eChapters

13.1. INTRODUCTION

Pearl millet crop has a wide adaptability to local environments. It is hardy and can be grown in areas which are very hot and dry and on soils too poor for sorghum. Pearl millet is considered more efficient in utilization of soil moisture and has a higher level of heat tolerance than even sorghum and maize. It is adapted to warm and dry climate but most of the area under the crop is in drought- prone areas of the world. In these areas, pearl millet is usually grown with limited inputs, sparse rainfall, low soil fertility, and also face disease and pest problems, with correspondingly poor yields.
 
The low average yields are primarily a result of the hot, dry conditions where pearl millet is mostly grown, rather than pearl millet plant’s capability. Pearl millet hybrids grown under better conditions yield 3000 to 4000 kg/ha compared to 300 to 800 kg/ha when moisture and soil fertility become limiting factors. A majority of the subsistence farmers who typically cultivate this crop are unable to take advantage of high yield potential because they have limited options for improving their management practices. Pearl millet production can be increased through growing varieties/hybrids with improved tolerance to drought, diseases and responding to higher rates of fertilizer applications.

12.1. INTRODUCTION

Sorghum [Sorghum bicolor (L.) Moench] is an important food/feed/fodder crop in more than 90 countries across the world and it is one of the cheapest sources of energy and micronutrients (Reddy et al., 2009; Ashok Kumar et al., 2011). Considerable efforts have been made to improve sorghum productivity through genetic enhancement and crop production and protection research all over the globe. Sorghum being an often cross-pollinated crop with cross pollination up to 2-15% depending on genotype and environment (House 1985), initially, pure-lines were the target products although phenomenon of heterosis was demonstrated in sorghum as early as in 1927 (Conner and Karper, 1927). Predominant self-pollinating nature of sorghum with tiny florets with single seed per emasculation and pollination prevented commercial exploitation of heterosis for commercial sorghum production. However, the discovery of a stable and heritable cytoplasmic-nuclear male-sterility (CMS) mechanism (Stephens and Holland, 1954), enabling large-scale, economic hybrid seed production gave a fillip to the exploitation of heterosis since early 1960s. The first commercial sorghum hybrid CSH 1 was released in 1964 in India. Using CMS mechanism, large number of commercial hybrids have been developed and released/marketed for commercial cultivation in all sorghum growing regions with strong Indian National Agricultural Research Systems (NARS).

11.1. INTRODUCTION

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop and is the dietary staple of more than 500 million people in over 90 countries, primarily in the developing world. It is grown on 47 m ha in 104 countries in Africa, Asia, Oceania, and the Americas. Among those, USA, Nigeria, India, Mexico, Sudan, China, and Argentina are the major sorghum producers globally. Sorghum grain is mostly used directly for food (55%), and is consumed in the form of porridges (thick or thin) and flat breads; however sorghum is also an important feed grain (33%), especially in Australia and the Americas. Stover (crop residue after grain harvest) is an important fodder source to both milch and draft animals in mixed crop-livestock systems. Sorghum is also a good source of green fodder due to its quick growth and high yield and quality of biomass. Of late, sorghum with sugar-rich juicy stalks (called sweet sorghum) is emerging as an important biofuel crop. Thus sorghum is a unique crop with multiple uses as food, feed, fodder, fuel and fiber. Sorghum is generally grown in rainy season (spring) but in India it is grown in both rainy and postrainy seasons. The postrainy season sorghum grain is prized for its food value (Reddy et al., 2009).

10.1. INTRODUCTION

The development of hybrid breeding methodology in maize and its successful application to exploit heterosis is considered as significant achievement of plant breeding in the present century. 
Even though Beal (1880) suggested for commercial cultivation of F1 varietal hybrids. It was Shull (1909) on the basis of his experiment gave pure line method of corn breeding, which laid foundation for present day hybrid breeding. Pure line methods of maize breeding involve three steps. 
    
·    Large scale inbreeding to obtain many homozygous/nearly homozygous inbred lines. 
    
·    Testing the selected inbred lines in all possible crosses.
    
·    Practical utilization of inbred lines in seed production of single cross hybrids.

9.1. INTRODUCTION

Maize (Zea mays L. ssp. mays 2n = 20), known as corn in some countries is an important cereal crop of the world. The scientific name from Greek word ‘Zea’ for a kind of grain and West Indian word ‘malnis’ for corn. Maize was domesticated in Mesoamerica and hence formed the Mesoamerican people’s identity and later it spread throughout American continent. Maize is widely cultivated throughout the world and a greater weight of maize is produced each year than any other cereal grain. USA produces almost half of the world’s harvest (42.5%) and other top producing countries include China, Brazil, Mexico, Argentina, India and France. During the year 2007, worldwide maize productivity was around 4970 kg per ha. Maize is the only cereal that can be harvested and used at various stages of plant development. The crop can be cultivated on a wide area from 580 N to 400 S from below sea level to altitudes higher than 3000 m and in areas with 250 mm to more than 5000 mm of rainfall per year (Shaw, 1988, Dowswell et al., 1996).

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).

7.1. INTRODUCTION

The cultivation of wheat (Triticum spp.) reaches far back into history. Wheat was one of the first domesticated food crops and for 8000 years has been the basic staple food of the major civilizations of Europe, West Asia and North Africa. Today, wheat is grown on more land area than any other commercial crop and continues to be the most important food grain source for humans. Its production leads all crops, including rice, maize and potatoes.

Wheat is special in several ways. It is grown on more than 240 million ha, larger than for any other crop, and world trade is greater than for all other crops combined. The raised bread loaf is possible because the wheat kernel contains gluten, an elastic form of protein that traps minute bubbles of carbon dioxide when fermentation occurs in leavened dough, causing the dough to rise (Hanson et al., 1982). It is the best of the cereal foods and provides more nourishment for humans than any other food source. Wheat is a major diet component because of the wheat plant’s agronomic adaptability, ease of grain storage and ease of converting grain into flour for making edible, palatable, interesting and satisfying foods.

6.1. INTRODUCTION

After introduction of TN-1 (Taichung Native-1), Jaya, IR8 and other high yielding rice varieties during sixties and seventies, the productivity increased drastically and remained at plateau since last three decades. With no possibility to extend land area for rice cultivation in Asia, there is some scope for production advantages in rice through further expansion of high yielding varieties coverage in Pakistan, Thailand and India, expansion of area under irrigation in Bangladesh, Cambodia, India, Myanmar, the Philippines, Thailand and Vietnam, or expansion of boro rice in Bangladesh, India and Myanmar. Thus, utilization of heterosis has become one of the main methods for increasing yield. Hybrid is one of the viable and proven technologies to improve rice productivity. China is the first successful country to produce hybrid rice in appreciable quantity. This technology not only helped China to increase the rice productivity, but also to save land for crop diversification. The 'National Food Security Mission' has been launched envisaging increase of annual rice production by 10 million tons by 2011-'12. Here, hybrid rice may play important role to achieve the assigned target.

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.

4.1. INTRODUCTION

Rice (Oryza sativa) is the major food crop in the world. Nearly 40% of the world population consumes rice as the major staple food. Most of the people, who depend on rice as primary food, live in the less developed countries.  Archeological evidence on rice in India dates back to 1500-1000 B.C. Since the dawn of civilization, rice has served humans as a life-giving cereal in the humid regions of Asia and, to a lesser extent, in West Africa. Introduction of rice into Europe and the America has led to its increased use in human diets. There are 42 rice producing countries throughout the world but China and India are major rice production centers. Rice is grown in wide range of agro-climatic conditions ranging from mountainous (Jammu) lands to low land delta areas (Sundarban), spanning an area from 53° latitude north to 35° south of the world but about 90% of the crop is grown and consumed in Asia. Rice provides fully 60% of the food intake in Southeast Asia and about 35% in East Asia and South Asia. The highest level of per capita rice consumption (130-180 kg per year, 55-80% of total caloric source) takes place in Bangladesh, Cambodia, Indonesia, Laos, Myanmar (Burma), Thailand, and Vietnam (Kenneth and Kriemhild, 2000). In many cultures of the world rice is the central part of people’s life and culture. Rice is an excellent food and is an excellent source of carbohydrates and energy.

3.1. INTRODUCTION

Heterosis is the superiority of the F1s over the parental forms. The term heterosis was first used by Shull (1910) to describe the interpretation of increased vigour, size, fruitfulness, speed of development, resistance to diseases and insect pests or some other characteristics manifested by out-breeding organisms as compared to corresponding inbreds. Exploitation of heterosis is gaining momentum due to increased yield, quality, uniformity, better desirable traits and management of biotic stresses. The future of most of the economic crops will be for hybrids for sustainable development of higher economic returns to the farmers. Sustainable increase in area under hybrid crops is witnessed by its popularity and adoption by the farmers.

2.1. INTRODUCTION

Pollination is the process of mating in plants, that is, the transfer of pollen from anther to stigma. In flowers, pollen delivered to the stigma through a wide range of mechanisms that ensure an appropriate balance in the genetic makeup of the species. Most plant species have evolved ways to ensure an appropriate degree of interchange of genetic material between individuals in the population, and cross-pollination is the normal type of pollination. Plants benefit most by being pollinated by other individuals because this broadens the genetic characteristics of individual plants. As a result, they are more adaptable to necessary changes. Self- and often-pollinated crops evolved from cross pollinated crops.

Pollination followed by fertilization is important in agriculture, particularly for the crops whose economic part is either fruit or seed, such as, rice, wheat, fruit vegetables etc. For other crops, these events are also important for production of seed for cultivation of next generation, for examples, green vegetables (amaranth, palak, cabbage, cauliflower etc).

The study of pollination brings together many disciplines, such as botany, plant breeding, horticulture, entomology, and ecology. The pollination process as an interaction between flower and vector was first addressed in the 18th century by Christian Konrad Sprengel. It is important in horticulture and agriculture, because fruiting is dependent on fertilization, which is the end result of pollination.

1.1. INTRODUCTION

During the last 30 years, India’s food production nearly doubled from 102 million tons. Almost all of this increase resulted from higher yield in all food grains rather than increase in area, particularly wheat, rice, maize and some extent in pulses and oil seed crops. This has contributed to a significant reduction in poverty from 55% to 26% (Dar, 2011). The increase in yield is the result of scientific innovations in India and other parts of the world and their adoption in India.

In 1871, the Government of India created Department of Agriculture. The impact of these departments in enhancement of crop productivity was not remarkable. Later, the Government of India established the Imperial Agricultural Research Institute in 1905 in Pusa, Bihar to enhance the agricultural research and education. Later, the headquarter of Imperial Agricultural Research Institute has been shifted to New Delhi in the year 1936. The name of the institute has been changed in 1946 as Indian Agricultural Research Institute. To boost the agricultural Research activities, Imperial Council of Agricultural Research was established in the year 1929, subsequently, the name of Imperial Council of Agricultural Research has been changed to its present form of Indian Council of Agricultural Research (ICAR) in 1946. Since then, ICAR playing significant role in all sphere of agricultural research, education and extension. A number of varieties and hybrids of different crops have been developed and released by the scientists of ICAR. To test the outcome of the agricultural research, ICAR has started All India Coordinated Crop Improvement Projects, which provide an efficient channel for multilocation testing of newly evolved strains.

1.     Isolation and Purification of DNA from E.coli
    
2.     Isolation of Plasmid DNA
    
3.     Gel Electrophoresis of DNA
    
4.     Southern Blotting
    
5.     Restriction Digestion

1.     Maintaining Embryonic Stem (ES) Cells
    
2.     Establishing ES Cells
    
3.     Freezing of ES Cells
    
4.     Thawing of Frozen ES Cells
    
5.     Production of Transgenic using ES Cells
    
6.     MTT Assay for Cell Viability

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

1.     Animal Biotechnology Laboratory
    
2.    Growing Cells with Serum-Basal Medium Eagle (BME), MEM
    
3.     Media Preparation and Sterilization
    
4.     Contaminations in Animal Tissue Culture

1.     Isolation of Plant DNA
    
2.     RAPD Analysis of Genomic DNA
    
3.    Agro Bacterium based Transformation in Plants
    
4.     Assay for Gus Operon
    
5.     Confirmation of Transformation using Polymerized Chain Reaction (PCR)
    
6.     Primer Designing
    
7.     Isolation, Purification and Identification of Plant Secondary Metabolites
    
8.     Evaluation of Antioxidant Activity of Plant Extract
    
9.     Estimation of Total Phenolic Content in A Plant Extract
    
10.     Estimation of Total Flavanoid Content

1.     Plant Tissue Culture Laboratory
    
2.     Cleaning and Sterilization of Glass Wares
    
3.     Media Sterilization
    
4.     Media Composition and Media Preparation
    
5.     Callus Culture in Carrot
    
6.     Culture of Shoot Tip (Vanilla)
    
7.     Anther Culture of Datura
    
8.     Subculture of Carrot Callus
    
9.     Hardening of Plantlets
    
10.     Isolation of Protoplast from Plant Leaves

1.     Preparation of Liquid and Solid Media
    
2.     Isolation of Pure Culture
    
3.     Analysis Bacterial Growth Curve
    
4.     Study of Effect of Carbon Source on Bacterial Growth
    
5.     Gram Staining
    
6.     Aseptic Cell Transfers
    
7.     Prokaryote Cell Number by Dilution Plating
    
8.     Cell Mass by Measurement of Turbidity
    
9.     Isolation of Bactriophage from Sewage Sample
    
10.     Standard Plate Count
    
11.     Imvic Test
    
12.     Antibiotic Sensitivity Test on Microbes
    
13.     Study of Transformation In Bacteria
    
14.     Study of Bacterial Conjugation
    
15.     Effect of pH and Temperature on Bacterial Growth
    
16.     Immobilization of Yeast Cells and Alcohol Production
    
17.     Citric Acid Production using Aspergillus Niger
    
18.     Alcohol Production from Yeast and Estimation of Alcohol

1.     Rules and Regulation for Safety in a Microbiology Laboratory
    
2.     Cleaning of Glass Wares
    
3.     Sterilization

1.     Extraction of b-galactosidase from Yeast Cells
    
2.     Measurement of Enzyme Activity
    
3.     Immobilization of Enzymes
    
4.     Precipitation of Enzyme and Proteins
    
5.     Protien Purification by Dialysis

1.     Asssay for Catalase
    
2.     Assay for Peroxidase
    
3.     Assay for Poly Phenol Oxidase
    
4.     Assay for Phosphatases

Enzymes are biocatalysts composed of amino acids. Enzyme reactions are highly specific. It binds to the substrate to form a reversible intermediate product called enzyme substrate complex. As the concentration of the substrate increases the rate of formation of the intermediate complex also increases. This increase in velocity of the reaction is in a hyperbolic manner till it achieves the maximum velocity called Vmax .At this point all the enzymes will be in the form of ES complex. Substrate concentration will be in at its optimum level i.e. further increase in substrate concentration will not affect the rate of the reaction. The substrate concentration at which the rate of the reaction is half the maximum velocity Vmax is called the Michaelis-Menten constant, Km. This is constant for the given enzyme acting on the same substrate.

1.     Chromatography
    
2.     Identification of Sugar in Fruit Juice by Thin Layer Chromatography
    
3.     SDS-PAGE
    
4.     Composition for Native PAGE
    
5.     Silver Staining of Protein Gels

1.     Determination of lmax
    
2.     Verification of Beer-Lambert Law
    
3.     Estimation of Carbohydrate by Anthrone Method
    
4.     Estimation of Reducing Sugar by Di Nitro Salicylic (DNS) Acid
    
5.     Estimation of Protein by Biuret Method
    
6.     Estimation of Protein by Lowry’s Method
    
7.     Estimation of Protein by Bradford Method
    
8.     Estimation of Cholesterol
    
9.     Estimation of DNA
    
10.     Estimation of RNA
    
11.     Determination of iso Electric Point of Amino Acid

1.     Common Solvents
    
2.     Common Buffer Compositions

1.     Centrifuge
    
2.     Spectrophotometer
    
3.     Microscope

1.     Equipments

1.     General Precautions
    
2.     General Requirements for Biotechnology Laboratory

1.     Concentration

1.     Length and Size
2.     Volume
3.     Weight

Introduction

Since the onset of human civilization molluscs have a tremendous impact on Indian tradition and economy. In India, molluscs have been in great demand as ornaments, currency, as popular panacea for illnesses and as mascot for ward off evil spirits in olden days. Now, molluscs have assumedgreater significance in our industrial, technological and aesthetic aspects of life, in addition to edible utility. Several species of gastropods and bivalves are traditionally fished for food and shell from time immemorial. About 80,000 - 1, 00,000 species of molluscs are recorded from the world over and a total of 3271 species are recorded from India. They are represented in 220 families and 591 general and the spectrum comprise of 1900 gastropods,1100 bivalves,210 cephalopods,41 polyplacophores and 20 scaphopods (edible and ornamental) and 14 species of cephalopods are exploited on commercial basis in India(Appukkuttan et al.,1989). It is difficult to categories shells satisfactorily according to their uses as many are collected for several purposes. The main categories are shown in the Table-1.

INTRODUCTION

Insects are the major group of arthropods and the most diverse group of animals across the Earth. Though some of them are beneficial to environment and to humans, many insects are considered as pests as they transmit diseases and damage the crops and forests. Chemical, biological, cultural and mechanical methods are being used to eradicate, control or manage these pests. The main strategy used for controlling pests has been the use of chemical pesticides because of their long residual action and wide spectrum toxicity (Casida and Quistad, 1998). However, the indiscriminate usage of chemical pesticides are toxic to mammals, birds and fish, also pollute the environment, besides the development of pest resistance and the emergence of secondary recalcitrant insect pest populations (Li et al., 2007). These negative impacts prompted the change of strategies in managing the pests by resorting to ecofriendly and cost effective pest control strategies (Ferre et al., 1991). 

SYSTEMS BIOLOGY

The ultimate goal of any biological experiment is to understand biological systems in sufficient detail to enable accurate, quantitative predictions about the behavior of the systems, including predictions of the effects of modifications of the systems. To precisely simulate the behavior of the system using a computer model is one of the ways to achieve the above goal and in this venture we are nowhere close to the goal. Systems biology will help us to get closer to this goal and it is expected that biologists to adopt to take advantage of the power of systems biology approach. Systems biology is an emergent field that aims at system-level understanding of biological systems. Systems Biology is the study of the interactions between the components of biological systems, and how these interactions give rise to the function and behavior of that system. For example, theenzymes and metabolites in a metabolic pathway.With the progress of genome sequence projects and range of other molecular biology projects that accumulate in-depth knowledge of molecular nature of biological system, we are now at the stage to seriously look into possibility of system-level understanding of solidly grounded on molecular-level understanding.Unlike molecular biology which focus on molecules, such as sequence of nucleic acids and proteins, systems biology focus on systems that are composed of molecular components. Although systems are composed of matters, the essence of system lies in dynamics and it cannot be described merely by enumerating components of the system.

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.

Abstract

A Mathematical Method for Artificial Neural Networks offers an original, broad and integrated approach that explains each tool in a manner that is independent of specific ANN systems. Artificial Neural Networks are abstract mathematical models of brain structure and functions. They are nothing but a mathematical model that relies on varying the strength of connections between the internal processing elements to interpret data. They can be applied to many pattern classification problems. In this paper, it has been used to predict the level of amino acid in protein sequences. Amino acids are the building blocks of proteins. It is any molecule that contains both amine and carboxylic acid functional groups. Here, known protein sequences of ingredients are taken as input patterns. The network is trained using back propagation algorithm with sigmoid function as activation function by generating random weights. It is tested again with unknown protein sequence. Error is calculated by the difference between actual network output and desired output. If the training is successful the patterns are correctly classified. The network is trained until the error is minimum. The amino acid level is thus predicted in a particular protein sequence.

Abstract

The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae)are obligate parasitic trematodes residing in the large biliary ducts of the herbivorous mammalian hosts causing fascioliasis worldwide. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the phylogenic location of Fasciola sp. of Assam (India) origin based on rDNA molecular data,ribosomal ITS regions were sequenced (Accession numbers- EF027103 and EF027104) and compared with other species of trematodes in the family Fasciolidae that includes, Fasciolopsis buski and Fascioloides magna besides the species of Fasciola. NCBI databases were used for sequence homology analysis using BLAST; multiple sequence alignments were performed using ClustalW program.The phylogenetic trees constructed based upon the ITS (I & II) sequences by multiple tree building methods in MEGA revealed a close relationship with isolates of F. gigantica from China, Indonesia , Japan, Egypt and Zambia, the isolate from China with significant bootstrap values being the closest. Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships 

Data Mining is the process of automatic discovery of novel and understandable models and patterns from large amounts of data. Bioinformatics is the science of storing, analyzing and utilizing information from biological data such as sequences, molecules, gene expressions, and pathways. Development of novel data mining methods will play a fundamental role in understanding these rapidly expanding sources of biological data. Data mining techniques are an automated means of reducing the complexity of data in large bioinformatics databases and of discovering meaningful and useful patterns and relationships in data. Bioinformatics, the application of computational techniques to analyze the information associated with biomolecules 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. It provides an introduction and overview of the current state of the field. The main principles that underpin bioinformatics analyses look at the Data Mining in Bioinformatics and databases that are commonly used, and finally examine some of the studies that are being conducted, particularly with reference to transcription regulatory systems.

The dream of having genomes completely sequenced is now a reality. The complete sequence of many genomes including the human one is known. However, the understanding of probably half a million human proteins encoded by less than 30’000 genes is still a long way away and the hard work to unravel the complexity of biological systems is yet to come. A new fundamental concept called proteome (PROTEin complement to a genOME) has recently emerged that should drastically help to unravel biochemical and physiological mechanisms of complex multivariate diseases at the functional molecular level. Proteomics involves the systematic study of proteins in order to provide a comprehensive view of the structure, function and regulation of biological systems. Coupled with advances in bioinformatics, this approach to comprehensively describing biological systems will undoubtedly have a major impact on our understanding of the phenotypes of both normal and diseased cells. Initially, proteomics focused on the generation of protein maps using two-dimensional polyacrylamide gel electrophoresis.

Keeping pace with latest technologies Central Institute of Freshwater Aquaculture (CIFA) has attempted to develop the following three databases on the following aspects for quick retrieval of information resources. The brief description of the databases is presented below for easy comprehension.

CD-ROM Database on Socio-Economic Aspects of Carp Culture in Kolleru Lake (Pictorial)

In the era of 21st century world is progressing fast towards the electronic media of communication and the real revolution has been brought about in the information technology. It has revolutionized the collection, storage and retrieval of information very speedily and accurately. One of the IT tools like CD-ROM (Compact Disc Read Only Memory) plays an important role in storing the huge data and can be easily carried to remote places. Since it is lightweight, pocket sized and can hold about 660 megabytes of data which is equivalent to 3 lakh pages. CD-ROM is a high capacity optical disc. It is 12 cm diameter, made of durable plastic with a reflective metal coating and lacquered surface. Considering all these advantages an attempt has been made to develop a database on socio-economic aspects of carp culture in Kolleru Lake which is immensely helpful to all scientific and farming community (Roy et al., 2004).

ABSTRACT

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Microarray expression analysis has become one of the most widely used functional genomics tools. Typical approaches to gene identification and functional characterization have and continue to involve protein characterization, peptide sequence determination, and identification of the corresponding DNA sequence. More recently, expressed sequence tags (ESTs), microarrays, large-scale gene expression (transcriptome) profiling, and associated informatics technologies are rapidly becoming commonplace in the sciences. These ‘genomic’ approaches typically take advantage of technologies for characterizing large numbers of nucleic acid sequences, bioinformatics, and the expanding collection of nucleic acid sequence data.

INTRODUCTION
 
Environment and ecological set up is maintained by the climatic conditions, presence and compositions of gases present in them, humidity level, temperature and the pollution. These conditions are responsible for the emerging of diseases in the environment. The diseases in plants, animals and human beings are due to the factors that affect the ecology. This also depends on the organism whether they are susceptible or resistant to the specific disease. This means the genetic level of the organism is an important factor.
Plant pathology or phytopathology is the study of diseases in plants. The disease evolution may be due to the climatic condition, humidity level, temperature and the genetic character of the plant and the pathogen. The parasitic adaptation of microorganisms to be plant pathogens includes acquisition of the following three abilities: 1) ability to enter into a plant, (2) ability to overcome the resistance of the host and (3) ability to evoke disease.

ANTIBIOTICS

Antibiotic is a drug used to treat infections caused by bacteria and other microorganisms. Technically an antibiotic is a substance produced by a microorganism that selectively inhibits the growth of another. Penicillin was the first antibiotic discovered by Alexander Fleming in 1928, a significant breakthrough for medical science. Antibiotics had saved thousands of wounded soldiers in the I and II world wars. Also, use of it made surgery safer and increased the average life expectancy of human beings. Antibiotics are among the most frequently prescribed medications in modern medicine. Some antibiotics are ‘bactericidal’, meaning that they work by killing bacteria. Each type of antibiotic affects different bacteria in a different way. Some antibiotics can be used to treat a wide range of infections and are known as ‘broad-spectrum’ antibiotics. Others are only effective against a few types of bacteria and are called ‘narrow-spectrum’ antibiotics.

Algae refer to an assemblage of polyphyletic organism that conducts oxygen evolving photosynthesis other than land plants. They are distributed widely throughout India in the sea, in fresh water and in moist situations on land. Algae also form an important component of biodiversity of Andaman and Nicobar Group of Islands. Database for Algae resources of Andaman and Nicobar Islands are created with an aim of providing an information pool to the researchers working in fields related to fresh water and marine water algae in Andaman and Nicobar Group of Islands. About 313 fresh water algal species belonging to 15 families and 57 marine algal species belonging to 18 families has included in this database among which 40 species has been found to be first time reported in India. Algae have a wide application in a variety of Industries such as Food, Fodder, and Fertilizer etc. They are also important sources of Protein, Iodine, Vitamins, Minerals and Substances of Antibiotic Nature.

The role of bioinformatics in genomics and molecular biology research can be likened to the role of intelligence gathering in battlefield. Intelligence is clearly very important in leading to a victory in the battlefield. Computational algorithms are the heart of bioinformatics as they enable predictions, understanding and interpretation of the data generated from laboratory experimental research carried by biologist. This article discusses one such approach called Decision tree induction and its application for generating rules from a dataset extracted from biological databases.

Decision Tree (DT) is one of the most popular choices for learning from feature based examples. They are especially attractive in data mining environment for several reasons. First due to their intuitive representation, the resulting classification model is easy to assimilate by humans. Second, DT does not require any parameter setting from the user and thus are especially suited for exploratory knowledge discovery. Third DT can be constructed relatively fast and accuracy of DT is comparable or superior to other classification models.

The coral reef ecosystem is one of the most diverse ecosystems, which is housing for an amazing diversity of organisms and estimation of species richness ranges from 650 000 to over 9 million. For this reason, coral reefs often are referred to as the “rainforests of the ocean”1.Prokaryotes represent overriding life form on the planet and are almost certainly the most diverse component of coral reef communities2. Corals have been known to harbour many different species of bacteria.

The rise in the number of drug-resistant pathogens and the limited success of strategies in providing new agents indicate an uncertain forecast for future antimicrobial therapy. So it is critical that new groups of microbes from unexplored habitats be pursued as sources of novel antibiotics. Marine actinomycetes serve as a logical target given the historical significance of their terrestrial counterparts in antibiotic production. Isolation strategies directed towards new marine-derived actinomycetes have been lacking, but it is clear that such procedures will increase the understanding of marine bacterial diversity and yield many novel marine natural products. Though recent literatures report the isolation of novel class of actinomycetes from marine sediments and sponges, reports on actinomycetes associated with corals are very scanty. Therefore in this study we attempted to characterize the actiomycetes diversity associated with the coral Acropora digitifera from the Gulf of Mannar, Southern coast of India. The antibacterial potential of the isolated actinomycetes was also investigated.

A fundamental problem facing researchers today is how to make effective use of available wealth of online background domain knowledge to improve their understanding of complex biological system. Effective use of such online background domain knowledge plays a crucial role in all stages of integrated biological studies.

In the past years, research in molecular biology and molecular medicine has accumulated enormous amounts of data. This includes genomic sequences gathered by the Human Genome Project, gene expression data from micro array experiments, protein identification and quantification data from proteomics experiments, and SNP data from high-throughput SNP arrays. However, the understanding of the biological processes underlying these data lags behind. There is a strong interest in employing methods of knowledge discovery and data mining to generate models of biological systems. Mining biological databases put forward challenges which knowledge discovery and data mining have to address in the future. Important background knowledge in bioinformatics is often contained in documents, such as scientific publications or database annotations. Analyzing data from biological databases often requires the consideration of data from multiple relations rather than from one single table. Recently, approaches (such as propositionalization algorithms) are being studied that utilize multi-relational data and yet meet the efficiency requirements of large-scale data mining problems.

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.