eChapters

Food is the basic requirement for maintaining the life process. Plants supply the bulk of foods required for human and animal. With limited cultivable area and ever increasing pressure of human population, the demand for food is constantly rising which can not be alone met by conventional plant breeding technologies. Novel techniques like plant genetic engineering are gaining momentum for production of superior plants or yield enhancement of a species.  It has been observed that the most commercially successful application of recombinant DNA technology is in genetic engineering of plants, which led development of multinational seed companies deriving monetary benefit from genetically modified crop and food products. From production of herbicide resistant or insect pest tolerant plants to alter the inherent quality composition of human food, plant genetic engineering has established firmly the commercial viability of recombinant DNA technology.

Several substrates, like proteins (enzymes), are very sensitive to alteration in the concentration of the solution they are placed in. Hence is the importance of a buffer which controls the chemical properties of the medium. Literally a “buffer” has the ability to resist changes in the hydrogen ion concentration. Although, buffers do contain other molecules, that might, in addition to the hydrogen ion concentration, influence the ionic strength, the activity of enzymes, and other parameters of the experiment.

In any biological experiment, appropriate buffer must be selected based on their effect on the experiment. Ideal buffers control pH and ionic strength without interacting adversely with the experiment undertaken. For example, although phosphate is a common buffer, it may not be suited when phosphate is a substrate or product of the reaction being studied. Also, some proteins interact poorly with some buffers. For example, Tris is not ideal as it exhibit high pKa and the large change in pKa when temperature changes, although it is cheap and most proteins are stable in Tris buffers, moreover it seldom reacts with reaction substrates hence, Tris buffer is commonly used in biochemical experiments.

Agriculture is the most important sector in India in terms of the population dependent on it. Although agriculture now accounts for on 14 per cent of GDP, it is still main source of livelihood for the majority of the rural population. Rapid growth of agriculture is critical for development of rural economy and viable development of rural economy will leads to overall development of country. Diversification in agriculture is need of the hour, any cropping system comprising crops with varied maturity period, crop canopy and high yielding potential is need for an average farmer. Again cropping systems depending upon the soil type, total rainfall and arrival of monsoon in the region. Low cost technology is essential for reducing financial burden on farmers and to increase production on sustainable manner.

There is no cereal in the world which has no immense patentability as in maize and that’s why it is called the “Queen of cereals”. It is the world’s leading cereals crop after rice and wheat. It is one of most important cereals of Nepal. At national level, it stands second position after rice in term of area and fourth in term of production after rice, potato and sugarcane. Maize is the most important cereals crop of hill and mid hills of Nepal. It is grown single as well as mixed cropping with millets or legumes or potato. Maize crop in hill is grown as rainfed farming. Generally, farmer of such region does not apply chemical fertilizer but they fertilize the land with organic manures in three seasons viz., rainy, winter and spring season. In rainy season it grown in upland while in spring season in low land. The winter maize is grown in Terai and inner Terai in low land as well as upland.

Abstract

Real-time PCR, also known as qPCR, is a highly sensitive technique used to determine the real-time amplification of a target DNA sequence. However, the presence of secondary structures or spurious amplicons can distort the results. When using SYBR Green chemistry, the features of qPCR primers differ from those of standard endpoint PCR primers. As a result, designing primers for SYBR Green qPCR requires extra caution and attention. This chapter outlines the essential features and conditions for designing qPCR primers, including primer length, melting temperature, GC content, specificity, and avoiding primer-dimer formation.

1.    Kernel type: Dent, Flint, Floury, Waxy, Sweet and Pop corn 
        •    Dent corn (Zea mays indentata Staurt.)
        •    Flint corn (Zea mays indurate Staurt.)
        •    Pop corn (Zea mays everta Staurt.)
        •    Sweet corn (Zea mays saccharata Staurt.)
        •    Flour/soft corn (Zea mays amylacea Staurt.)
        •    Waxy corn (Zea mays ceatina Kulesh)

Modern agriculture faces unprecedented challenges due to climate change, unsustainable farming practices, and declining soil health. In response, nanoparticle-bioinoculants (nano-bioinoculants) have emerged as a promising innovation that integrates nanotechnology with microbial inoculants to enhance plant productivity and sustainability. Conventional agriculture contributes significantly to greenhouse gas emissions, degrades microbial diversity, and compromises ecological balance. Beneficial microbes, known as bioinoculants, play a vital role in improving plant health through nutrient cycling, hormone production, and disease suppression. However, their field performance is often limited by environmental instability and low survival rates. Nanotechnology provides a solution by enabling the encapsulation of bioinoculants within nanoparticles, enhancing their stability, targeted delivery, and effectiveness. These nano-scale carriers exhibit high surface-area-to-volume ratios, improved reactivity, and strong adhesion properties, making them ideal for enhancing microbial colonization and activity in the rhizosphere. Additionally, nanoparticles function as nano-fertilizers and nano-pesticides, supporting both plant nutrition and protection against pathogens. Plant-based nanoparticle synthesis further offers an eco-friendly alternative, minimizing ecological and health risks. Studies demonstrated that nano-bioinoculants improve seed germination, stress resilience, photosynthetic activity, and crop yield across various species. They also mitigate abiotic stresses such as drought, salinity, and heavy metal toxicity while promoting systemic resistance against biotic threats. The synergistic combination of nanoparticles and microbial agents enables multifunctional benefits—supporting soil health, reducing chemical dependency, and enhancing agricultural resilience. While challenges remain in understanding

Maize is a tall, determinate annual C₄ plant varying in height from (1-4) meters producing large, narrow, opposing leaves (about a tenth as wide as they are long), borne alternately along the length of a solid stem. The botanical features of various plant parts are as follows: 

Root

Root system of maize consists of seminal roots, crown or coronal or adventitious or fibrous roots and brace, pop or aerial roots. Seminal roots - which develop from radical and persist for long period. Crown roots developing from the lower nodes of stem below ground level which are the effective and active roots of plant and.  Brace or prop roots, produced by lower two nodes. The roots grow very rapidly and almost equally outwards and downwards. Favorable soils may allow corn root growth up to 60 cm laterally and in depth.

Abstract

FASTA, which stands for “Fast All”, is a sequence alignment tool developed by William R. Pearson and David J. Lipman in 1985. It is commonly used to identify similarities between DNA and protein sequences. FASTA employs a “hashing” strategy to locate matches for short stretches of identical residues with a length of k, referred to as k-tuples or k-tups. This method enables FASTA to quickly search large databases for sequence similarities, making it a popular tool for identifying homologous sequences, predicting gene functions, and analyzing evolutionary relationships. This chapter elaborates some basics of FASTA.

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.

Progeny test

Progeny trials involve large numbers of progenies of a family type, such as full-sib, half-sib, or S1 lines. The progenies are evaluated to identify those that may be used to generate synthetic or experimental varieties, or recombined to form an improved population in a recurrent selection program. Progenies in the trials are normally a random sample from the particular population under study. Therefore, data obtained from progeny trials may be used to estimate genetic variances and covariances from which heritability estimates, predicted responses to selection, genetic correlation coefficients, and correlated responses to selection may be obtained. Progeny trials are normally researcher-managed. Progeny trials involve complex field designs, such as balanced incomplete block, lattice, and alpha-lattice. Some examples of lattice are 11 × 11 for 121 progenies, 14 ×14, 16 × 16, etc. Because of the large number of entries, single-row plots with only 2–3 replications in a few environments are used in progeny trials.

Transfer 1.5 mL overnight culture to a 1.5 mL microfuge tube, centrifuge for 30 sec, and decant supernatant.

Resuspend cells in 400 µL TE by vortexing, add 50 µL 10% SDS, 50 µL proteinase K (20 mg/mL in TE). Incubate for 1 hour at 37^oC.

Shear DNA by 3-5 passages through a 26 G needle.
Extract twice with 500 µL phenol: chloroform (1:1), and twice with 500 µL chloroform. 
Precipitate nucleic acids by adding 25 µL 5 M NaCl and 1 mL 95% EtOH, vortex, and centrifuge for 10 min, decant supernatant. Dry pellet.

Abstract

Synthetic biology is a multidisciplinary field of study that seeks to understand living systems and organisms, and utilizes engineering principles to design and create new biological components, devices, and systems, as well as modify existing natural systems. This chapter provides an introduction to synthetic biology and describes the procedures and methodologies involved in the design and construction of novel biological systems. The applications of synthetic biology are vast and include the development of biosensors, gene circuits, metabolic pathways, and genetically modified organisms for use in a variety of industries, including healthcare, agriculture, energy, and environmental remediation.

Introduction
Project title:
Objective (S):

Reagents

Nuclease-Free Water: 14µl

10X Restriction Buffer: 2µl

Acetylated BSA (1mg/ml): 2µl

DNA (~1µg): 1µl

Restriction Enzyme (10u): 1µl

Final Volume: 20µl

Reagents

Restriction enzymes of choice, such as BamH1 and EcoRI

Restriction enzyme reaction buffer,

70 % Ethanol

100 % Ethanol

3 M Sodium acetate (pH 5.2)

Distilled water

Plasmid DNA isolated from bacteria, such as pGFP(R) and pBC(R)

Start with a 1:2 molar ratio of vector: insert DNA when cloning a fragment into a plasmid vector. This ratio will vary with other types of vectors, for example, cDNA and genomic cloning vectors. The following example illustrates the conversion of molar ratios to mass ratios for a 3.0kb plasmid and a 0.5kb insert DNA fragment.

Synthesis of Zn Oxide Nanoparticle

Aim

To synthesize Zn oxide nanoparticle

Introduction

Zinc oxide nanoparticle are effective anti-bacterial and antiodur agent. They can be synthesized by number of techniques including hydrothermal methods. Their synthesis using solvothermal process is described, (Aneesh et al., 2007).

Principle

Plasmids requires hosts to replicate, hence it has to be inserted into bacteria. But efficiency of uptake of plasmid DNA by bacteria is low and will not do so without getting degraded. Therefore, to enhance the probability of uptake of the plasmid DNA by bacteria it is necessary to make the bacterial cells “competent” to absorb the plasmid DNA. One of the methods to increase efficiency of cell competence is given below. It should be noted that competent cells are more fragile than normal bacteria. Vortexing the cells, heating the cells above 42ºC or to 42°C for prolonged periods, or exposure of the cells to abusive treatments may kill them

Aim

To synthesize iron (III) oxide (Fe₂O₃) nanoparticles

Introduction

Iron oxide nanoparticles have a number of applications in catalysis, sensors and high sensitive biomolecular magnetic resonance imaging (MRI) for medical diagnosis and therapeutics. They can be synthesize by the bottom-up approaches including the sol-gel technique.