eChapters

Abstract

Sequence alignment is the positioning of DNA, RNA, or protein sequences with each other to identify the regions of identity, which may be the result of functional, structural, or evolutionary relationships between the sequences. Therefore, sequence alignment is the process of aligning two sequences to achieve the maximum levels of identity and conservation. This chapter deals with the basic concept of sequence alignment and the tools associated with multiple sequence alignment. Further, it describes various matrices used in sequence alignment.

Principle

The infectivity of a virus may be neutralized by specific antibody when they are mixed and incubated. In some cases, the addition of homologous or guinea pig complement to the mixture enhances neutralization, particularly when early antiserum is used. Serum must be inactivated by heating at 560C for 30 minutes to inactivate complement or to remove non-specific virus inhibitors. Serum-virus mixtures are inoculated into appropriate cell cultures, which are then incubated until the only virus controls develop cytopathic effects. Antibody by neutralizing the infectivity of the virus, protects the cells against virus destruction.

Sex Chromosomes

Sex can be considered at chromosomal, gonadal, phenotypic, and gender identity levels.

Human females are homogametic (XX) and males are heterogametic (XY).

The Y chromosome contains few identified genes, while the larger X chromosome contains several thousand genes. Pseudoautosomal regions at both tips of the Y chromosome contain genes that have counterparts on the X chromosome.

The male determining gene, SRY, has been found on the Y chromosome.

Some traits are carried on the sex chromosomes, X and Y. Most traits carried are present on only the X-chromosome. The Y-chromosome is smaller, and so, very few genes are located on this chromosome. Sex traits can be categorized into three types of inheritance:
Sex limited,
Sex-linked, and
Sex-influenced.
Sex-limited traits are traits that are visible only within one sex. For instance, barred colouring in chickens normally is visible only in the roosters. Sex-linked traits would be considered traits like sickle cell anemia and colour blindness. They are said to be linked because more males (XY) develop these traits than females (XX). This is because the females have a second X gene to counteract the recessive trait. Thus, the trait is more likely to be visible in the male.
Sex Influenced Inheritance
The condition in which the same gene acts as dominant in one sex and recessive in other sex is called as sex influenced dominance. That is, the sex influences the gene either to be dominant or recessive. The sex influenced genes are present in autosomes. This differential behaviour of the gene is due to female and male sex hormones. For example, in human being baldness is due to sex influenced gene. This trait is dominant in men and recessive in women. A man is bald in homozygous recessive as well on heterozygous condition for baldness. Whereas women exhibit baldness only in homozygous recessive condition for baldness and heterozygous condition for baldness in female sex produce normal phenotype. HN, HN -Normal female and normal male

According to the karyotyping the domestic sheep (Ovis aries) has 54 chromosomes. The following is a brief summary of their chromosome composition:

Autosomes: There are one pair of sex chromosomes, 52 autosomes and three pairs of these autosomes are submetacentric (having a centromere slightly off centre), while the rest are acrocentric (with the centromere near one end).

Sex Chromosomes: The X chromosome is acrocentric and the Y chromosome varies from submetacentric to metacentric.

Important features

• According to the Food and Agriculture Organization Corporate Statistical (FAOSTAT) Database (2019) and database of the United Nations Food and Agriculture Organization, the top three countries by the number of heads of sheep were: China (163.48 million heads), India (74.26 million) and Australia (65.75 million). • India has second largest sheep population in the World.

• Sheep milk is an important product in the Near East and North Africa (9% of total milk production) and sub-Saharan Africa (4%).

• The countries with the most dairy sheep are China, Sudan, Turkey and Algeria (FAO).

• Major sheep milk producers are China, Turkey and Greece.

• More than half of the world’s sheep population is found in developing countries. Sheep are more prevalent than goats in cold climatic conditions. The major produce from Sheep production are milk, meat, skin, fibre and manure. However, most of the small-scale producers in developing countries raise sheep for meat or sale.

The principle of silver nitrate staining of proteins is based on the reduction of silver ions to its metallic form. (Silver ions in alkaline conditions bind with proteins through å-amino group of lysine and sulphur groups of cysteine and methionine residues). When the complexed silver ions are reduced in the presence of formaldehyde, they become metallic silver, which is seen on the gel as bands. Staining of proteins with silver nitrate after SDS-PAGE is quicker and ~ 10 times more sensitive than Coomassie brilliant blue staining and that is the reason it is widely used in research laboratories these days.

The procedure is as follows:

True/False

Q.1.    Two independent random variables (X,Y) are always uncorrelated but reverse may not be true

A simple random sample (SRS) of size n consists of n individuals from the population chosen in such a way that every set of n individuals has an equal chance to be the sample actually selected.

A simple random sample is a subset of a statistical population in which each member of the subset has an equal probability of being chosen. An example of a simple random sample would be the names of 25 employees being chosen out of a hat from a company of 250 employees. In this case, the population is all 250 employees, and the sample is random because each employee has an equal chance of being chosen.

The concept of single cell micro-gel electrophoresis (SCGE)/comet assay is f irst introduced by Ostling and Johanson (1984) as a method to measure DNA single-strand breaks under neutral conditions. Singh et al. (1988) modified this technique by using alkaline conditions (>13 pH) of electrophoresis, which enabled detection of not only frank strands breaks but also alkali labile sites, DNA cross- linking and incomplete excision repair sites. Now-a-days, this technique is extensively used to study the genotoxic effects of various chemicals. The advantages of SCGE technique include: (1) collection of data at the level of individual cell, allowing for more robust types of statistical analysis; (2) need for small number of cells per sample (<10,000); (3) its sensitivity for detecting DNA damage; and (4) that virtually any eukaryotic cell population is amenable to analysis. The idea is to combine DNA gel electrophoresis with fluorescence microscopy to visualize migration of DNA strands from individual agarose-embedded cells. If the negatively charged DNA contained breaks, DNA supercoils are relaxed and broken ends are able to migrate toward the anode during a brief electrophoresis. If the DNA is undamaged, the lack of free ends and large size of the fragments prevented migration. Determination of the relative amount of DNA that migrated provided a simple way to measure the number of DNA breaks in an individual cell.

Genotoxic effects of any xenobiotics in PMNC and splenocytes of Wistar rats can be studied according to the working protocol of Dhawan et al.

Abstract

The sires have been evaluated and ranked on the basis of solutions obtained through univariate and multivariate REML using animal model and BLUP value for sire effects under mode l 8. The data considered from 1214 animals descendent from 110 sires of chokla sheep maintained at CSWRI, Avikanagar, Rajasthan. The traits were considered birth weight, weaning weight, 6 months weight and first greasy fleece yield for the present study. Three solutions were used: Best linear unbiased Predication (BLUP1) values of Model 8, and univariate (BLUP₂) and multivariate (BLUP₃) solutions of REML animal models. Less than half of the sires were superior to the populations mean under BLUP₁ for the traits studied. The corresponding values were above 60% under BLUP₂, which was much higher than BLUP₁.

10.1 Introduction

The assumptions on which analysis of large samples is done generally do not hold well in case of small samples (n < 30). In case of large samples we had presumed that the random sampling distributions of statistics are approximately normal and further that the values obtained by sampling study are close to the population values and can be used in their place for the calculation of the standard error of the estimate. These assumptions do not hold well if the size of the samples may or may not be normally distributed and similarly it is not possible to substitute the mean or the standard deviation of a small sample in place of the parameter mean or standard deviation for the calculation of standard errors. Under such circumstances the analysis of small samples has to be done by techniques which are different from those applicable in case of large samples.

I. Definition

Solute transport in plants, translocation, primarily occurs in the phloem, but it can occur in the xylem.

II. Solute Transport in the Xylem

Some solutes are transported in the xylem

Water and dissolved ions are the main substances in vessels/tracheids

These materials are transported via transpiration stream

Xylem sap may also contain organic materials, usually in relatively low concentration (with a notable exception being maple sap in the spring which is comprised of 2% or more sucrose).

Substances move at different rates depending on matrix effects, metabolic needs, etc.

Abstract

The Sonadi is an important breed of sheep in southern Rajasthan. Three districts namely Udaipur, Rajsamand and Chittorgarh were selected from major and Bhilwara from minor breeding tract for complete enumeration. Finally 450 shepherds were selected to collect the information with respect to demographical and geographical distribution as well as management practices. Among selected tehsils, two tehsils from each district were chosen for breed characterization. In all 6979 sheep from 147 shepherds of 49 villages in 8 tehsils were registered for breed characterization.

Split-plot Design

In field experiments, sometimes a factor has to be applied to a large experimental unit. This is true when the different methods of ploughing or irrigation are to be compared. And in such cases it is possible to introduce a second factor, which does not require large plots, with a small number of levels into the same experiment, at a little extra cost. This is done by splitting the plots (called whole plots of the first factor into as many sub-plots as there are levels of the second factor.)

A split-plot design with an RBD for the first set of treatments (called “the whole-plot treatments”) is obtained by allotting the whole-plot treatments at random to the whole plots of a block and then randomizing the second set of treatments (called “the sub-plot treatments”) to the sub-plots within each whole plot.

This enables us to test for the main effects of the sub-plot treatments and the interaction of the whole-plot treatments and the sub-plot treatments more efficiently than the main effects of the whole-plot treatments in a split-plot design.

1. Introduction
Good Laboratory Practice (GLP) is a systematic quality system essential for
ensuring the reliability, consistency, and integrity of laboratory data, particularly when the findings are used for regulatory decision-making. GLP ensures that laboratory studies are conducted in a scientific manner, maintaining high standards of ethical practice, precision, and reproducibility, with a primary focus on ensuring public and environmental safety. Introduced by the U.S. Food and Drug Administration (FDA) in 1978, GLP gained global recognition through the Organisation for Economic Cooperation and Development (OECD), which established guidelines for its implementation. GLP principles are now widely adopted in regulatory testing for pharmaceuticals, chemicals, food safety, and environmental testing. The OECD’s guidance on GLP has been instrumental in developing standards across the globe, ensuring that test results are scientifically valid and can be accepted internationally. In Asia, particularly in India and other developing countries, GLP compliance has gained increasing importance as pharmaceutical, environmental, and chemical industries expand. Regulatory bodies in these regions have gradually aligned their standards with international norms to ensure their competitiveness in global markets. This chapter discusses the key SOPs necessary for GLP compliance and provides a regional perspective, focusing on India and other Asian nations, where GLP frameworks are evolving to meet international standards.
2. Objective of GLP
The overarching objective of GLP is to ensure that laboratory data is accurate, reliable, and reproducible across different studies. The scientific and regulatory communities rely on GLP to ensure that findings from preclinical studies and safety evaluations can be trusted and utilized for regulatory approval.
The key objectives of GLP include
• Accuracy and Integrity of Data: GLP ensures that every aspect of data collection, analysis, and reporting is conducted with integrity and accuracy, preventing errors or falsification that could affect regulatory decisions.