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.

SCARs are DNA fragments amplified by the Polymerase Chain Reaction (PCR) using specific 15-30 bp primers, designed from nucleotide sequences established in cloned RAPD (Random Amplified Polymorphic DNA) fragments linked to a trait of interest. By using longer PCR primers, SCARs do not face the problem of low reproducibility generally encountered with RAPDs. Obtaining a codominant marker may be an additional advantage of converting RAPDs into SCARs. However, SCARs may exhibit dominance when one or both primers partially overlap the site of sequence variation. SCARs are locus specific and have been widely applied in gene mapping studies and marker assisted selection (Paran & Michelmore, 1993).

Introduction

DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. The most commonly used sequencing method is the dideoxy method. This method uses dideoxynucleotide triphosphates (ddNTPs) which have an H on the 3’ carbon of the ribose sugar instead of the normal OH found in deoxynucleotide triphosphates (dNTPs). Dideoxynucleotides are chain terminators. In a synthesis reaction, if a dideoxynucleotide is added instead of the normal deoxynucleotide, the synthesis stops at that point because the 3’OH necessary for the addition of the next nucleotide is absent (Sanger et al., 1977).

6.1  Write True/False

Q.1    A procedure to make an inference about the unknown values of parameters of one or more than one distribution in which the sample size say n is a ramdom variable, is known as “Sequential procedure.”
Q.2    The principal feature of sequential procedure is a ‘Sampling Scheme’ which provides a rule under which one decides at each stage of sampling whether to stop or continue the sampling work.

Introduction

Silk also known as the “Golden Fibre” is admired all over the world for its lustre, strength and smoothness. Sericulture industry is an ecofriendly agro based activity of mulberry cultivation, silkworm rearing and production. It is a labour intensive, rural cottage industry providing subsidiary employment and supplementing the income of semi-literate and semi-skilled poor workers throughout the year [Chanotraet al., 2019]. The term ‘sericulture’ includes economic activities which receive poor workers in the value addition at each stage like (i) raising plants for feeding the silk-worms (in the form of the mulberry plantation); (ii) production of disease-free silkworm layings (dfls), eggs, or seeds; (iii) indoor rearing of silkworms till the cocoon stage which produces silk (about 30-day egg-to-cocoon cycle), and (iv) sale of silk cocoons produced.

Silk industry can be broadly classified into; (a) sericulture, (b) post-cocoon technology – reeling (yarn production), spinning and twisting of silk yarn from the cocoons; and (c) weaving, fabric production, printing and dyeing, finishing, garment designing, marketing etc. These activities also provide the auxiliary enterprises of by-product utilization and machine manufacture including spun silk yarn manufacture and pupae oil extraction, thus creating livelihood for the small and marginal farmers and labour force.

Asia is the key producer of silk in the world producing over 98.5 per cent of the global output. There are more than 40 silk producing countries, but the majority of its production comes from China and India, followed by Brazil, Uzbekistan, Thailand, Vietnam, Korea and Japan. Unlike temperate countries, India has a distinct advantage of practising sericulture all around the year, as a result of its tropical climate, yielding a stream of about 4-6 crops (Savithri and Sujathamma, 2019).

Silk is a way of life in India. Over thousands of years, it has become an inseparable part of Indian culture and tradition. No ritual is complete without silk being used as a wear in some form or the other. Sericulture and Silk Textiles Industry is one of the major sub-sectors comprising the textiles sector. Sericulture is an agro-based cottage industry. Sericulture refers to the mass-scale rearing of silk producing organisms in order to obtain silk. Sericulture is an agro-based labour intensive industry. The major activities involved in a sericulture industry are:

1. Cultivation of silkworm food plants
2. Rearing of silkworms for the production of raw silk
3. Reeling the cocoons for unwinding the silk filament and
4. Other post-cocoon processes such as twisting, dyeing, weaving, printing and finishing.

India occupies second position among the silk producing countries of the world, next only to China. Sericulture as a farm enterprise is highly suited to rural poor, especially small and marginal farmers and other weaker sections of the society, since it requires low investments but provides good and quick returns at individual family level. Several socio-economic studies have established that cost-benefit ratio in sericulture is highest compared to agricultural crops. Though there are limitations to the number of broods that can be raised per year in Himalayan region due to ecological conditions, net returns from sericulture activities are quite remunerative and effectively supplement the rural economy through part-time employment opportunities and utilization of local resources.

Introduction

Ever since its discovery, silk as a unique product of a plant-animal interface, continues to reign supreme despite the onslaught of natural and man-made textile fibres, because it is exclusive and the most beautiful of all textile fibres. It is associated with comfort, festivity and fashion.

Sericulture has established itself as an economic activity with a rural-base. It presents an intriguing example of an agro-industry whose potential to act as a safety-net for the poor in rural areas is unquestionable. From “Soil to Silk” activities, sericulture creates around 6 million person-years of incomegenerating opportunities. It generates employment @ 11 man-days per kg of raw silk production in a year in associated upstream and downstream activities. Sericulture is thus a labour-intensive cottage industry in all its phases, namely, host plant cultivation, silkworm rearing, silk reeling, and other post-cocoon processes such as twisting, dyeing, weaving, printing and finishing.

Introduction

Sericulture is regarded as a significant rural and cottage industry in India. It can generate more income in addition to agricultural crops. Although being viewed as a secondary occupation, sericulture may now be practiced on a large scale due to technological advancements. Since it provides a steady source of revenue, cocoon production and cultivation could be seen as a vital economic tool for the improvement of rural communities. It spreads its welfare-raising distributive impact both in the rural and urban sectors of society throughout its vertical process of production (from the rearing of silkworms to the fabrication of silk goods). Although farmers in rural regions engage in sericulture operations, most of the silk is produced in urban towns and cities through weaving. As a result, silk and sericulture are interconnected with both the agrarian and cottage industries, having a broad-based distributive effect on the creation of jobs and revenue. The employment generation pattern of the sericulture sector has been divided into two main categories by the Indian Sericulture Industry: 1) Direct employment, which includes mulberry cultivation, leaf harvesting, and silkworm rearing. 2) Indirect employment examples include reeling, twisting, weaving, printing, dyeing, finishing, and processing silk waste.

1. …. . involves rearing of silkworms.

 a) Lac culture b) Sericulture  

 c) Apiculture d) Pisciculture

 2. ‘Silk Samagra’ scheme was launched by …. . .

 a) Government of Karnataka b) Government of Tamil Nadu  

 c) Government of Punjab  d) Government of India

 3. Match the pairs

 a) Mulberry silkworm          1. Antheraea paphia

 b) Tasar silkworm                  2.  Attacus ricinii

 c) Muga silkworm                 3.  Antheraea pernyi

 d) Eri silkworm                        4.  Attacus altas

 e) Oak silkworm                     5.  Bombyx mori

 f) Giant silkworm                  6.  Antheraea assama

 a) a=5, b=2,c=3,d=4,e=1, f=6 b) a=5, b=1, c=6, d=2, e=3, f=4

 c) a=2, b=4, c=3, d=1, e=6, f=5 d) a=2, b=3, c=2, d=1, e=4, f=6

 4. ‘Silk Samagra’ scheme was launched for period of …. . .

 a) 2017-2020 b) 2016-2019 

 c) 2014-2017 d) 2021-2024

In many experimental situations, it becomes necessary to repeat an experiment over time ( for a number of seasons or years ) and / or over space ( a number of places). This repetition ( or replication ) of the experiment broadens the scope of the experiment in the sense that our recommendations will be applicable for a number of seasons /or a number of places . A single experiment performed in one place for only one season will provide recommendations for that place and for that season . It may not be applicable to other places or for other seasons . In the case of agricultural experiments , for example , there may be present treatment x place interaction and/ or treatment x season interaction . So the results of a series of experiments , performed over different places for different seasons with the same set of treatments,will have wider applicability .

We shall consider the simplest case of repetition of experiments of identical structure over a number of places ( it is the same for a number of seasons ). Let us consider randomized block experiments with t treatments in r blocks and conducted in p places. The analysis of the experiment in a place is based on the linear model . Before attempting a combined analysis for the p experiments ,it is necessary to perform the analysis for the p places separately and interpret the results separately .It may be of interest to find out whether differences among the treatments are the same in the different places so that a ‘ best ‘ treatment may be recommended for all the places, or whether different treatments are to be recommended for different places . The model for this combined analysis may be written as

Series of experiments are conducted at different locations, times, or combinations of locations and years to evaluate the spatial and temporal performance of treatments. Such experiments are especially important in forestry and agricultural research when conclusions are intended to apply across wider geographical or environmental conditions. This chapter explains combined analysis of a series of experiments after individual experiments have first been analysed according to their respective designs. Particular attention is given to testing the homogeneity of error variances, including Bartlett’s test. When variances are homogeneous, pooled analysis can assess treatment effects, location or year effects, and treatment-by-location or treatment-by-year interactions, thereby evaluating consistency of treatment responses.

The questions related to different series like perfect squares, perfect cubes, geometric, arithmetic, two stage types etc. are given to quantify the aptitude of the students. These series have a definite pattern and require to stressed upon the basic knowledge and aptitude of the candidates to find out the proper answer. The series may follow different pattern either additive, deductive or multiple based on earlier values given in the series. Some of the tips are given below for better understanding of the students and also these tips will help you to solve some of the ticklish questions.

This chapter deals with the principles and applications of serological tests used to detect antigens and antibodies. It distinguishes primary, secondary and tertiary binding tests and explains antibody titre, affinity, avidity, sensitivity and specificity. Important techniques include precipitation, agglutination, complement fixation, neutralization, immunofluorescence, ELISA, radioimmunoassay, Western blotting and the radioallergosorbent test. The chapter also addresses serum decomplementation and the interpretation of positive and negative reactions. These methods are central to the laboratory diagnosis, surveillance and control of infectious diseases. The objective questions enable readers to compare diagnostic techniques and select appropriate tests according to their principles, applications and analytical performance.

A. Answer the following.

Q.1.     What are the different enzymes used to couple with antibodies to prepare conjugates for use in ELISA?
Ans.     HRPO, Alkaline phosphate, b galactosidase, penicillinase etc.

Q.2.     What does it indicate if any woman has HI titre of > 10 for rubella ?
Ans.     It means that the woman is immune to rubella. If it is less than 10 it indicates that the woman needs to be immunized against rubella.

The application or utility of serology in solving taxonomic problems is called serotaxonomy or systematic serology. The study of antigen-antibody reactions is called serology. It had its origin towards the end of 20th century with the discovery of serological reactions and development of the discipline of immunology. The substance capable of stimulating the formation of an antibody is called antigen. A highly specific protein molecule produced by plasma cells in the immune system is called antibody. The antibodies combine chemically with specific kinds of antigens. Proteins are the useful carriers of
taxonomic information and are most widely used antigens in serotaxonomy.
Serology is Useful in The Following Ways
1. It expresses similarities and dissimilarities amongst different taxa, and these data are helpful in taxonomy. It determines the degree of similarity between species, genera, families, etc. by comparing the reactions of antigens from various plant taxa with antibodies raised against the antigen of a given taxon.
2. It helps in comparing non-morphological characteristics, the knowledge of which is useful in taxonomy.
3. Single proteins from different plant taxa are also compared by serology techniques.

Members of the genus Serpulina (Treponema) are host-associated spirochaetes found in the oral cavity, intestinal tract and genital region of animals and humans. The cells are wider, are not as tightly coiled as th e leptospires and can be stained by aniline dyes.
The species of veterinary significance are S. Hyodysenleriae (swine dysentery) and T. paraluiscunicllii (ventdisease of rabbits). S. innocens, present in the faecesof pigs and dogs, is thought to be non- athogenic,although some workers regard S. innocens as a strainof S. hyodysenteriae of lower virulence. S. hyodysenteriae and S. innocens are s imilarmorphologically, culturally as well as biochemicallyand can be grown on laboratory media. T. Paraluiscuniculi has not been cultured in vitro.
Normal Habitat
T. paraluiscliniculi produces a benign venereal disease of rabbits and is present in lesions in the genito-perineal area of rabbits. It causes latentin fection in mice, guinea- pigs and hamsters. The treponemes can be found in the lymph nodes of these animals. The reservoir of S. hyodysenteriae is the intestinal tract of pigs, wild rats and mice. Recovered, asymptomatic pigs can excrete these organisms in faeces for 3 months or more. Survival of S. hyodysenteriae in soil or voided pig faeces is short, about 24 48 hours. Infection is by the faecal-oral route.

Etiology

It is an uncommon endocrine related skin disorder. It is very rarely encountered in neutered dogs.It is always associated with cryptorchidism and sertoli cell tumor. This condition is closely accompanied with endocrine related testicular tumor followed by skin lesion and feminization.

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.

5.1. Emergence of Service Area Approach

During the five years ended 1985-86

Gross value added in agricultural sector: 2.70% per annum.

Share of agriculture in total net domestic product declined from 39.80% to 35.40%.

Food grains production increased from 133.30 million tons to 150.50 million tons by 18%

In contrast, there was 41% increase in outstanding level of credit for agriculture from rural lending agencies viz., Co-operatives, RRBs and CBs between June 1981 and June 1986.

Share of Haryana, Punjab and U.P. in total food grains production was around 38% accounted for 75% increase in food grains output.

However, their share in the total institutional credit was 22% only.

Introduction

Cultivated sesame (Sesamum indicum L.), has originated in India (Bedigian,1984; Bedigian et al., 1985; Bedigian and Harlan,1986) and is considered to be the oldest oilseed crop known to man (Ram et al 1990). Archaeological records indicate that it was known and used in India for more than 5,000 years and is recorded as a crop in Babylon and Assyria some 4,000 years ago (Borchani et al., 2010). Sesame crop is being grown in many parts of the world. Sesame seed is an important source of edible oil and is also widely used as a spice and condiment. The seed contains 50-60% oil which has excellent stability due to the presence of natural antioxidants such as sesamolin, sesamin and sesamol (Brar and Ahuja 1979).

Sesamum indicum L., belongs to the family Pedaliaceae, which contains sixteen genera and sixty species under the generic name Sesamum. The other species related to sesame viz., Sesamum angustifolium, Sesamum radiatum and Certotheca sesamoides (false sesame) are cultivated in Africa. The fact that the crop is cultivated in India from times immemorial is testified by the excavations of Harappa and Mohenjo-Daro of undivided India (Watt,1966). The crop was introduced into Brazil by the Portuguese (Weiss, 2000).

World production of sesame seed didn’t show any marked increase for the past three decades, although sesame oil is used largely in Asia and Africa. The current world production of sesame stands at 6.1 million tons as in the year 2016. The sesame production declined world over since the crop had to face a tough competition against other oilseed crops (Weiss, 2000). Most of the world trade on sesame revolves around the seed. The shipments of seed cake and oil are negligible.