eChapters

Introduction to Metabolism Metabolism is the sum of all biochemical reactions (physical and chemical processes) occurring within the body to sustain life. In total, it encompasses all the processes converting the energy from nutrients into usable forms, thereby facilitating the synthesis of biomolecules necessary for sustaining life. This process occurring in all living organisms ensures that a continuous supply of energy and precursors is maintained to perform cellular functions, such as growth, reproduction, maintenance and response to environmental stimuli. Therefore, studying the body’s metabolism provides insights into the physiology, mechanism of disease occurrence and potential therapeutic interventions. Specifically, metabolism is a highly regulated process involving a set of biochemical reactions that can be broadly grouped into: a) Catabolism involves the breakdown of complex molecules into simpler components, releasing energy in the form of adenosine triphosphate (ATP). Catabolic reactions assist in the extraction

Metabolomic databases provide essential information for identifying metabolites, interpreting experimental results, analyzing pathways, and understanding biochemical relationships. This chapter introduces major databases used in metabolomics and explains their roles in modern biological research. Resources such as KEGG, BRENDA, HMDB, MetaboLights, METLIN, and LIPID MAPS provide information on metabolites, enzymes, pathways, structures, spectra, diseases, and experimental datasets. The chapter discusses their applications in metabolite identification, pathway analysis, biomarker discovery, systems biology, and translational research. It also considers challenges including data volume, database completeness, continuous updating, standardization, and integration with other omics resources.

Metabolomic research depends on analytical technologies capable of detecting and characterizing large numbers of chemically diverse metabolites. This chapter introduces the principal analytical platforms used for metabolite analysis, with emphasis on mass spectrometry and nuclear magnetic resonance spectroscopy. Gas chromatography–mass spectrometry, liquid chromatography–mass spectrometry, capillary electrophoresis–mass spectrometry, and NMR are examined in relation to metabolite separation, identification, and quantification. The chapter also considers sample preparation, analytical workflows, advantages and limitations of different platforms, and complementary approaches for achieving broader metabolome coverage. These techniques provide the analytical foundation for metabolic profiling, biomarker discovery, pathway analysis, and systems-level biological investigations.

Abstract

Dietary phytochemicals and herbal medicines are under intensive investigation for their potential as chemopreventive agents against various diseases due to the wide variety of microbial and plant functionally relevant secondary metabolites. The chemical diversity of phytochemicals, as well as phytochemicals and complex metabolic interactions between the biological systems may exceed the capacity of the platforms of traditional analysis, and therefore pose major challenges in the study of chemopreventive phytochemical compounds.

Summary

Metagenomics is a rapidly developing field of research that enables the study of microbes that have not been cultured or cannot be cultured easily. It has greatly advanced the understanding of ecology and diversity of natural microbial communities and has led to the discovery of many new genes and geneproducts. The various aspects of metagenomics – history, techniques for identification, different approaches of data analysis, comparative and functional genomics, applications in the areas of medicine, agriculture, biotechnology, ecology, bioprospecting, bioremediation, future advances and challenges and issues related to intellectual property, have been discussed.

Surface-Enhanced Raman Spectroscopy (SERS) may detect and identify chemical and biological species ultrasensitively. Through localized surface plasmon resonance (LSPR) effects, metal nanostructures boost analyte Raman signals. This chapter covers current advances and essential principles in metal nanostructures for SERS chemical detection. It discusses SERS fundamentals and enhancing processes, such as metal nanostructure size, shape, and composition. Top-down and bottom-up processes including lithography, chemical synthesis, and self-assembly are used to create repeatable and controllable metal nanostructures. The complex interactions between light, metal nanostructures, and analyte molecules are best understood by combining theoretical modeling and experimental observations. 

Developments in recombinant DNA technology have made it possible to transfer gene from any source across species barrier. In fact, transfer and expression of foreign genes in plant cells is now a routine procedure. Of the several methods tried so far, the system based on Ti plasmid of Aprobacterium tumefaciens appears to be most successful for transformation of plant cells.

Atoms and molecules are the essential building blocks of every object. The manner in which things are constructed with these basic units is vitally important to understand their properties and their reciprocal interactions. An efficient control of the synthetic pathways is essential during the preparation of nanobuilding blocks with different sizes and shapes that can lead to the creation of new devices and technologies with improved performances. Traditionally nanoparticles were produced only by physical and chemical methods. Some of the commonly used physical and chemical methods are ion sputtering, solvothermal synthesis, reduction and sol gel technique

Basically there are two approaches for nanoparticle synthesis namely the Bottom up approach and the Top down approach. In the Top down approach, scientists try to formulate nanoparticles using larger ones to direct their assembly. The Bottom up approach is a process that builds towards larger and more complex systems by starting at the molecular level and maintaining precise control of molecular structure.

These two different methods highlight the organization level of nanosystems as the crossing point hanging between the worlds of molecular objects and bulk materials.

The top-down approach has been advanced by Richard Feynman in his often-cited 1959 lecture stating that “there is plenty of room at the bottom” and it is ideal for obtaining structures with long-range order and for making connections with macroscopic world. Conversely, the bottom-up approach was pioneered by Jean-Marie Lehn (revealing that “there is plenty of room at the top”) and it is best suited for assembly and establishing short-range order at the nanoscale. The integration of the two techniques is expected to provide, atleast in principle, thewidest combination of tools for nanofabrication.

In genetics, microRNAs (miRNA) are single-stranded RNA molecules of 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (i.e. they are non-coding RNAs); instead each primary transcript (a pri-miRNA) is processed into a short stem-loop structure called a pre-miRNA and finally into a functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression. They were first described in 1993 by Lee and colleagues in the Victor Ambros lab .

MicroRNAs can be encoded by independent genes, but also be processed (via the enzyme Dicer) from a variety of different RNA species, including introns, 3' UTRs of mRNAs, long noncoding RNAs, snoRNAs and transposons.

The genes encoding miRNAs are much longer than the processed mature miRNA molecule; miRNAs are first transcribed as primary transcripts or pri- miRNA with a cap and poly-A tail and processed to short, 70-nucleotide stem-loop structures known as pre-miRNA in the cell nucleus. These pre- miRNAs are then processed to mature miRNAs in the cytoplasm by interaction with the endonuclease Dicer, which also initiates the formation of the RNA-induced silencing complex (RISC). This complex is responsible for the gene silencing observed due to miRNA expression and RNA interference. The pathway in plants varies slightly due to their lack of Drosha homologs; instead, Dicer homologs alone effect several processing steps. The pathway is also different for miRNAs derived from intronic stem-loops; these are processed by Dicer but not by Drosha. Either the sense strand or antisense strand of DNA can function as templates to give rise to miRNA.

Abstract

Microorganisms execute many key functions that regulate the processes related to the fertility status, nutrient transformation, nutrient conservation, and soil health management that are crucial for agronomic sustainability. Rice soils offer peculiar conditions for microorganisms that support diametrically opposite biochemical reactions under flooded conditions. It is pertinent to note that both reduction and oxidation reactions of several essential nutrients mediated by microbes occur simultaneously in the flooded soils at various depths, profiles and stages of rice crop growth in concurrence. This is peculiar and specific to rice soils as the cultivation process demands changes in water regimes, operative and management practices.

Abstract

Discovery of the agricultural utility of microbes during the later part of the eighteenth century, led to the formulation and utilization of superior microbial strains as biofertilizers, for a wide variety of crops and growing conditions across the world. Though microbial inoculants have been in usage for almost two centuries, they are yet to capture the collective imagination of farmers across the globe, which is essential to meet the larger objective of reducing chemical input usage in cropping systems. One probable reason for this is the existence of large growing tracts that are subject to various abiotic stresses of atmospheric and edaphic origin, which limit the proliferation and efficiency of the microbial strains that are commonly used in inoculant production.  This is obvious, since unlike chemical fertilizers, microbial cells being living systems need to grow and thrive in the introduced eco-systems in order to achieve the desired effects of inoculation. But unfortunately microbial inoculant technology has largely adopted the one size-fit all mindset, which had led to failures of microbial inoculants especially in abiotically stressed growing environments. In such a scenario it would be wise to adopt a location or region specific approach for the selection of superior and locally adapted microbial strains for inoculant production.

The increase in population and global industrialization has led to environmental pollution, which is a significant threat to the health of the ecological system. Different measures are recommended to remediate polluted areas effectively. The applications of nanotechnology in medicine, cosmetics, sports, textiles, and pharmaceuticals have increased over the years. Another approach to remediate the adverse effects of pollutants on the environment is by utilizing nanotechnology for contaminant remediation. Biogenic nanoparticles are tiny particles produced by biological entities such as fungi, bacteria, yeast, and algae. These biogenic nanoparticles are efficient in removing pollutants like heavy metals, pharmaceutical waste, dyes, and hydrocarbon waste. 

The induction of mutations in polygenes controlling quantitative characters can be detected by the estimation of mean and variance of progenies from normal looking mutagen treated populations. Induction of micromutations in different crop plants have been reviewed by various investigators like Gregory (1955, 1968) in peanut, Rawlings et al. (1958) in soybean, Oka et al. (1985) in rice, Brock and Latter (1961) in Trifolium, Borojevic (1966) and Scossiroli (1966) in wheat, Gaul (1961a, 1966), Astveit (1966) in barley and Brock (1967) in Arabidopsis.

Though more reliable results can be obtained from the study of quantitative variation in the advanced generations than in M₂ (Aastveit, 1968, and Scossiroli, 1977), an estimation of the extent of induced genetic variability in quantitative traits in M₂ itself will be valuable in providing information for future selection programme. It was therefore considered worthwhile to study the shift of mean values and to gather information on induced genotypic variance heritability and genetic advance for different quantitative traits from families of M₁ from different mutagenic treatments.

Principle

Micropropagation is especially useful for include propagation of high value plants that grow slowly (bulbs, ferns, orchids, palms, etc), new cultivars having limited stock and high market demand (new cultivars produced via conventional breeding or genetic engineering), cultivars that are difficult to root by conventional techniques, and endangered plant species. In addition, virus elimination is possible via culture initiation from meristem explants. Also, micropropagation provides a source of sterile tissues that can be used for other tissue culture protocols, including genetic transformation.

Micropropagation is possible using multiple types of cultures; however, shoot cultures are typically employed, in which case five stages to the micropropagation process are typically recognized as outlined below. Nodal explants of rose are used for culture initiation. Three media, differing in hormone content, is employed and the explants should be evaluated for differences in axillary shoot growth and proliferation.

Abstract

Bamboo is nature’s unique gift to mankind. It has tremendous scope for use in eco-friendly agro-forestry programmes, to bring marginal lands into use. The requirement for bamboo is increasing for various traditional and industrial requirements. In India almost 99% of annual bamboo production comes from the natural forests and only about 1% is derived from plantations.

Experiment - 1
 
Aim: Micropropagation of Tobacco plant by leaf disc culture

Principle: The totipotency of the plant cells and tissues form the basis for in vitro cloning i.e., generation or multiplication of genetically identical plants in in vitro culture. The ability to propagate new plants from a cells or tissues of parent plant has many interesting possibilities.

Micropropagation /Clonal propagation

Micropropagation or clonal propagation is the growing of plants from meristematic tissue or somatic cells of superior plants on nutrient suitable media under controlled aseptic physical conditions. Sexually propagated plants (through generation of seeds) demonstrate a high amount of heterogeneity since their seed progenies are not true to type whereas asexual reproduction (by multiplication of vegetative parts) gives rise to genetically identical copies of parent plant. Thus, it permits perpetuation of the parental characters of the cultivars among the plants resulting from micropropagation. Micropropagation proves useful for propagation of: 

BC

1750 The Sumerians brew beer.

500 The Chinese use moldy soybean curds as an antibiotic to treat boils.

250 The Greeks practice crop rotation to maximize soil fertility.

100 Powdered chrysanthemum is used in China as an insecticide.

AD: Before the 20^th Century

1590 The microscope is invented by Janssen.

1663 Cells are first described by Robert Hooke.

1675 Leeuwenhoek discovers protozoa and bacteria.

1745 Maupertuis proposes an adaptationist account of organic design

1797 Jenner inoculates a child with a viral vaccine to protect him from smallpox.

1802 The word “biology” first appears.

PLANT NUTRITION

Plants use inorganic minerals for nutrition, whether grown in the field or in a container. Complex interactions involving weathering of rock minerals, decaying organic matter, animals, and microbes take place to form inorganic minerals in soil. Roots absorb mineral nutrients as ions in soil water. Many factors influence nutrient uptake for plants. Ions can be readily available to roots or could be “tied up” by other elements or the soil itself. Soil too high in pH (alkaline) or too low (acid) makes minerals unavailable to plants.