eChapters

Abstract

Drug design is a complex computational process that involves studying the structural and physicochemical properties of biological moieties in order to identify new chemical or biochemical substances that can be used as drugs with specific pharmacological properties. The drug discovery pipeline is a crucial aspect of drug design that requires a detailed understanding of the various phases involved. In this chapter, we discuss the fundamental principles and phases of drug design. Additionally, we delve into the concept of docking, a critical step in the drug discovery process that involves predicting the orientation and affinity of a ligand binding to a protein target. The use of computational tools and techniques in drug design has revolutionized the field and is essential for the development of safe and effective drugs.

Restriction enzymes cut only at specific sequences of 4 to 8 bases

A long restriction site is rare. Cutting rare sites will produce a few large pieces of DNA.

Restriction enzymes with long sites → small number of large fragments

Restriction enzymes with short sites → large number of small fragments

Objectives

• To study working principles of compound microscope
• Study different parts of compound microscope

Introduction

A compound microscope is an optical instrument consisting of two short focal-length convex lenses that are used to observe the highly magnified images of small objects by naked eyes. The compound microscope is capable of magnifying up to 1000 the image of a small object by complex system of lens arrangement. The working distance varies from 0.14 to 4 mm. Compound microscopes generally require the sample to be seen to be sufficiently thin, or translucent, to allow the light to pass. Such microscopes provide high magnification, but the view is two-dimensional.

Introduction
Cytoplasmic male sterility (CMS), a condition under which a plant is unable to produce functional pollen, is widespread among higher plants. CMS systems represent a valuable tool in the production of hybrid seed in self-pollinating crop species, including maize, rice, cotton, and a number of vegetable crops. Hybrids often exhibit heterosis, more commonly known as hybrid vigor, whereby hybrid progeny exhibit superior growth characteristics relative to either of the parental lines. CMS systems can be of considerable value in facilitating efficient hybrid seed production.
Male-sterility-inducing cytoplasms were recognized in the 1900s. Bateson and Gairdner reported male sterility in flax in 1921, was inherited from the female parent, although genes passed from both the male and female parents affected its expression. Chittenden and Pellow (1927) recognized that male sterility in flax was due to an interaction between the cytoplasm and nucleus, with the male sterility conditioned by the homozygous recessive nuclear genotype in combination with the sterility-inducing cytoplasm.

Introduction

This section of the manual contains instructions for preparing stock solutions that are commonly used in laboratory protocols for the analysis of DNA, RNA and proteins and visualization of gene or protein expression. Each of these stock solutions is provided as either the most convenient concentration or the most frequently used stock concentrations to be used in the protocols of an individual laboratory.

All chemicals must be reagent grade or molecular biology grade, and the water used in the preparation of all solutions must be the highest quality available. Use sterile-glass distilled deionised water whenever possible. Unless otherwise stated, most solutions required sterilization either by filtration or autoclaving.

The first step in applying the correct rate of fertilizer is calculating crop nutrient requirements. A soil test is the only way to measure how much P₂ O₅ and K₂ O are available in soils, and soil tests are available through several private and public laboratories.

Fertilizer Calculation

To compute the equivalent amount of fertilizer necessary to supply the corresponding amounts of nutrients, the following formula is used:

Introduction

In order to use a fine quality of DNA for various molecular biological work like sequencing, cDNA synthesis and cloning, RNA transcription, transfection, nucleic acid labeling (random primer labeling), etc., quality and quantity of DNA is extremely important to have the defined template concentration. Failure to produce results from the above techniques can sometimes be attributed to an incorrect estimate of the DNA template used.

History and Recent Developments

Richard P. Feynman in 1959 suggested that it should be possible to build machines small enough to manufacture objects with atomic precision. His talk “There is plenty of Room at the Bottom” is widely considered to be the foreshadowing of Nanotechnology. He delivered this talk at the annual meeting of the American Physical Society at California Institute of Technology (Caltech), In 1990, a team of IBM Physicists revealed that they could write (arrange) the letter IBM using 35 individual atoms of Xenon.

In 1992 a book entitled Nanosystems: Molecular Machinery, Manufacturing and Computation was published by Eric Drexler where he outlined a way to manufacture extremely high performance machines out of molecular carbon lattice (diamondoid).

Around year 2000, federal funding for Nanotechnology in the United States began with National Nanotechnology Initiative (NNI). NNI defined nanotechnology as dealing with materials with sizes between 1 and 100 nanometers exhibiting novel properties.

The Government of India, in May 2007 launched a mission on Nano sceince and nano technology (Nano Mission) with an allocation of `1,000 crores.

Solid state materials can exists in various forms namely:

1. Single crystals (preferred for authentic characterization of structure and physical properties)
2. Polycrystalline powders that are agglomerates of large number of crystallites and are used for characterization when single crystal cannot be easily obtained
3. Nanocrystalline or nanostructured materials that posses large surface area
4. Thin films that can be grown in the best crystalline form for many applications
5. Amorphous systems that have no long-range translational order

Principle

The rate of joining of DNA fragments is affected by seven parameters:

DNA concentration,

Concentration of compatible ends,

Size of the fragments,

Presence or absence of complementary, single-stranded ends (some nucleases form blunt ends and in these cases special techniques are needed for joining),

G + C content and length of the complementary single strands,

Temperature of the reaction and

Ionic composition of the solution.

Steps for Cloning

Prepare DNA.

Select restriction enzymes for your insert and vector, and determine the appropriate reaction buffers.

Combine the following in a microfuge tube (30 µL total volume):
2 µg DNA
1 µL Each Restriction Enzyme
3 µL 10x Buffer
3 µL 10x BSA
x µL H₂O (to bring total volume to 30 µL)

Principle

To retrieve and purify any specific DNA fragment from an agarose gel slice; the expected yield is from 50-75% of the amount in the gel slice.

Time required

Restriction digest - minimum of 2 hours

Electrophoresis - approx. 4 hours

Elution - 2-5 hours depending on fragment size

DNA Purification -2 hours

Principle

RNA is negatively charged at neutral pH and when an electric field is applied, it migrates towards the anode. RNA retains much of its secondary structure during electrophoresis unless it is first denatured. The addition of formaldehyde to the agarose gel maintains the RNA in its linear (denatured) form. The following protocol is based on Formaldehyde Agarose Gel Method.

This is an international convention governing the recognition of deposits in officially approved culture collections for the purpose of patent applications in any country that is a party to it. Because of the difficulties and on occasion of virtual impossibility of reproducing a microorganism from a description of it in a patent specification, it is essential to deposit a strain in a culture collection centre for testing and examination by others.

This was the year, 1974, the Director General of WIPO convened a committee of Experts to discuss the possibilities of international cooperation over the deposit of microorganisms for patent purposes

The Patent Cooperation Treaty provides an overview of an International Treaty which is administered by the World Intellectual Property Organization. The Patent Cooperation Treaty is an international treaty with more than 157 Contracting States by 2022. India deposited its instrument of accession on 7 September 1998 to both international treaties of WIPO in Geneva i.e. Paris convention for the protection of Industrial Property and Patent Cooperation treaty. PCT provides a system for filing a patent application and allow us to obtain patents in multiple countries around the world on the basis of a single patent application.

Introduction

Rick (1984) used the term pre-breeding or developmental breeding to describe the same activity. Thus "genetic enhancement" or "pre-breeding" refers to the transfer or introgression of genes or gene combinations from unadapted sources into breeding materials (FAO, 1996)

However, enhancement has been more popularly adopted by PGR scientists. It is an emerging concept emphasizing the use of plant genetic resources

• To meet the market requirement, plant breeders have to develop improved cultivars.

• Crop improvement has led to narrowing down of genetic base resulting in slower progress (genetic gain) in plant breeding and increased risk of genetic vulnerability

Need for Genetic Enhancement

• In improving the level of resistance to biotic and abiotic stress.

• In improving quality characters such as fibre length, strength, fineness, maturity and uniformity.

• In developing early maturing genotypes, which can fit well in multiple cropping systems.

• In developing plant types suitable to machine picking etc.

• Use of germplasm will help in broadening the genetic base of cultivars as well as in creating vast genetic variability.

Biological Diversity Act, 2002 was passed by Indian government in pursuance of Convention on Biological Diversity, 1993 The Convention on Biological Diversity (CBD) is a legally binding multilateral environmental agreement that has 194 contracting Parties (Countries) as its members with three objectives mentioned below:

1. Conservation of biological diversity
2. Sustainable use of the diversity and
3. Ensuring fair and equitable sharing of benefits of such use.

This protocol is designed for potato stem internodes on ZIG medium, but might work for leaf pieces as well.

Plant Material

Cut stem internode explants from 5-6-week-old in vitro plants (or leaf explants from 3-4-week-old in vitro plants) grown on 15 ml PROP in 25 x 150 mm test tubes.

Day 1

Streak out desired Agrobacterium strain on YEP + antibiotic to obtain a single colony. Grow at 28 C for 2 days. Alternatively, skip this step and use frozen stock for next step.

Day 3

Use a single Agrobacterium colony to inoculate 20 ml YEP + antibiotic in 250-ml flask. Grow overnight at 28 C with vigorous shaking (~200 rpm). Some Agrobacterium strains require an additional day to reach sufficient density.

Traditional knowledge is a type of Intellectual property. It is also known as indigenous knowledge generated from the local communities and tradition of regional technology areas. This knowledge is orally passed over generation from person to person. According to world intellectual property organization, Traditional knowledge is an indigenous, cultural and intellectual property. The biodiversity of a country, the uses and applications of biological resources and prevalent practices are examples of traditional knowledge associated with life science. TK has the tremendous potential of being transformed into commercial opportunity by the development of products and processes. Hence, a share of benefits must accrue to creators and holders of Traditional Knowledge.

8.1. Phytosanitary Capacity Evaluation (PCE): The Tool, and Its Relation to Invasive Alien Species

Phytosanitary Capacity Evaluation (PCE) is a diagnostic tool enabling a country to assess the weaknesses and strengths of its phytosanitary system in relation to its ability to fully implement the International Plant Protection Convention and other international phytosanitary obligations. PCE has also been applied as a cross-disciplinary tool among the sanitary, phytosanitary and food safety areas in the Andean subregion. Since “quarantine pests”, as defined by the convention, constitute a subset of invasive alien species, PCE results are already useful in relation to invasive alien species. PCE methodology has the potential to be further developed to cover a country’s needs in implementing Article 8(h) of the Convention on Biological Diversity.

Article XX of the International Plant Protection Convention establishes the agreement by contracting parties to promote the provision of technical assistance to facilitate implementation of the IPPC. Phytosanitary Capacity Evaluation (PCE) is the first tool approved by the Interim Commission of Phytosanitary Measures to address that commitment, assisting contracting parties to perform a needs assessment and identification of their constraints for achieving full implementation of the IPPC at the national level.