eChapters

Abstract

Quercus species of family Fagaceae are very important from both economic and ecological perspectives. These exhibit irregular fruiting, and produce seeds recalcitrant to storage, thereby difficult to propagate through conventional procedures. Again because of their very difficult to root nature, extremely limited success has been observed in vegetative propagation. Application of new technological approaches like in vitro propagation may be of interest for accelerating tree improvement programs to these hardwood species. This review provides a summary of the advancement in the application of in vitro propagation to oak species of Kumaun West Himalaya India.

Principle

Orchid seeds are produced in large numbers but are exceedingly small, hence are also called “dust seeds” may be as small as 0.01 by 0.05 mm in dimension and weigh as little as 10-30 ug. Seedling development is generally a slow process in orchids, with the seedlings passing through an initial stage, termed the protocorm stage, prior to the production of distinct vegetative organs (leaves, roots, etc). The protocorms of terrestrial orchids are subterranean and entirely heterotrophic, with all of the nutritional needs of the orchid being supplied by the mycorrhizae (the symbiotic fungus). The length of the protocorm stage is variable, however, in many cases, months, or even years, elapse before leaves and roots are produced.

The combination of a small seed size and fungal symbiont requirement largely precludes the propagation via conventional seed propagation protocols. Accordingly, most of the early research on the development of orchid seed germination protocols focused on in vitro germination with the seeds and fungal symbiont being sown on the same petri plate. Successful protocols were developed for several species; however, the process was complicated by the diversity of fungal symbionts required (across orchid taxa) and the difficulty in isolating and culturing these fungi.

In the 1920’s the process of orchid seed propagation was revolutionized by Lewis Knudson with the demonstration that nutrient media that could be used as a substitute for fungal infection. The isolation and culture of multiple fungal strains was no longer required, and improvements in germination frequency, germination speed, and seedling vigor were generally observed. To date, successful asymbiotic germination techniques, termed ‘flasking’, have been developed for many epiphytic orchids, with several species being saved from extinction via the application of these techniques.

Aplant collector and conservationist faces many problems. These include adverse weather, limited availability of personnel, insufficient material because of poor growing season, general scarcity of the plant in the target region, grazing of the plant by animals, damage by pests or diseases or immaturity of the material. These problems are common to both seeds and vegetative propagules. The vegetatively propagated plant material face another unique problem related to excessive weight and bulk. The cost and inconvenience of transporting large amounts of material can be a limitation on the scope of a plant exploration mission. There is additional need to maintain selected clones in a disease-free condition for distribution to national programmes.

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.

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.

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.

8.1. INTRODUCTION

Exploitation of heterosis through development of hybrid wheat is one of the most attractive options to increase wheat productivity. The efforts on developments of hybrid wheat started in early fifties (Kihara, 1951; Fukasawa, 1953) through cytoplasmic male sterility system (Livers and Heyne, 1968). Later, in seventies, research works from public as well as private sectors have shifted their efforts to the use of gametocide (chemically hybridizing agent-CHA), and a number of gametocides were tested in eighties. In wheat, heterosis is especially interesting for grain yield and for the resistance of plants to both parasites and climate risks (Rousset, 1986). With this advantage in mind, the first phase of hybrid wheat development started in the United States in 1975. Chronological events of wheat hybrid development have been given in Table 8.1. Subsequently, a number of hybrid wheat has been released in countries such as Argentina, France, and United States (Pickett, 1993).

Objectives
    
·    Creation and use of large databases of Biological information to augment traditional laboratory based biology.
    
·    Analysis and interpretation of genomic and structural data using computational techniques from Mathematics, Statistics and Computer Science.
    
·    Explain the process and mechanism of evolution by comparing the Genomes of different species.
    
·    Development of new methods and technologies for understanding and diagnosis of genetic diseases and design of drugs for their treatment.

Biological sequences like the nucleotide and amino acid sequences can be analyzed by means of the sequence alignment. The objective behind this is to obtain knowledge regarding the similarity between the query and the target sequence to decipher the structure, function, homology of the query sequence.

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.

1.     Tissue Collection and Culture
    
2.     Trypsinization of Cells
    
3.     Cell Separation by Density Gradient Method
    
4.     Low Speed Separation of Cells
    
5.     Isolation of Lymphocyte
    
6.     Cryo Preservation
    
7.     Isolation of Spleen Cells
    
8.     Isolation of Peritoneal Macrophage
    
9.     Isolation of Blood Dna
    
10.     Differential Count of Leucocytes
    
11.     Slide Gel Electrophoresis
    
12.     Haemagglutination Assay
    
13.     Elisa
    
14.     Western Blotting
    
15.     Widal Test
    
16.     Identification of Y-chromosomes in Cattle using Pcr

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

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.

ANN is a Mathematical model or Computational model based on biological neural networks. It consists of an interconnected group of artificial neurons and processes information using a connectionist approach to computation. Neural Networks are non-linear statistical data modeling tools. That can be used to model complex relationships between inputs and outputs or to find patterns in data.

Bioinformatics is a discipline that deals with computation of biological information. Bioinformatics is a newly emerging interdisciplinary research area spanning a range of specialties that include biology, biophysics, computer science, mathematics & statistics. It makes use of scientific and technological advances in the area of computer science, information technology and communication technology to solve complex problems in life sciences particularly problem in Biotechnology.

Explosive growth in biological data from large sequencing projects that are producing nucleotide sequences continuously at a faster rate and the content of the nucleotide database is doubling in every 14 months. The latest release of Gene bank (v.102) exceeded one billion base pairs. To cope with this huge volume of data, a new scientific discipline has emerged comprising bioinformatics, biocomputing & computational biology.

Introduction

After the advent of Post Genomic era, Biological data is accumulating at an electrifying pace every day. Storage and analysis of these data serve as a major source for scientific research to understand the phenomena of origin, evolution and existence of various forms of life. The management of these data requires different statistical techniques used for retrieval, storage, analysis and extraction of precise information from small as well as large biological datasets. Application of statistical tools in Bioinformatics especially in fisheries data has been reported (Roy and Martha, 2008).

Abstract

The protein classification prediction is an important Problem in molecular biology, and one that has attracted a lot of attention, because there is a gap between sequence and structure of proteins from various resources. The proteins can be usually classified into one of the four structural classes; they are all-a, all-b, a/b and a+b. To address the problem of protein classification, many different algorithms and efforts have been made so far. In this paper, a new rule based data mining method for the prediction of protein structural classes is constructed using Rough Sets algorithm. Rough Sets Theory (RST) is a new mathematical approach to study the realistic information (Z. Pawlak, 1982). It focuses on knowledge reasoning by the whole set directly approximating to the incomplete and uncertain information. There are studies on the knowledge reduction and features selection of mass data. To apply rough sets algorithm, a decision table is constructed using Amino acid compositions and eight physicochemical properties data as conditional attributes. The generated decision rules after reducing the decision system can be used to classify new objects.The classification results of Rough Sets is verified by using self-consistency and jackknife tests on the datasets constructed by G.P. Zhou and comparison is made with some of the previous works.

5.1. INTRODUCTION
     
Rice is an important provider of nourishment for the world’s population. Indian scented rice, ‘Basmati’ has dominated the domestic and international market for aroma. Aromatic rice is an important commodity worldwide and command premium price over non-scented varieties. Most of the trade in aromatic rice is from India, Pakistan and Thailand. Bulk of aromatic rice from India and Pakistan consist of Basmati, while Thailand is the supplier of Jasmine rice. The Indian subcontinent has the Natural Gift of basmati rice that has been accepted as the best scented, long and slender grain in the world markets and gets high price. In addition to Basmati, many local landraces are grown traditionally, which excel in aroma, grain quality and cooking quality. Most of these genotypes are short bold to medium bold grain and hence not traded in the international market. However, in the domestic market its demand is greater than the Basmati rice. These are mainly used for special preparation, such as Khir in Bengal.

Influenza a Pandemics