eChapters

Abstract

The conventional methods of pathogen identification have often depended on identification of disease symptoms, isolation and culturing of the organisms, and identification by morphology and biochemical tests. The major limitations of these culture based morphological approaches, however, are the reliance on the ability of the organism to be cultured, the time consuming nature and requirement of extensive taxonomic expertise. Furthermore, diagnosis of plant diseases can be even more difficult with asymptomatically infected propagative materials such as tree grafting stocks or potato tubers. The use of molecular methods can circumvent many of these shortcomings. Accordingly, there have been significant developments in the area of molecular detection of plant pathogens in the last three decades. The polymerase chain reaction (PCR) which revolutionised molecular diagnostics and biological sciences. In the last decade the range of targets that can be diagnosed using diagnostic PCR have grown tremendously. The very flexibility and application specific variations in the basic theme of the system have allowed the development of many PCR variants adapted to wide range of applications. Furthermore, diagnostic PCR has been greatly improved by the introduction of the second generation PCR, known as the Real time PCR where closed-tube fluorescence detection and quantification during PCR amplification (in real time) is possible eliminating the need for laborious post-PCR sample processing steps which greatly reduces the risk of carryover contamination. Using Real Time PCR, it is possible not only to detect the presence or absence ofthe target pathogen, but it is also possible to quantify the amount present in the sample allowing the quantitative assessment of the number of the pathogen in the sample. Enumerating the pathogen upon detection is crucial to estimate the potential risks with respect to disease development and provides a useful basis for diseases management decisions. Crops can be attacked by many pathogens which, in addition, often occur in complexes. Therefore, many disease diagnostic applications require simultaneous detection and quantification of several targets. Methodological limitations, however, are in many cases the reason for developing simplex or assays designed for only few targets. The DNA Microarray technology, originally designed to study gene expression and generate single nucleotide polymorphism (SNP) profiles, is currently a new and emerging pathogen diagnostic technology, which in theory, offers a platform for unlimited multiplexing capability. It is viewed as a technology that fundamentally alters molecular diagnostics. The fast growing databases generated by genomics and biosystematics research provides unique opportunity for the design of more versatile, high-throughput, sensitive and specific molecular assays which will address the major limitations of the current technologies and benefit plant pathology.

ABSTRACT

Central Plantation Crops Research Institute at Kasaragod maintains largest collection of coconut germplasm accessions representing different geographical regions. So far, morphological and isozyme markers were employed for germplasm characterization. To overcome the difficulties associated with the morphological markers, DNA based molecular markers are presently employed for germplasm characterization. In the present study, Inter Simple Sequence Repeat (ISSR) markers are utilized to estimate the genetic diversity among South East Asian germplasm accessions. Nineteen ISSR primers were used to amplify 8 germplasm accessions (4 palms per accession referred as population). The PCR products were electrophoresed in 1.80 % agarose gels. Binary data were analyzed using the software POPGENE ver. 1.32. Dendrogram was constructed based on Nei’s unbiased measure of genetic distance. Nineteen ISSR primers detected a total of 85 polymorphic markers across 32 individuals belonging to eight populations. The average genetic distance among the eight populations ranged from 0.7908 to 0.9327 with a mean of 0.8540. Of the 28 pair wise comparisons the accessions Laguna Tall and Kongthienyong Tall (KTYT) showed the highest genetic identity (0.9327). The lowest identity (0.7908) was between San Roman Tall (SNRT) and Philippines Dalig Tall (PDLT). The Shannon’s index ranged from 0.1615 to 0.299. Diversity parameters viz. number of effective alleles, gene diversity, number of polymorphic markers were calculated for each population. The dendrogram constructed based on the genetic distance revealed clustering of Kongthienyong Tall (KTYT) and Laguna Tall (LAGT) while Philippines Dalig Tall (PDLT) was positioned separately. In the genetic improvement programmes the diverse accessions can be used in hybridization for increased heterosis.

ABSTRACT

Purine Nucleoside Phosphorylase (PNP) is an enzyme that functions in the purine salvage pathway by catalyzing the phosphorolysis of purine nucleoside thereby releasing the purine bases and phosphorylated sugar. Interest in PNP as a drug target arises from its role in T-cell proliferation and T-cell mediated autoimmune diseases. Recently, we have isolated the compound, coixol, from the plant Scoparia dulcis L. and its three-dimensional structure has been elucidated. As the structure of the coixol mimics the structure of PNP inhibitors, we have undertaken the molecular modeling studies of this compound with Human PNP, as a screening test for further in vivo studies. Generally PNP inhibitors have been synthesized with a ribose sugar moiety attached to them. As the plant Scoparia dulcis L. contains glucose and rhamnose (six membered ring), these sugar moieties are also included along with ribose in the presen study. In order to understand the binding mode and interactions of the isolated compound attached with different sugar groups, we have carried out the docking studies with Human PNP. The interactions between the ligand molecules and active site residues of Human PNP are similar to those of solved complexes and the energy values are also comparable, which clearly indicate that these ligands may act as inhibitors.

Summary

Molecular evolution is the process of evolution at the scale of DNA, RNA, and Protein. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology, and population genetics sought to understand recent discoveries on the structure and function of nucleic acids and protein. It covers two broad areas of study : the evolution of macromolecules, and reconstruction of the evolutionary history of genes and organisms. The evolution of macromolecules refer to the characterization of the changes in the genetic material (DNA or RNA sequences) and its products (Proteins of RNA molecules) during evolutionary process, and to the rates and patterns with which such changes occur, and also the mechanism responsible for such changes. The second area also known as “molecular phylogenetics”, deals with the evolutionary history of organisms and macromolecules as inferred from molecular data and the methodology of tree reconstruction.

Summary

Molecular farming is the large scale production of pharmaceutically important and commercially valuable proteins in plants and animals. Molecular farming in plants has the potential to provide an inexpensive and convenient system in the production of unlimited quantities of recombinant proteins for use as therapeutics, diagnostics, vaccines, antibodies, plasma proteins, cytokines and growth factors. Plants are also being used for the production of oils, starches, plastics, enzymes for food processing and other uses and spider silk etc. However, quality and safety of the final product and wider effects of molecular farming on health and environment need to be addressed. The benefits of molecular farming should not be outweighed by risks to human health and environment.

4.1 Introduction

Many important traits such as yield, quality and some forms of disease resistance are controlled by many genes and are known as quantitative traits or characters (also called ‘metric’,‘polygenic,’ ‘multifactorial’ or ‘complex’ traits). The regions within genomes that contain genes associated with a particular quantitative trait are known as quantitative trait loci (QTLs). The identification of QTLs based only on conventional phenotypic evaluation is not possible. A major breakthrough in the characterization of quantitative traits that created opportunities to select for QTLs was initiated by the development of DNA (also called molecular) markers in the 1980s.

One of the main uses of DNA markers in agri-horticultural research has been in the construction of linkage maps for diverse crop species. Linkage maps have been utilised for identifying chromosomal regions that contain genes controlling simple traits (controlled by a single gene) and quantitative traits using QTL analysis. The process of constructing linkage maps and conducting QTL analysis–to identify genomic regions associated with traits–is known as QTL mapping (also called ‘genetic,’ ‘gene’ or ‘genome’ mapping). DNA markers that are tightly linked to agronomically important genes (called gene ‘tagging’) may be used as molecular tools for marker-assisted selection (MAS) in plant breeding. MAS involves using the presence/absence of a marker as a substitute for or to assist in phenotypic selection, in a way which may make it more efficient, effective, reliable and cost-effective compared to the more conventional plant breeding methods. The use of DNA markers in plant (and animal) breeding has opened a new realm in agriculture and horticulture called ‘molecular breeding’.

5.1 Introduction

The development of quantitative trait loci (QTL) mapping methods to identify genes or QTLs controlling quantitative traits was a landmark achievement in plant genetics research in the late 1980s. Since then literally thousands of research papers have reported the identification of genes or QTLs for important traits across a diverse range of plant species. This wealth of genetic information was built on the foundation of decades of research in crop molecular genetics and genomics.

The selection and enrichment of QTLs within breeding material was the inevitable next step from QTL discovery to application, and there have been numerous reports of successful tracking of genes and QTLs within breeding programmes. DNA (or molecular) markers have enabled selection of major genes or QTLs for critical or important traits in a process called marker-assisted selection (MAS), which has revolutionized plant breeding. DNA markers are used as tools by breeders to improve the accuracy or efficiency of selection as well cost and time efficiency. Apart from MAS, DNA markers have numerous applications including DNA fingerprinting, genetic diversity analysis and parental characterization.

Recent developments in genotyping platforms and systems to implement molecular breeding schemes offer new tools for modern plant breeders. Single nucleotide polymorphism (SNP) markers are biallelic, co-dominant markers which are abundant in the genome. Insertion-deletion (Indel) markers are also prevalent and can be screened using high-throughput genotyping platforms. These platforms are cost-efficient, can handle large sample sizes and provide fast data turn-around time. The availability of genome sequences and genomic resources continues to provide a wealth of SNP and Indel markers which will undoubtedly be the marker type of choice for decades to come.

The availability of high-throughput SNP platforms in conjunction with advances in computational methods has also led to the molecular dissection of traits using genome-wide association studies (GWASs) across diversity panels and the development of genomics-based molecular breeding strategies. Association mapping (AM) has now emerged as a standard method for gene and QTL discovery for major crops.

Rice (Oryza sativa L.) is the most popular crop and source of food for more than one-third of the world’s population. About 90 % of the world’s rice is grown in Asia and more than 3 billion Asians rely on rice for 30–75 % of their total calories (Braun and Bos 2004). It has been cultivated in four different ecosystems viz., irrigated, rainfed low land, upland and flood-prone (Halwart and Gupta, 2004). Since rice planting has been started around 8,000 to 9,000 years ago, the level of diversity would be more than it expected. The genetic diversity plays a major role in survival and adaptability of a species, as changes happen in environment. Organism needs to make changes in the phenotype that enables it to adapt and survive in unfavorable conditions. The inadequate knowledge on diversity of a species reduces the chance of widening the genetic base of that species. The venture of green revolution in Indian agriculture has narrowed down the genetic base of any popular crops. Therefore, collection, conservation and utilization of germplasm are very much needed in the present scenario for improving the varieties against biotic and abiotic stress.

Morphological and biochemical trait based diversity studies being largely influenced by environment as phenotype and/or enzymes are altered by the environmental and developmental changes. Therefore, adapting DNA based molecular markers for genetic diversity studies would be more reliable to overcome the environmental influence. Being molecular markers as a versatile tool, it establishes its strong holds in several fields of life science. Molecular marker based technique does not require DNA sequencing but it is generally based on nucleic acid hybridization or polymerase chain reaction (PCR). The PCR based tests has several advantages over hybridization technique as it is cheaper, speedy and sensitivity. Therefore, PCR based markers have been used extensively in genetic diversity study for assessing genetic variation within the species. The recent advent of molecular and computational tools now enables the estimation of genetic diversity and allele frequency between the genotypes easy.

DNA is the master molecule which carries the genetic information from one generation to the other. Study of Molecular Genetics accelerated since April 25th, 1953 when James Watson and Francis Crick proposed the structure of DNA which was published in Journal called ‘Nature’. Molecular Genetics deals with the flow of genetic information and its regulation. In simple terms it can be defined as the field of biology which studies the structure and function of genes at molecular level.
Scope of Molecular Genetics
Development of techniques like nucleic acid hybridisation, cloning, sequencing etc. brought a revolutionary change in Molecular Genetics. It is of major interest to the students of biology and medicine. Though it has a lot of significance in many fields, we’ll confine ourselves to the applications of molecular genetics to the mankind. They are as follows:
i) Diagnosis of infectious diseases: Normally microorganisms are detected in the laboratory using biochemical methods. In case of molecular techniques, microorganisms are detected by using probes (short DNA or RNA sequence) which are complementary to a part of genome of the microbe. The advantage of using molecular methods is:
• Identification of pathogen is done within a short time;
• No need to cultivate the microbes;
• Latent infections can also be identified when no antibody is formed; and
• The technique can be used even when the microorganism cannot be cultured.
ii) Diagnosis of genetic diseases : Before the advent of the above techniques, counselors used to give risk estimate like one fourth risk of getting the disease, if the parents are heterozygous for an autosomal trait. But now by directly testing for the mutation, they are able to confirm the presence or absence of mutation in the fetus. It is of immense help in prenatal diagnosis.

Molecular markers or DNA markers are considered to be one of the most successfully applied component of molecular biology techniques that have relevance in almost every sphere of biology, from paleobotany to transgenic technology. In true sense, a marker is a characteristic of an individual that differentiates the individual from others. Morphological descriptions like cotyledon colour of Pea, eye colour of Drosophila, shape and size of fruits in summer squash etc. are examples of typical morphological markers. However, a single morphological marker is not sufficient for describing the uniqueness of an individual, for many pea plants will have green cotyledon or many Drosophila may have red eye. To define the uniqueness of an individual, we have to find a number of marker traits characteristic of that individual. Unfortunately, morphological variations are not sufficient to differentiate between a large number of individuals, or between groups or sub groups within a species, simply because the level of polymorphism is low. Besides, morphological characters or phenotypic expressions are affected by environmental changes, so stability of expression is low and sometimes uncertain.

Introduction

Plant genetic resources management essentially consists of two phases; its conservation and utilization. Germplasm conservation includes acquisition, in which germplasm is safeguarded in situ (by establishing reserves) or ex situ (by assembling collections through exchange or exploration). It also involves maintenance, protecting germplasm in situ in reserves or storing it ex situ under controlled conditions, propagating it while preserving its original genetic profile with maximum fidelity, monitoring its viability and health in storage or in situ and maintaining associated passport information and other data. Germplasm conservation also involves characterization, assessing highly heritable morphological and molecular traits for taxonomic, genetic, quality assurance and other management purposes. The second phase of germplasm management, encouraging utilization, includes evaluation, assessing agronomically or horticulturally important traits with relatively low heritability and high components of environmental variance e.g. yield adaptation and host-plant resistance to certain abiotic/biotic stress. It also includes genetic enhancement, making particular genes more accessible and usable to breeders by adopting exotic germplasm to local environments without losing its essential exotic genetic profile and/or introgressing high value traits from exotic germplasm into adapted varieties. Genetic enhancement can be subdivided into introgression i.e. backcrossing a few genes controlling desired characters into adapted stocks and incorporation i.e. the large scale development of locally adapted populations good enough to enter the adapted genetic bases of the crops concerned.

Plant breeding is considered as current phase of crop evolution. It is a combination of art and science, which involves designers activity, conventionally, economically important traits dispersed in different parental lines are combined together to develop a new variety or cultivar and to change the genetic constitution of a plant to make it more suitable for human need with available scientific knowledge. Although plant breeding has been existing since time immemorial, modern plant breeding methods are based on scientific principles begins only with the rediscovery of Mendel’s laws of inheritance in 1900 and chromosomal theory of inheritance in 1902. Significant achievements have been made in crop improvement through phenotypic selections for agronomically important traits, considerable difficulties are often encountered during this process, primarily due to genotype-environment interactions.

Molecular markers may be a short DNA sequence that flanks base pairs like SNP, a Single Nucleotude Polymorphism, small fragment or SSR Single Sequence Repeat or an extended site as in the case of microsatellites. Schematic representation of the SSR assay is shown in Fig. 1. Genetic markers have to be easily identified, linked to a specific locus and polymorphic. Molecular markers are subdivided into codominant monolocus and polyallelic markers and the second group contains dominant, polyallelic and biallelic markers. 

ABSTRACT

Genetic improvement of crop plants through conventional plant breeding has made tremendous contributions to the breakthrough in the global agricultural production. Recently, an array tools and techniques in the field of molecular biology has become available for supplementing the conventional genetic approaches. Consequently, new integrated approaches are being designed. One of the approaches employs molecular markers for genome mapping, gene tagging and marker assisted selection (MAS). With the complete sequencing of whole plant-genomes and a large number of random cDNAs in many different crop species, newer opportunities are emerging. This presentation is an attempt to briefly describe the current applications of molecular markers and to highlight their future prospects.

Molecular markers

Molecular markers are heritable differences in nucleotide sequences of DNA at corresponding position on homologous chromosomes of two different individuals, which follow a simple Mendelian pattern of inheritance. These differences are detected employing two basic techniques: (a) Southern blot hybridization and (b) Polymerase chain reaction (PCR). Restriction Fragment Length Polymorphism (RFLP) is the first molecular marker system to be conceived and developed. It is based on the southern blot technique. Markers such as random amplified polymorphic DNA (RAPD), sequence tagged site (STS) and amplified fragment length polymorphism (AFLP) are generated by enzymatic amplification of DNA by extension of oligo nucleotide primers and therefore, are based on PCR. Single/simple nucleotide polymorphism (SNP) markers are based on DNA sequence differences as revealed by sequencing and assayed by various techniques.

Abstract

Molecular markers play key role in crop improvement. There are severalmarkers such as RAPD, SSR, AFLP, SNP, DArT and many more are available for their practical uses. From the past markers like RAPD, AFLP, and SSR have been used extensively in the crop breeding. Recently new markers such as SNP and DArT have become popular among the researchers of molecular biology for use in genomics-assisted crop breeding. These markers have been applied for study of genetic diversity, germplasm management, cultivar identification, genetic mapping, gene tagging and genomics etc. Though the conventional method of breeding willcontinue to play a primary role in the crop improvement, molecular marker technology is becoming one of its integral components. Agarose-based DNA markers like ISSR, CAPS, RAPD, SCAR and AS (allele specific) have the potential for faster and accurate breeding for target traits through MAS.

Introduction

Genetic markers are genes or DNA sequences associated with a specific gene or trait, often arising from mutations or alterations in genomic loci (Samarai and Kazaz, 2015). Recently, there has been a growing interest in molecular markers, which reveal polymorphisms at the DNA level. These markers play a crucial role in animal genetics studies, as they help identify genetic resources and differences between domesticated and wild animals. Cytological markers, which use chromosome karyotypes, bandings, repeats, translocations, deletions, and inversions, are widely used for elucidating species origin and classification (Becak et al., 1971; Jonker et al., 1982).

Abstract

People dealing with forest tree seeds are very much concern with the collection and supply of pure and quality seed. Assessing genetic purity of tree seed is always a challenge. Besides, studying tree diversity and tree improvement are also the key components of forestry. With the discovery of DNA based molecular markers these tasks have been made easier and authentic. So, the basic concepts behind different molecular markers were the principal concerns of this chapter. It has been focused here about the pros and cons of the markers along with their applicability. The application may be expanded towards hybrid seed testing and even to clonal forestry.

Introduction

Fresh and processed products derived from fruit crops provide vital contributions to human nutrition, health, and well-being, and collectively their production constitutes the economic backbone of many rural communities worldwide. Rapid development and distribution of new cultivars with improved characteristics which meet the industry, market (both domestic and export), and consumer preferences is the need of the day. Conventional methods of perennial fruit crop improvement have almost exclusively relied on traditional breeding techniques. These techniques are expensive, time consuming and space requiring, especially for tree species due to the need of a large population of seedlings from which only a few promising ones are selected. The juvenile period of tree crops may last three to five years before onset of fruits so that 20 years or more are common before the successful introduction of a gene of interest (Baird et al., 1996). Therefore in this context, molecular tools recently made available for breeders have become tools of choice because they permit to reduce cost by fastening the selection process of woody fruit plants. Further, traits of importance like fruit quality, resistance to diseases, high yield etc. are polygenic in nature for which classical breeding is generally not suitable for detection and selection of traits. A quantitative trait locus (QTL) analysis with help of markers and linkage maps may be more appropriate for detection of such traits of interest. Also, molecular markers are being used for maintenance of core collections, for the assessment of genetic diversity between genotypes and fingerprinting.

Introduction
Molecular markers have revolutionized various fields of biological research by providing precise tools to elucidate genetic diversity, map genes, and facilitate marker-assisted selection (MAS) in breeding programs. These markers, ranging from simple sequence repeats (SSRs) to single nucleotide polymorphisms (SNPs), offer invaluable insights into the genetic architecture of organisms, enabling researchers to link specific DNA sequences to desired traits. By harnessing the power of molecular markers, scientists can expedite the development of stress-tolerant crops, enhance agricultural productivity, and address global challenges such as food security and climate change.
A. Definition of molecular markers: Molecular markers play a crucial role in identifying genetic variations or disparities among individuals, populations, or species. These markers are specific sequences of DNA (or RNA) that can be found in blood, other body fluids, or tissues, serving as indicators of normal or abnormal processes, conditions, or diseases. Additionally, they can be fragments of DNA associated with a genome, aiding in the identification of specific DNA sequences. Molecular markers are indispensable tools in the fields of genetics, molecular biology, and biotechnology, enabling the identification of specific DNA sequences and genetic variations within populations.

Molecular markers, including DNA based genetic markers have found their applications in almost all areas of biology, more so in evolutionary biology, genetics and breeding in order to identify a particular sequence of DNA in a pool of unknown DNA. For many applications, DNA markers are preferred over other molecular markers since DNA is stable within an organism over time and among stages of development whereas other molecules are dynamic. A molecular marker is a DNA sequence that is readily detected and whose inheritance can be easily monitored. The uses of molecular markers are based on the naturally occurring DNA polymorphism. Most commonly used molecular markers in biological science include:

1. Restriction Fragment Length Polymorphism (RFLP)

RFLP is the first molecular marker technique which was invented by Botstein et al. (1980). The technique is based on restriction fragment length polymorphism; a molecular marker based on the differential hybridization of cloned DNA to DNA fragments in a sample of restriction enzyme digested DNAs; the marker is specific to a single clone/restriction enzyme combination. It consists of the following steps:

Introduction

Millions of dollars are lost each year due to insect crop devastation, and the use of chemical pesticides has unwanted side effects such as resistance and unintentional impacts on species that are beneficial (Kumar et al. 2019). For farmers, authorities, and academics, finding additional target-selective pest management techniques is of utmost importance. Enhancing performance, cost-effectiveness, and increasing the markets for bio pesticides are all made possible by biotechnology. Molecular methods are used to detect and track the emergence and spread of particular types that are natural enemies (Tipvadee, 2002). It offers chances for the growth of beneficial insect natural enemies with features including pesticide resistance, cold tolerance, and sex ratio change.

The diversity of the haloarchaea found within a crystallizer pond of a solar saltern located in Siridao and Ribandar, Goa, India was examined. Both cultured-based and culture independent methodology were employed which included  surface spreading of samples on different media containing 25% crude salt/NaCl, DNA extraction from sediment and water samples, amplification of 16S rRNA gene and DGGE.

Abstract

Molecular modeling is a computational technique used to simulate the three-dimensional interactions between atoms and molecules. It allows for the visualization, manipulation, and prediction of molecular structures and chemical reactions. In this chapter, we discuss the different types of molecular models used in computational chemistry, including ball-and-stick models, space-filling models, wireframe models, and ribbon models. Ball- and-stick models depict atoms as spheres and bonds as sticks. Molecular modeling has numerous applications in drug discovery, materials science, and other fields of research, making it a valuable tool for computational chemists and molecular biologists. Here, this chapter focuses on different types of molecular models.

Abstract

Molecular phylogeny is an important method for understanding the evolutionary relationships between different organisms. Molecular phylogeny is based on the idea that organisms that share a more recent common ancestor will have more similarities in their DNA or protein sequences. The chapter seems to cover the basic concepts and terminology used in molecular phylogeny, including the difference between rooted and unrooted trees, as well as various methods used for constructing phylogenetic trees. Further, chapter also covers some common tools and software used for analyzing molecular data and constructing phylogenetic trees. Overall, this chapter provides a useful introduction to molecular phylogeny and the methods used for understanding the evolutionary relationships between different organisms. Understanding these concepts is important for many areas of biological research, including evolutionary biology, ecology, and biotechnology.

Antimicrobial resistance (AMR) is a mounting global health emergency that threatens the effectiveness of modern medicine and veterinary care. In India, the challenge is compounded by high antibiotic consumption, unregulated access to antimicrobials, and widespread use in agriculture and animal husbandry. The World Health Organization has identified the Eskape pathogens— Enterococcus faecium, Staphylococcus aureus, Klebsiellapneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp, as priority organisms due to their ability to “escape” the effects of antibiotics and cause life-threatening infections. Simultaneously, zoonotic transmission of resistant bacteria from animals to humans is emerging as a critical concern, particularly in regions with close human-animal interfaces like Jammu & Kashmir. The importance of Eskape pathogens to the establishment and promotion of antimicrobial resistance in hospitalized patients was first recognized in a 2008 by Rice. The morbidity and mortality associated with Gram-negative Eskape pathogens is particularly concerning, as new antimicrobial agentsthose with activity against multidrug-resistant and pan-resistant Gram-negative strainshave not emerged as quickly as needed. Consequently, nosocomial infections continue to pose a serious threat to patient health, especially among critically ill inpatients and those undergoing invasive procedures or requiring the placement of medical devices. Eskape pathogens are well known for their intricate resistance mechanisms, often leaving clinicians with limited therapeutic options. Due to their significant role in driving antimicrobial resistance within hospital settings, consistent and systematic monitoring of their resistance profiles is crucial for guiding effective infection control and therapeutic strategies.This also serves as a critical indicator of regional resistance trends among hospitalized populations. In animal sector, the wastewater of livestock slaughterhouses, animal products (raw or processed) have been considered a source of multidrugresistant bacteria with clinical implications as well as their dissemination into the environment and entry into human food chain.Bacteria from the livestock can act as opportunistic pathogens and carry resistance genes that are important for both veterinary and human health. Since many antibiotics are used in both human and animal health fields, the resistant bacteria enter the environmentespecially through wastewater treatment plants affected by slaughterhouse wasteposing risks to public health. Among the various sources, the water used during poultry slaughtering often contains multidrug-resistant bacteria and can expose slaughterhouse workers to infection. To reduce these risks, it’s important to develop strategies that limit bacterial release into the water systems and prevent their spread to people and the environment. The development of AMR has been attributed to several factors comprising of microbial mutations rendering the antibiotics ineffective, human interference such as over use and over-prescription of antimicrobials, agricultural and commercial application of antimicrobials in the animal sector, and human behavioural factors (Vijayalaxmi et al., 2021). An expected annual rise of antimicrobial resistance (AMR) by 5–10 % annually has been predicted by the Indian Council of Medical Research (ICMR) Annual Report 2021 due to wide spread abusive use of broad-spectrum antibiotics (ICMR Annual Report 2021). Twelve families of priority drug-resistant bacteria (critical, high and medium) posing great threat to human health in terms of resistance to selected antimicrobials have been identified in priority pathogen list (PPL) of Global Action Plan, World Health Organisation (WHO) to stimulate the research towards the development of new antimicrobials against a particular drug-resistance (WHO,2017). From the Indian perspective, AMR is a grave concern as the Indian population is the highest consumer of antibiotics in the world (10.7 units per person). The poor public health systems, hospital infections, high rate of infectious diseases, easy availability of inexpensive

Introduction

The term ‘lectin’ was coined by William C. Boyd in 1954 for their property of selectivity (Latin ‘legere’, to pick up or choose). In 1888 H. Stillmark of Russia gave the first description of what we now know as lectin. While investigating the toxic effects on blood of extracts of the castor bean (Ricinus communis), Stillmark observed that the red blood cells were being agglutinated by a protein and gave it the name ‘ricin’. Shortly afterward ‘arbin’ was extracted from Arbus precatorius. Because they were first isolated from plants, lectins came to be known as phytohaemaglutinin. Now it has become clear that lectins are present not only in plants but also in some bacteria, vertebrates and invertebrates. However, lectins are most widely distributed in plants, reported in almost 1000 plant species.

Plant lectins are a very heterogeneous group of proteins; as far as their occurrence within the plant kingdom and distribution over tissues are concerned. They show high degree of heterogeneity with respect to biochemical and physiological roles, because of their widely different carbohydrate binding specificities (Etzler 1986; Rüdiger 1988; Goldstein and Hayes, 1978). Besides the fact that they all exhibit carbohydrate binding activity, most of the plant lectins behave as typical storage proteins (Peumans and Van Damme, 1995 b).

The harmony between human beings and plants is one of the evergreen reasons that maintains and supports life on earth. This fact clearly explains why any hazard to the life of plants prominently affects man. One important feature distinguishing plants from other complex multicellular organisms is that plants are sessile and thus have to endure environmental challenges (Zhu, 2001).

Crop productivity is limited by stress factors. The stresses which pose major threats to survival of plants belong to two categories- abiotic and biotic stress. Drought, salinity, high or low temperatures, light, deficient or excess nutrients, heavy metals, pollutants etc., either individually or in combination causes abiotic stresses. Biotic stress refers to any stress provided by living organisms, be it unicellular or multicellular. Plants facing a variety of biotic and abiotic stresses are able to protect themselves by means of tolerance mechanisms which result from changes at the molecular level. They are often confronted by a multitude of stresses in their natural environment. To overcome this, plants have evolved various defence strategies, which involve comprehensive reprogramming of the cellular metabolism.

Introduction

Genetic resistance to diseases is a great resource to control and prevent diseases, and to improve the productivity in livestock and poultry. The emergence of virulent and drug resistant pathogens, restriction on use of antimicrobials and appearance of certain diseases associated with selection for production traits emphasize the possible exploration for genetic resistance to diseases (Pinard et al., 1992). Genetic resistance to diseases is a composite trait and difficult to measure directly. The disease resistance measurement was first started as difference in mortality among populations. Later on, several other criteria related to expression of infection such as antibody response, tumour production count or expression in quantitative scale such as survival time and density of pathogen in target organs were used as a measure of disease resistance.

ABSTRACT

Frankia is a gram-positive, microaerophilic, actinomycete that enters into symbiotic associations with a number of woody dicotyledonous plants called actinorhizal plants. Frankia can fix atmospheric nitrogen through such associations. The actinorhizal-Frankia association is beneficial for the environment, since it increases the fertility of soils. Extensive studies on the biochemical and molecular aspects helped in the classification of Frankia. PCR-RFLP studies of the 16S rRNA and the nif regions of Frankia revealed considerable information regarding the diversity of Frankia strains, isolated from different parts of the world. The completion of three whole genomes of Frankia has bolstered the study of the molecular organization of the genome. Comparative genomics study of the three complete genomes revealed that, the strains reflected the biogeographical history of the host plants they infected. Striking similarity in the codon usage patterns highlights the fact that they may have evolved as a unit. In the present review we highlighted the taxonomy of Frankia and the host plants, the Frankia-actinorhizal association, regulation of infectivity, biochemical and molecular characterization, phylogeny and genomics of Frankia and stressed the need for metabolomic study of the Frankia-actinorhizal association.

In recent years several plant pathological laboratories have been using molecular techniques for identification of the fungal plant pathogens isolated from the diseased plants. These are specifically used for the confirmation of the pathogen identified based on their cultural and microscopic characteristics. With the help of fungal genomic studies, not only the genus but also the species of the pathogen is identified based on the genomic sequences available with NCBI, and provide the accurate identification of the fungal isolate. This identification method involves the following steps:a

1. Introduction
Molecular techniques are laboratory methods used to study and manipulate DNA, RNA, and proteins. These techniques are crucial for analyzing and understanding the molecular basis of biological processes and have applications in various fields like medicine, agriculture, and forensics.
2. Molecular Marker Analysis
Molecular markers can be expressed as a DNA sequence or gene expression product that represents differences in genomic level in relation to a gene or a property. Molecular markers are markers that can be used to monitor differences at the DNA level and for a gene that is being investigated. DNA markers are also DNA regions in which polymorphism in individuals within a species can be determined.
Molecular markers are nontissue-specific DNA regions that are reliable, repeatable, standardizable, capable of identifying multiple regions in the genome, capable of identifying more than one region in the genome, independent of environmental conditions, dominant and codominant.
Molecular markers are classified as dominant and codominant markers. Heterozygous individuals cannot be distinguished from homozygous dominant individuals, since dominant markers are not suitable for identification of heterozygous individuals when related to dominance between alleles is dominated by dominant markers. Thus, three different individuals (AA, AA and AA) can be distinguished for any marker at any point.
The use of molecular marker systems based on this meta-analysis has become more prevalent in genetic studies conducted by the discovery of the polymerase chain reaction (PCR). The rapid development of technology and the accompanying needs, the facilities of the laboratories where the applications will occur, the biological properties of the species and the abundance of markers in the genome have contributed to the development of DNA markers [5]. Restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA markers (RAPD), amplified fragment length polymorphism (AFLP), sequence labeled sequences (STS), microsatellites (SSR), cleaved polymorphic sequence (CAPS), single strand such as complementary polymorphism (SSCP), amplicon length polymorphism (ALP), interspecific sequence repeat polymorphism (ISSR),

Introduction

In the ever-evolving realm of fisheries and aquaculture, the infusion of molecular technology has become a beacon of hope, transforming the way we diagnose diseases and identify pathogens. Imagine it as a kind of genetic detective work that not only helps us understand the health of aquatic life but also empowers us to protect it. It all begins with the delicate dance of DNA extraction, a bit like teasing out the secrets locked within the cells of aquatic organisms. This biological treasure map, once unveiled, guides us through the labyrinth of diseases. Enter the PCR protocol for Carp Edema Virus (CEV) detection—a sort of molecular magnifying glass that allows us to zoom in on specific genetic footprints of trouble. It’s like deciphering a genetic code, helping us pinpoint potential issues swiftly.

Use of morphological markers has continued till today for characterization of several crops including horticultural crops with the Mendel’s principles of inheritance by following visible traits in the progenies of sexual crosses. Genetic markers play an essential role  in the study of variability and diversity, in the construction of linkage maps, and in the diagnosis of individuals or lines carrying certain linked genes. Within this context, the limitations of morphological markers became quickly apparent. They tend to be restricted to relatively a few traits, display a low degree of polymorphism, are often environmentally variable in their manifestation, and can depend on the expression of several unlinked genes. Furthermore, some may affect plant viability or seed set, distorting gene frequencies in the progeny. Morphological markers were largely supplemented by biochemical markers, particularly isoenzymes that could be easily scored by electrophoresis (Ganapathy and Scandalios 1973; Tanksley 1983). The limitations of isoenzmyes as markers, in particular both the limited number of polymorphic enzymes that can be conveniently stained and the environmental effects on expression pattern, were apparent already twenty years ago (Tanksley 1983).

Introduction

Indian agriculture accounts for nearly 65% of the country’s employment, 23% of the total GDP and nearly 20% of total export earning and supplier of raw material to major industries. Agriculture is not only the backbone of Indian economy and food security but also a way of life, a tradition and anchor of overall livelihood opportunity for about 700 million of our one billion populations. Agriculture, therefore, is and will continue to be central to all strategies for planned socio-economic development of the country.

Losses due to insect pests represent one of the single largest constraints to crop productivity estimated at 14% of the total agricultural production. Besides, insects also serve as vectors of plant pathogens. The annual global cost of pest management through insecticides is more than US$10 billion per annum. However, over-reliance of insecticides creates agricultural, environmental and pest management problems, such as frequent evolution of insect resistance, destabilization of multitrophic interactions and environmental contamination. Broad spectrum insecticides often compound these problems. Insecticides often interfere with biological control, causing secondary pest outbreaks or catastrophic resurgence of insecticide resistant herbivores. The vicious cycle of pesticide treadmill effect is observed when more pesticides lead to insects developing resistance, which in turn necessitates use of more and newer pesticides. Therefore, now it is imperative to develop a holistic system of tackling pests to make it more eco-friendly, economically viable and socially acceptable for the farmers.

Two types of molecular weight (MW) standards are routinely used. The Lambda/HindIII and PhiX174/HaeIII MW standards provide a useful reference for calculating molecular weights of large and small DNA fragments, respectively, after electrophoretic separation; the “internal MW standards” provide a means for normalizing fragment migration distances within each lane to facilitate comparisons between lanes on the same or different luminographs in fingerprinting studies.

Recent years have seen a rapid increase in the application of the various techniques of molecular, cytogenetical and serological approaches to problems in plant Nematology. The application of these approaches has been considered to problems of genetic variation and classical taxonomy. Two principal approaches are available. Firstly the use of “random” techniques which aim to sample the entire genome of the animaIs or populations of interest and which are mostly used in studies of genetic variation. Secondly “non-random “ techniques which target defined regions of the genome such as particular genes or gene products and are most frequently used in identification to species or sub-species level. The defined region ofthe genome may be the ribosomal genes, the mitochondrial genome or a conserved nuc1ear gene. Whilst analysis of these regions may allow information about taxonomic relationships to be gathered, focusing on one region of the genome imposes certain limitations on the experimenter.

Vegetables have always been looked upon as an essential part of diet and are necessary for human health and well-being. Vegetables supply many kinds of nutrients, e.g., carbohydrates, proteins, minerals, vitamins, fibers, phytochemicals, etc. and also add flavour, colour and crispness to foodstuffs. For developing modern day vegetables, breeders have utilized an understanding of genetic principles and applied them for the improvement of these crops. They often make crosses (hybridization) between a crop plant and a related or wild species (a wide cross) enabling valuable genes to be used for genetic improvement of the crops. Over the last few decades, molecular breeding is supplementing plant breeder’s efforts for accelerated genetic enhancement bringing about a revolution in this area. This approach demands efficient procedures for the routine introduction of foreign DNA into plant genomes and utilizing them for the production of novel types of vegetable. In this chapter, attempts have been made to review most of the available molecular breeding techniques, which can routinely be employed in various aspects of vegetable improvement.

Cultivars are developed by selecting for desired traits or by removing undesirable traits that are controlled by genes (the blueprint for all characteristics in living organisms) from existing varieties or breeding lines. The plant species, varieties and clones are identified or selected by their physical features since olden times. However, these traits would change with respect to environmental and climatic conditions. The biochemical parameters like enzymes, proteins, alkaloids, etc. are also likely to change due to the stages of development of plant tissue. Successful selection strategies are dependent on the breeder’s ability to distinguish genetic effects from environmental effects on a visible or measurable trait. Therefore, the scientists resorted to use ‘genetic marker’, i.e., any stable and inheritable variation that can be measured or detected by a suitable method and can be used subsequently to detect the presence of a specific genotype or phenotype, which otherwise is very difficult to detect. Presently, the breeders and scientists all over the world are pursuing mostly DNA or molecular markers.

Introduction

Commercially laying of poultry birds carried out for a laying year or cycle after that as egg production decreases then they are usually culled when birds starts shedding of feathers. If we still keep these birds after allowing shedding and renewing of feathers birds take sufficient rest to builds up its body reserve of nutrients for next laying cycles. Their production regains 80-83% of the first laying cycle therefore recycling of laying can be carried out by shedding and renewing of feathers which is nothing but the “molting.”

Moments

In statistics, moments are measures of the shape and variability of a data set. They are used to describe the location and dispersion of the data. There are several types of moments that can be calculated, each providing different information about the data set.

Moments is a term which refers to a measure of force with respect to its tendency which provides rotation. The strength of the tendency depends upon the amount of force and distance from the point of origin where force is exerted.

So total moments of all the forces about origin, if total moment is divided by the total force, which is called moment actually arithmetic mean for frequency distribution.

Hence, arithmetic mean is called first moment about the origin

• Arithmetic mean of various powers expressed as deviation from mean in any distribution is called the moment of the distribution.

Introduction

Monetary policies are the policies used to regulate the money supply, cost, and availability of credit in the economy. Monetary policy is considered as an important tool of controlling inflation in the economy.

Central banks use monetary policy to guide the economy. They set interest rates, control the amount of money in circulation, and take other actions to affect inflation, encourage economic growth, and ensure financial stability. The ability of monetary policy to influence the economy is not absolute. It is affected by several variables, such as how adaptable the economy can expand or contract (supply and demand) and the link between monetary policy and economic development. It plays a significant role in shaping the effectiveness of monetary policy. For example, when people have more pessimistic expectations of inflation, they tend to hold less money and monetize more debt. Economic growth tends to be positively correlated with certain financial factors. For instance, higher inflation, an increased money supply, and lower interest rates are often associated with stronger economic growth. Plus, people's expectations regarding future inflation can also impact economic growth. A reduction in available money can weaken the impact of monetary policy. To accurately assess the effectiveness of monetary policy, it's important to consider. Flexibility and limitations in economic supply and demand. The relationship between monetary policy and economic growth. Expectations of inflation It's also essential to account for potential drawbacks and unexpected effects of monetary policy. Additionally, monetary policy should consider the interaction between monetary and fiscal policies. In formulating domestic monetary policy, the global economic landscape holds significant sway. Factors such as the global economy, currency exchange rates, and international trade can profoundly influence a country's monetary policy framework. Moreover, in today's interconnected financial system, central banks must be cognizant of the broader implications their monetary actions may have on other economies, highlighting the need for a global perspective in monetary policy decision making.

Money

Money has made rapid economic progress possible in this modern age. In the early stages, exchange took the form of barter The direct exchange of one good for another is known as barter. For instance, the potter received paddy from the farmer in exchange for cooking pots. Barter became more challenging as there were more items to trade. Silver and other precious metals were thus utilised as currency. Then the paper currencies were used as legal money, i.e., an instrument of exchange, by the governments.

Definition of Money

Anything that the general public readily accepts as payment for products, services, other assets, and the discharge of debt is referred to as money. Robertson defned money, “as anything that is acceptable in discharge of obligations”.

According to Crowther, “Money is anything that is generally acceptable as a means

18.1. Meaning
When the human civilization was not developed, people used to exchange those goods which they produced for those which others produced. Such an act of exchanging goods for goods is called barter. But as the years rolled by and when the social organization became more complex, barter system was found to be not practicable. The following are the main difficulties which were found in the barter system.
1. Double coincidence of wants
2. Lack of a standard unit of account
3. Impossibility of subdivision of goods
4. Lack of information
5. Production of large and very costly goods not feasible
The difficulties in barter system were replaced with the introduction of money. Money has been defined as the medium of exchange. According to Robertson money is defined as “Anything which is widely acceptable in discharge of obligations”. The different stages in the development of money are as follows.
1. Commodity Money: The earliest form of money consisted of goods like rice, wheat, cattle, skins, elephant tusks etc. These were accepted as they were all desired by all the people.
2. Metallic Money: As the civilization advanced, people found it difficult to carry on the exchange transaction with commodities, as they were found to be very inconvenient. Commodity money gave way for the metals to be used as money. These metals include gold, silver, copper, bronze, etc. From the beginning of their introduction, Government kept the right to issue coins and certify their weight and quality. Metals were converted into coins for this purpose.

Definition of Monitoring and Evaluation

Systematic recording of observations, information, gathering, analysis, documentation, reflection, action and re-planning is called monitoring.

It provides programme/projects managers and key stakeholders with regular feedback and early indications of progress or lack of in the achievement of intended results.

Introduction

The ‘cutting edge’ of any development is the projects. No matter how well planned, a poorly executed project will waste valuable resources. India has pioneered many poverty-reduction programmes in agriculture, rural development, health and family welfare, education, women’s and children’s development, drinking water, and other fields. According to an analysis of these initiatives, monitoring and suitable mid-course corrective measures are crucial to accomplishing project objectives.

Monitoring and evaluation constitute systematic processes of tracking, assessing, and learning from program implementation and outcomes to improve performance, demonstrate accountability, and inform decision-making. These complementary yet distinct functions serve as essential management tools that enable organizations and programs to understand whether they are achieving their intended objectives, efficiently using resources, and creating desired changes in target populations or systems. The integration of monitoring and evaluation creates powerful feedback loops that enhance program effectiveness while providing evidence for policy development, resource allocation, and strategic planning. Monitoring is defined as the systematic and continuous collection, analysis, and use of information about program implementation, progress toward objectives, and changes in context that may affect program performance. It represents an ongoing process that tracks inputs, activities,

Key words : GPS, GIS, DSS, SDSS, RS, Digital Elevation Model (DEM), Ground Water Exploration, Conjunctive Use of Surface and Ground Water, Digital Terrain Modeling (DTM).

Introduction

Water is one of the most precious gifts of nature to living beings and particularly to the mankind. On account of erratic distribution of rainfall both in time and space, the country is subjected to cycles of floods and droughts. With the increase in demand for water for various purposes and to mitigate the twin problems of floods and droughts faced by the country, a coordinated approach for optimum utilization and proper management of this precious resource is of prime importance. In addition, proper development and management of both irrigation and drainage systems are essential. This would require integrated management of surface water as well as gorund water. All the water related problems whether mitigating droughts or floods or better irrigation management practices, dictate for adoption of state of the art water management practices. Water management deals with the control, distribution and allocation of water flows and the treatment of rivers and catchments, consequently, solutions to many of the problems in water management require the knowledge and expertise from diverse sources.

Abstract

While harnessing the benefits of genetically modified (GM) crops, in terms of increased yield, better nutritional quality and resistance to biotic and abiotic stresses, it is important to undertake biosafety and risk assessment studies in a systematic manner to allay the concerns of their impact on the environment and especially on the genetic diversity. Since Bt cotton is the only commercialized GM crop in India, this paper reports on the monitoring of unintentional introgression of transgene(s)/ regulatory elements of four commercialized Bt cotton events, covering 99.5% of the area under cultivation, in 180 ex situ cotton accessions conserved in the National Gene Bank at National Bureau of Plant Genetic Resources (NBPGR), New Delhi, using polymerase chain reaction (PCR)-based assays. Based on the real-time event-specific and conventional transgene-specific PCR assays, no amplification signals specific to two major Bt cotton events MON531, MON15985; transgenes/markers/ regulatory elements of 4 widely cultivated commercialized Bt cotton events, i.e., cry1Ac, cry2Ab, marker genes, i.e., nptII (neomycin phosphotransferase), aadA (aminoglycoside-3’-adenyltransferase) and uidA (?-D-glucuronidase) marker genes, CaMV35S, nos (nopaline synthase) promoters and nos terminator were detected in any of the cotton accessions. The study shows that the cotton accessions conserved in National Gene Bank are GM free and the study can be used as a model for monitoring the adventitious presence of unintended mixing of cotton seed during seed production or harvesting in Bt cotton growing states of India. On similar lines, adventitious presence of transgenes can be checked in ex situ collections of different crops conserved in the genebanks.

Monitoring the microclimate inside protected cultivation systems—such as greenhouses, polyhouses, net houses, and other semi-controlled environments— plays a crucial role in modern agricultural practices that aim to enhance crop productivity, quality, and resource efficiency. As global demand for high-quality and high-yield crops continues to rise, protected agriculture has become a key solution for mitigating the effects of climate variability, pest infestations, and limited available land. However, the effectiveness of these systems largely depends on the ability to continuously monitor and regulate the essential microclimatic factors that directly influence plant health, disease resistance, and overall productivity. Microclimate refers to the localized climate conditions within a specific area— in this case, within the protected structure—that can differ significantly from external environmental conditions. Key parameters typically monitored include temperature, relative humidity, solar radiation or light intensity, carbon dioxide (CO?) concentration, vapor pressure deficit (VPD), and air movement or circulation. These factors are interrelated, and even minor fluctuations can greatly impact plant health, photosynthesis, transpiration, and reproduction. Thus, accurate and continuous monitoring of these variables is essential for effective climate control and optimal crop growth.
Temperature is arguably the most critical variable, as it controls metabolic processes, enzyme function, flowering time, and fruit development. A deviation from the ideal temperature range can either accelerate or stunt plant growth, leading to reduced yields or even crop failure. In tropical or semi-arid climates, temperature spikes inside protected structures can result in heat stress, while in temperate or mountainous regions, low temperatures can hinder growth. To mitigate this, temperature sensors—such as thermistors, RTDs, or thermocouples— are placed at different heights and zones within the structure to ensure uniform monitoring. These sensors typically transmit real-time data to centralized systems that control heating, cooling, and ventilation systems. Along with temperature,

Project monitoring is the process of keeping a close eye on the entire project management life cycle and ensuring project activities are on the right track. It is a continuous function that aims primary to provide functionaries with required feedback and early indication of progress or lack of their achievements of intended results.

Digestion is the process by which food is converted into substances that can be absorbed and assimilated by a living organism. In most animals it is accomplished in the digestive tract by the mechanical and enzymatic breakdown of foods into simpler chemical compounds. Digestion usually consists of two elements: a mechanical/ physical stage, e.g. mastication, churning, emulsification, in which no chemical bonds are broken and no enzymes are required; and a chemical stage requiring enzymes in which complex food molecules are broken down by hydrolysis into a state in which they can be absorbed.