron boundaries, can also be considered as consensus sequences. Defining a consensus DNA binding site by examining consensus sequences is a key work carried out by biologists (Harley et al., 1994). Rareness or anomaly detection followed by in depth analyses in such sequences may reveal significant information regarding the structural, functional and biochemical mechanisms of the genes which are of much importance to biologists.

Two schemes of labeling are in common use today. One variant labels a single sample, either radioactively or fluorescently. Radioactive labeling is used, e.g., in conjunction with hybridization on nylon membranes (Lennon and Lehrach, 1991). The company Affymetrix synthesizes sets of short oligomers on a glass wafer and uses a single fluorescent label (Lipshutz et al., 1999). Alternatively, two samples are labeled with a green and a red fluorescent dye, respectively. The mixture of the two mRNA preparations is then hybridized simultaneously to a common array on a glass slide. This technology is usually referred to as the Stanford technology (David Duggan et al., 1999). Quantification utilizes a laser scanner that determines the intensities of each of the two labels over the entire array. Recently, companies like Agilent have immobilized long oligomers of 60 to 70 base pairs length and used two-color labeling.

Mitochondria are key energy generators in most eukaryotic cells. In recent years a number of mitochondrial genomes have been completely sequenced, contributing to the knowledge of molecular features related to function and evolution of this peculiar genome (Boore, 1999). The pathways of mitochondrial DNA evolution are obscured by their extraordinary size. Gene content, gene rearrangement and mode of expression are the characteristics of mitochondrial genomes. The mitochondrial genomes from eukaryotes reveal large size differences between animal, fungal and plant species. The average size of animal mtDNA is ~ 16 kb (Boore, 1999), whereas plant mtDNAs range from 200 to 2500 kb (Palmer, 1990). The size of fungal mtDNA’s range from 19 kb to 176 kb (Hudspeth, 1995).The mtDNA genome has a limited number of protein coding genes such as NADH ubiquinone oxidoreductase (ND2 to ND5), cytochrome c oxidase (COX), succinate dehydrogenease (SDH), ATP synthase (ATP6), cytochrome (CYTB), etc. Among non-coding genes only rRNA and tRNA genes are found.Ribosomal RNA (rRNA) is a component of the ribosomes, the protein synthetic factories in the cell. rRNA molecules are extremely abundant. They make up at least 80% of the RNA molecules found in a typical eukaryotic cell. Synthesis of the three nucleolar rRNA molecules is unusual as they are made on one primary transcript that is chopped up into three mature rRNA molecules.

The development of bio-informatics started with the working of computers and accumulation of data on genes and proteins. There are 100,000 proteins in the human body or 1 million. In the last decade the number of protein sequences gathered in databases increased tremendously, but the key to understand the function of a protein is not its sequence but its structure. Experimental determination of 3 dimensional native folded structure of a protein usually can be done via crystallography techniques. But such experiments are time consuming. Currently there are hundreds of different fully automated approaches to protein 3D structure prediction.

All proteins are polymers of Amino acids. The polymers also known as polypeptides consist of a sequence of 20 different L-m-amino acids also referred to as residues. For chains under 40 residues the term peptide is frequently used instead of protein. To be able to perform their biological function, proteins fold into one that is driven by a number of non covalent interactions such as hydrogen bonding, ionic interaction, Vander Waal’s forces and hydrophobic packing. In order to understand the functions of proteins at a molecular level, it is often necessary to determine the three dimensional structure of proteins. The modern Information Technology techniques like Artificial Intelligence have opened new pathways to researchers. Once ANN has been trained it is capable of producing accurate output for the unknown inputs. Many researchers have tried to analyze the large sequence sized gene to determine the protein, predict the secondary structure of the protein and model its three dimensional (3D) view [11].

Today, when the collection of biological data has been increasing at explosive rate, the processing of these data is needed. It would be extremely valuable if the specialists who know what the data mean were also able to imagine ways to collect, process and exploit these data. Biological and agricultural scientists should note that concepts from computer science, discrete mathematics and statistics are being used increasingly to study and describe biological systems. The specialists, who know the subjects of mathematics, statistics and computer programming, are needed for solving the computational problems in biology. Statistical data mining approaches seem ideally suited for bioinformatics, since it is data rich, but lacks a comprehensive theory of life organization at molecular level, or in the words of I.E. Alcamo “ Keeping up with the directions and application of DNA is a never ending job.” Starting with possible definitions of statistical data mining and bioinformatics, this chapter will give a general side view of both the fields on the statistical data mining part and its technologies and discuss how statistical data mining may be used in bioinformatics.

Bioinformatics is the application of information technology to the field of molecular biology. The term Bioinformatics was coined by Paulien Hogewag, in 1978 for the study of informatic processes in biotic systems. Bioinformatics nowadays, entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. Bioinformatics deals with storing and searching of large biological data sets and analysis of these data sets using computers to determine various relationships. 
The rapid developments in genomic and other molecular research technologies and developments in information technologies have been combined to produce tremendous amount of information related to molecular biologists. Now bioinformatics has developed and deals with many other types of biological data like protein structures, sequence alignment, gene finding, genome assembly, gene expression profiles, structure alignment, protein structure prediction, protein–protein interactions and the modelling of evolution. Being an interface between modern biology and informatics, it involves detection, expansion and implementation of computational algorithms and some of the software tools used to provide applications primarily in agriculture and healthcare divisions. In developing countries, bioinformatics play a major role in agricultural area where it can be used for increasing the nutritional content, and increasing the volume of the agricultural products etc.

r DNA Biotechnology
    
Concept of r DNA
    
DNA Preparation from Tissue
    
Reagents
    
Preparation
    
DNA Buffer (Tris-EDTA)
    
RNase A (20 mg/ml)
    
Toe DNA Preparation for Southern Blots
    
Southern Blot
    
PCR
    
Polymerase Chain Reaction
    
The Cycling Reactions
    
Denaturation at 94°C
    
Annealing at 54°C
    
Extension at 72°C
    
DNA Sequencing
    
The Sequencing Reaction
    
Denaturation at 94°C
    
Annealing at 50°C
    
Extension at 60°C
    
Separation of the Molecules
    
Detection on An Automated Sequencer
    
Assembling of The Sequenced Parts of a Gene
    
Freezing of Buffalo Semen (Jindal, 1995)
    
Tissue Culture
    
Preparation of Media
    
Laboratory Procedure for IVF (Kharche et al., 2008)
    
Source of Oocytes
    
Preparation of Estrous Goat Serum
    
Collection of Oocytes
    
Laparoscopic Ovum Pick-up
    
Oocyte Retrieval from Ovaries Collected form Slaughter 
    
House
    
Slicing Technique
    
Follicle Puncture Technique
    
Follicle Aspiration Technique
    
Follicle Isolation Technique
    
Evaluation of Oocytes
    
In vitro Maturation of Oocytes
    
Preparation of Cells for Co-culture
    
Assessment of Nuclear Maturation After in vitro Maturation of Oocytes
    
Analysis of Nuclear Status is Ascribed to One of the Following
    
Sperm Preparation for in vitro Fertilization of Oocytes
    
In vitro Fertilization of Oocytes
    
Assessment of in vitro Fertilization of Oocytes
    
Assessment of Cleavage
    
In vitro embryo culture

Animal Science Biotechnology Research Centres
    
Current Status and Some of the Achievements in Animal Heatlh
    
National Bioresource Development Board
    
Animal Biotechnology
    
Biotechnology Parks and Incubators
    
National Institute of Immunology, New Delhi
    
Bose Institute, Kolkata
    
Jawahar Lal Nehru University, New Delhi
    
National Centre For Cell Science, Pune
    
Centre for Dna Fingerprinting and Diagnostics (Cdfd) Hyderabad
    
National Institute for Plant Genome Research (Nipgr) New Delhi
    
Institute of Bioresources and Sustainable Development,Imphal
    
Institute of Life Sciences, Bhubaneshwar
    
Bharat Immunologicals and Biologicals Corporation Limited
    
International Centre for Genetic Engineering and Biotechnolgoy (Icgeb), New Delhi
    
Animal Biotechnology Research Abroad

Checks and Balances in Biotechnology Applications
    
Biosafety Issues in Animal Biotechnology Application
    
World Organization for Animal Health (OIE)
    
Recombinant DNA Safety Guidelines (1990)
    
Foreign Trade (Development and Regulation) Act, 1992 (2006)(Draft Amendment)
    
Revised Guidelines for Research in Transgenic Plants and Guidelines for Toxicity and Allergenicity Evaluation of Transgenic Seeds, Plants and Plant Parts (1998)
    
Guidelines for Generating Preclinical and Clinical Data for rDNA Vaccines, Diagnostics and other Biologicals (1999)
    
The Food Safety and Standards Act (2006)
    
Transgenic Animals Bioreactors
    
First Patent in Biotechnology
    
Biotechnology - Ethical Concerns
    
Some Priority Areas in the Field of Biotechnology
    
Suggestions for Future Development of Biotechnology Activities in the Field of Animal Health and Production in India
    
Epilogue

Information Sources for Biotechnology
    
Books
    
General Biotechnology Books
    
Animal Biotechnology Books
    
Review Articles
    
Journals
    
Animal Biotechnology Journals
    
Biotechnology Job Listings
    
The Scientist
    
Patents
    
Requirements for Setting up a Biotechnology Laboratory
    
Essential
    
Beneficial
    
Useful
    
PCR
    
Specifications of a Good PCR Macine
    
Gel Documentation System Electrophoresis
    
Laboratory Safety and Hazards

Environmental Biotechnology
    
Global Warming and Animal Health and Production
    
Genome Mapping
    
Human Genome
    
Livestock Genomics
    
Cattle Genome
    
Pig Genome
    
Bioinformatics
    
Major Branches of Bioinformatics Include
    
List of Bioinformatics Software Commonly Used in Animal Genomics Research
    
Sequence Analysis Software
    
Genetics Analysis Software
    
Functional Genomics Software
    
Biofuels
    
Advantages of Bioethanol
    
Ecological
    
Economical
    
Looking to the Future: The Potential of Second-Generation Biofuels
    
Future Role of Biofuels Depends on Profitability and New Technologies

Vaccines
    
Veterinary v/s Human Vaccines
    
Modern Veterinary Vaccines
    
rDNA Technology to Prepare Vaccines
    
Veterinary Viral Vaccines
    
Live Vaccines
    
Killed Vaccines
    
Genetically Engineered Viral Vaccines
    
Veterinary Bacterial Diseases Vaccines
    
Veterinary Parasitic Vaccines
    
Vaccines against cancer
    
Swine Flu
    
Foot and Mouth Disease
    
Adenovirus Vector Vaccine
    
Johne’s Disease
    
Diseases of Poultry
    
Newcastle Disease in Poultry
    
Avian Influenza (Bird Flu)
    
Rabies
    
Disease Diagnostics
    
The Nucleic Acid-hybridization Technique
    
Diagnostics Based on pcr
    
Diagnosis by Restriction Fragment Length Polymorphisms and Related DNA-based Approaches
    
Diagnosis by DNA Probes and DNA Microarray Technology
    
Antigen-Capture Enzyme-Linked Immunosorbent Assay (ELISA) Proteomics
    
Disease Diagnosis Kits Developed
    
Brucelosis
    
Rabies
    
Canine Distemper and Canine Parvo Virus
    
Canine Hepatitis Virus
    
Foot and Mouth Disease
    
New Castle Disease
    
Egg Drop Syndrome Virus-76 (EDS-76)
    
Proteomics for Disease Diagnostics
    
Nanotechnologies in Diagnosis and Vaccine Development
    
Monoclonal Antibodies
    
Immunotherapy
    
Problems
    
Animal Genomics for Disease Resistance
    
Gene Knockout Technology
    
Gene Pharming
    
Gene Therapy
    
Types of Gene Therapy
    
Germ Line Gene Therapy
    
Somatic Gene Therapy

Reproductive Biotechnology
    
Artificial Insemination (AI)
    
History and Future Perspectives of Artificial Insemination
    
Semen Cryopreservation
    
Buffalo
    
Goat
    
Cryoprotection and Anti Oxidants
    
Cryopreservation and Genetic Stability of Livestock Spermatozoa
    
Insemination Technique
    
Cattle and Buffalo
    
Sheep and Goat
    
Conception Rate with Artificial Insemination
    
Multiple Ovulation and Embryo Transfer (MOET)
    
Advantages of Embryo Transfer
    
MOET Includes the Following Steps
    
Superovulatory Treatments
    
Insemination
    
Recovery of Embryos
    
Synchronization of Recipients
    
Cattle
    
Buffaloes
    
Goats
    
Horses
    
In vitro Maturation, fertilization and culture of Oocytes
    
Historical Development
    
In Vitro Maturation of Oocytes
    
In vitro Sperm Capacitation
    
Scope
    
Limitations
    
Embryo Cryopreservation
    
Ultrasonography in Reproductive Management
    
Ultrasound-guided Transvaginal Oocyte Pick-up (OPU)
    
Embryo Cloning or Nuclear Transfer
    
Blastomere Separation
    
Embryo Splitting
    
Nuclear Transfer Cloning (NT)
    
Embryonic Stem Cell Complementations
    
Limitations and Future Prospects of Cloning
    
Sexing of Embryos and Separation of X and Y Chromosomes Bearing Sperms
    
PCR  in Sex Determination
    
Transgenic Animal Production
    
Gene Transfer Through Direct DNA Microinjection
    
Gene Transfer with Retroviral-Vector Assistance
    
Gene Transfer through Production of Germ-line Chimeras
    
Parthenogenetic Embryos: An Emerging Tool in Reproductive Biotechnology for Multiplication of Superior Germ Plasm
    
Applications of Parthenogenesis
    
Livestock Genomics and Marker Assisted Selection (Use of DNA Level Markers)
    
Stem Cells
    
Vaccine for Fertility Control and Increase Prolificacy
    
Auto-immunization to Increase Prolificacy
    
Biotechnology of Conservation of Livestock Breed Biodiversity
    
Gene for Prolificity: Booroola Merino
    
Role of Biotechnology in Enhancing Production
    
Milk
    
Biotechnology of Rumen Manipulation
    
Genetically Modified Ruminal Microorganisms

Biotechnology of Animal Feeding
    
Probiotics
    
Biotechnology Crops as Animal Feed
    
Biotechnology of Animal Products
    
Some New Products made Possible by Biotechnology Include