eChapters

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.

Abstract
This chapter describes how modern quantum mechanical methods can be applied in a systematic manner to understand pharmacophore and mechanistic aspects of drugs. This chapter also explains why accurate computation of drug-receptor interactions is important for in silico drug designing and testing.

WHY in silico DESIGNING?
Drug designing is the inventive art of finding a new lead compound based on knowledge of its biological target and then its slow conversion to a compound of therapeutic benefit to patient termed as “drug”. This whole process comprises of long sequels of synthesizing compounds followed by their testing and activity evaluation procedures; often a seemingly endless task until desired potency level is achieved.

Evolution is a self-occurring natural phenomenon by which new organisms develop gradually as a result of change in genetic pool of a population. It is a very widely and historically studied phenomenon which still surprises scientists due to its underlying complexity. The three processes which contribute most to evolution are genetic drift (also known as random drift or allelic drift), natural selection and mutations. Genetic drift and natural selection act at a population level, whereas mutations act at individual level. For evolution to occur, the changes these processes bring about must be heritable, which they are.
 
Genes are present on chromosomes inside nucleus of the cell and the collection of all the genes in a cell is known as the genome of that cell. Genome size and complexity varies from species to species. Simple organisms, such as bacteria and protozoans have a very simple genome, with very few genes, whereas complex higher organisms such as humans have a large genome, with thousands of genes. The position of a gene on a chromosome is known as a locus. Organisms may have more than one copy of a chromosome in the cell.

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 

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.

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.

The success of any crop improvement programme springs mainly from sound and genetically investigations carried out in the fields. However, the moment such biological populations are subjected to field evaluation, some external and non-heritable agencies come into active role. As a result, these agencies or factors mask real differences among the tested populations which stem purely from heritable or genetic factors. Their influence gets confounded with the latter. Consequently authentic data related to genetic differences are not available due to controllable and non-controllable errors. Further, physical data that are assembled in an experiment are often so voluminous and so vast that is perhaps humanly not possible to arrive at meaningful conclusions. Hence, an adequate knowledge of statistical principles and their appropriate use warrant perfection to a point where all possible sources of error can be well accounted for.

Nanotechnology is a field of applied science focused on the design, synthesis, characterization and application of materials and devices on the nanoscale. It is a sub classification of technology in colloidal science, biology, physics, chemistry and other scientific fields and involves the study of phenomena and manipulation of material at the nanoscale. This is involved in the creation of useful materials, devices, and systems used to manipulate matter at an incredibly small scale; between 1 and 100 nanometers. With nanotechnology, a large set of materials with distinct properties (optical, electrical, or magnetic) can be fabricated. Nanotechnologically improved products rely on a change in the physical properties when the feature sizes are shrunk.

1.1. INTRODUCTION

In this chapter, we will know how to classify raw data. The purpose of classifying raw data is to bring order in them so that they can be statistically analysed easily. Classification of objects or things saves our valuable time and effort. It is done in a logical manner and similar things are arranged into a group or class.

6.1    Copyrights
    
6.2    Trademarks
    
6.3    Geographical Indications
    
6.4    Trade Secrets

Introduction
At the beginning of the 21^st century, with a population of 6.1 billion in 2000 and expected to be headed for 9.1 billion by 2050 (UN News Centre, 2005), the challenge of yet again increase food production by many folds only in 50 years has become a daunting task in itself. The situation is further worsen because now, we need to increase food production in sustainable way by 2050 on approximately the same area of arable land using less resources, particularly, fossil fuel, water and nitrogen, at a time when we must also mitigate some of the enormous challenges associated with climate change. Furthermore, there is the critical and urgent humanitarian need to alleviate poverty, hunger and malnutrition which is afflicting more than 1 billion people

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

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)

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

Introduction

Microbes (bacteria, archea and eukarya) are single celled organisms that rule the planet. Microbes occupy every possible niche, from the high atmosphere to the deep ocean, from hot springs to artic ice, from hot deserts to deep forests including many regions that cannot yet be accessed for study. The biosphere contains between 1030 and 1031 microbial genomes, which is about 2-3 times more than the number of plant and animal cells combined (67). In fact, studies have shown that microbes associated with the human body are about ten times more than the number of human cells (5).  Microbes play a critical role in the life cycle of all living organism and environment in general.  Some microbes cause disease, but the most of them are either innocuous or play a role in physiology and cellular response including immune response, digestion and vitamin production of various organisms.

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.

Abstract

DNA barcoding, an additional global standard taxonomic tool for identifying plant species helps the non-taxonomists also to identify the plant species in a more reliable way with the help of devices including nanotechnology. Researchers proposed various genes or gene portions as potential barcodes either singly or in combination, yet there is no standard/ universal barcode DNA region for plants. The more accurate plant DNA barcode region would have to be from highly variable markers in the nuclear genome preferably from multiple loci and in combination with variable DNA regions of chloroplast genome, to resolve the problems that arise due to hybridization, allopolyploidization and introgression. Nonetheless, the phylogenetically informative sites might not be the potential DNA barcode regions as the former requires synapomorphies unlike autapomorphies with high levels of informative characters in the latter DNA taxonomy, but could provide insights into genetic distances between species.

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.

Introduction

India is an agriculture based country with 60% of the manpower employed in agriculture (World Bank, 2010). Few of the main environmental issues are soil erosion, water pollution from raw sewage and runoff of agricultural pesticides. There is a need to maintain a sustainable environment and a sustainable agricultural system.  Sustainable Agricultural system is a self sustaining system, is dependent up the ability to bring together and manage simultaneously the soil, water, plant and animal resources with the limitation of climatic and environment in such a way that the agricultural production/profitability can be maintained in the future too. So initiatives need to be taken to achieve a sustainable agricultural system. Tools have been developed to aid agriculturist, extension personnel and policy makers. The World Wide Web has made the tools easy accessible.

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].