eChapters

1    Introduction to Patent Laws    540

2.    An Overview of the Patenting Process    541

    2.1.    Inventor’s disclosure, 542
    2.2.    Patentability search, 542
    2.3.    Patent application preparation, 542
    2.4.    Patent application amendment, 542
    2.5.    Patent application examination, 543
    2.6    Main parts of a patent, 543
    2.7.    Granting of patent, 544
    2.8.    Date and term of patent, 544
    2.9.    Provisional specification, 544
    2.10.    Complete specification, 545
    2.11.      Cost of patenting, 545

Section 3.1 Biotechnology Patents – Scope and Controversies
3.1.1 Introduction
Biotechnology, a field at the intersection of biology and technology, generates innovations that are often groundbreaking and commercially significant. As such, patents have become a vital tool in protecting biotechnological inventions. However, the unique nature of biological materials and living systems presents unprecedented legal, ethical, and commercial challenges, sparking ongoing debates globally. This section delves into the scope of patenting in biotechnology and explores the controversies surrounding such patents.
3.1.2 Scope of Biotechnology Patents
Biotechnology patents cover a wide array of inventions that are novel, non-obvious, and industrially applicable. These may include:
1. Genetic Materials and Constructs
• Isolated DNA/RNA sequences, including genes and promoters
• Synthetic nucleic acids and gene editing tools (e.g., CRISPR-Cas systems)
2. Microbial Inventions
• Genetically modified microorganisms (GMMs) for bioremediation, fermentation, or synthesis of pharmaceuticals

Sanger Method for DNA Sequencing

One necessity first know a little about the structure of DNA:

1. A segment of DNA, which is ordinarily double stranded, has a specific orientation, as it has a 5' (read as “5 prime”) and a 3' (“3 prime”) end. This can be simply thought of as a front and tail end to the DNA segment.
2. When DNA is synthesized in the lab, the two strands are separated and new bases are added to the 3' end-thus DNA is assembled from the 5' to 3' end.
3. DNA cannot be synthesized from scratch. A short piece of DNA, called a primer, is required for the reaction to begin.
4. Primers are designed such that they are able to bind to the target DNA, the binding of which is the initiator for DNA synthesis.

Objective: To study peroxidase isozyme variation in rice seedlings by electrophoresis.

Background information

For electrophoresis and PAGE please see practical no. 4. For peroxidase please see practical no. 7.(Page 17-22)

Isozymes (isoenzymes or more generally as multiple forms of enzymes) are the enzymes that are differing in the sequence of amino acids but they work on same substrate or in other words catalyze same biochemical reaction. The isozymes have difference in K_M values and regulatory properties. Isozymes are very useful for proper tuning of metabolic activities and to meet the specific need of particular tissue or developmental stage, e.g. lactate dehydrogenase (LDH). Isozymes are coded by homologous genes that have diversity during evolutionary process. Although, strictly speaking, allozymes represent enzymes from different alleles of the same gene, and isozymes represent enzymes from different genes that process or catalyse the same reaction, the two words are usually used interchangeably.

In agricultural practices pesticide application is an inevitable factor for maintaining high crop productivity and is currently an integral part of modern farming. Pests (insects, microbes and weeds) cause approximately 20-30% loss in crop production so making pesticide use indispensable for crop protection.
 
Pesticide : A pesticide may be defined as ‘any agent or chemical or a mixture of chemicals/ substances intended to prevent, destroy, repel or irritate one or more pest populations causing economic loss in crop production’. Worldwide more than 450 active pesticide chemicals formulated into more than 10,000 commercial products are currently used by farmers. The most worrying aspect is that about two-third of the 800 chemicals tested so far have been found involved in causing or promoting tumor in rodents. Yet more than 50,000 synthetic chemicals/formulations remain untested so far.

Introduction

Mosquito-borne diseases such as malaria, filariasis, Japaneseencephalitis, chikungunya and dengue hemorrhagic fever cause extensive morbidity and take heavy toll of life in the developing nations particularly in the tropics. Every year about 300-500 million people are estimated to be affected by malaria alone (WHO report, 2000). In India around two million cases of malaria are being reported annually although real burden is many fold higher (Kumar et al. 2007). Similarly, lymphatic filariasis caused by Wuchereria bancrofti affects about 120 million people worldwide. India contributes about 40%  to  the total global burden of filariasis and accounts for about 50% of the people at risk of infection (ICMR bulletin, 2002). Anopheles stephensi is recognized as a major vector for urban malaria in India (Kumar 1997).

Introduction

Increased population pressure, reduced length of fallow, deforestation and improper agricultural practices have led to widespread soil degradation in many parts of the developing world which has culminated in appearance of determinative manifestations of environmental damage in form of inadequate replenishment of soil nutrients and organic matter. Phosphorus is second major plant growth limiting nutrient and despite being in abundance in soil (organic and inorganic form), P deficiency is becoming critical in many soils throughout world as these soils have free available P concentration (generally) not higher than 10mM even at most soluble slight acidic pH (Arnou, 1953). Moreover, consistent P deficiency threatens to disturb the use efficiency of applying other nutrients. Hence to preserve the sustainability of agriculture it is foremost to rebuild soil fertility and maintain/improve the soil biodiversity to reap hiked current levels of productivity and farm income.

Phosphorus is only second to nitrogen as an inorganic nutrient required by both plants and microorganisms. It stimulates growth of young plants, giving them a good and vigorous start. Phosphorus management and nutrition has both economic and environmental implications. Phosphate constitutes nearly 0.1% of the earth’s crust. They occur in soil in inorganic and organic forms. The organic phosphorus containing compounds are derived from plants and microorganisms and are composed of nucleic acids, phospholipids, lecithin, phytin and related compounds. In soil, 15-85 % of the total P is organic and soils rich in organic matter contain abundant organic P. The inorganic forms are derived from parent rocks or through fertilizers application and manuring with bone meal. They are soluble in water when present as phosphates of Na, K, Ca, Mg etc. Phosphorus exists mainly as apatites, with the basic formula M₁₀ (PO₄) ₆ X₂. Commonly the mineral (M) is Ca, less often Al or Fe. The anion (X) is either F^-, Cl^-, OH^- or CO^2- ₃. Diverse combinations of M and X results in 200 forms of P.

It is a major constituent of nucleic acids in all living systems essential in the accumulation and release of energy during cellular metabolism. This element is added to the soil in the form of chemical fertilizers, or in the form of organic phosphates present in plant and animal residues. In cultivated soils it is present in abundance (i.e. 1100 kg/ha), but most of which is not available to plants, only 15 % of total soil phosphorus is in available form. Both inorganic and organic phosphates exist in soil and occupy a critical position both in plant growth and in the biology of soil.

MOST OF THE ENERGY FOR LIFE COMES FROM SUNLIGHT

Total rate of energy delivery from sun to earth (at the top of the atmosphere) = 175,000 terrawatts

Terrawatt = 10^12 watts

Rate of energy capture by plants from the sun = net primary productivity (NPP) = 100 terrawatts

Only ~ 0.06% of sunlight is captured

Captured in chemical bonds, especially in sugar

Small amounts of energy are available to specialized microorganisms from chemical reactions not linked to sunlight

It is estimated that 99% of the energy used by living cells comes from the sun

Incorporation of sunlight into chemical bonds occurs through the process of photosynthesis

“Invented” by cyanobacteria about 2 billion years ago

1. Introduction
Water is the most essential resource for life, supporting the survival of allliving beings, including humans, and playing a crucial role in food productionand economic progress. Currently, many cities around theworld are facingsignificant water shortages. About 40 % of global food production dependson irrigation, and countless industrial operations rely heavily on water. Theavailability and quality of water, whether surface or groundwater, have amajor impact on environmental health, economic development, and societagrowth. Human activities like urban expansion, population increase, industrialoutput, and climate shifts are causing a decline in water quality. As nationsdevelop, industrial activities increasingly lead to the pollution of watersources, resulting in negative consequences such as widespread disease and
diminished beauty of water bodies. This pollution is a significant threat toboth the planet and its inhabitants. Higher temperatures are interfering with themetabolic processes of aquatic life, while changes in water pH create unstableconditions. Additionally, increased cloudiness in water reduces oxygen levels,affecting deep-water species and contributing to health issues for both animalsand humans. Polluted water also hinders growth and development in allliving organisms Haldar et al., 2015 and Arif et al., 2020. A study conductedby Halder et al. (2015) highlighted severe health challenges faced bylocalcommunities due to pollution in the Turag River, Dhaka, caused by thedischarge of untreated wastewater into the river. It was revealed that elevatedpH levels in the water, resulting from the use ofcaustic chemicals such assoda ash and caustic soda in industrial processes, were associated with skinirritation and sores. Dietary exposure to polluted crops and fish was found
to contribute to stomach ailments, including gastric ulcers. Concerns wereraised about potential groundwater contamination through the infiltration ofindustrial waste. Microbial contamination was identified as a likely cause ofdiarrhoea and dysentery. The use of river water for bathing and laundry wasobserved to facilitate the spread of waterborne diseases. Outbreaks of yellow
fever, cholera, dengue, malaria, and other epidemics were noted as prevalent inthe area. Respiratory problems and foul odours were attributed to air pollutioncaused by industrial discharge. Maternal and child health in riverbank slumsfound to be vulnerable, emphasizing the urgent need for interventions to addressthese public health concerns.Wastewater produced by industries, agriculture,and domestic activities contains high levels of nutrients, heavy metals, andchemicals, which harm the environment by polluting land, air, and water,

Abstract

Photosynthetic blooms of toxin producing marine algae are often referred to as “red tides”. Proliferations of freshwater toxin-producing cyanobacteria are simply called “cyanobacterial blooms” or “toxic algal blooms.” Biotoxins of cyanobacteria are water-soluble and heat stable and they are released upon aging or lysis of the cells. The primary types of cyanobacterial biotoxins involves three types of toxins: hepatotoxins (microcystin; cylindrospermopsin and nodularin), which are taken up by the liver and cause weakness and anorexia (loss of appetite); neurotoxins (usually anatoxin and saxitoxin), which effect the nervous system and dermatotoxins (aplysiatoxin and lyngbyatoxin, LPS), which cause skin and mucous irritations upon contact. Unlike freshwater toxic algal blooms, marine algal toxins become a problem primarily because they may concentrate in shellfish and fish that are subsequently eaten by humans, causing syndromes known as paralytic shellfish poisoning/PSP (paralysis due to saxitoxin and gonyaulatoxins), diarrhetic shellfish poisoning/DSP (diarrhea due to okadaic acid) , amnesic shellfish poisoning /ASP(memory disturbances due to domoic acid), neurotoxic shellfish poisoning/NSP (paresthesia due to brevetoxin; also bronchial spasms). Coral reef fishes are the vectors of another algal poisoning, the ciguatera fish poisoning/CFP (paresthesia, warm-cold sense inversion etc., due to ciguatoxins and maitotoxin).

Plant hormones - They are defined as:

1. Small
2. Organic compounds;
3. Synthesized by the plant;
4. Active in low concentration (<10^-6);
5. Promote or inhibit growth and developmental responses;
6. Often show a separation of the site of production and the site of action (although this isn’t as clear a distinction as in animals).

Based on these criteria, would the following substances be considered hormones? Ca²⁺, sucrose, 2 4 - D, glycine, or K⁺?

Abstract

Any environmental variable, can adversely affect the optimal growth conditions of the plants. The stressed environment makes the plants to alter their physiology for survival rather than reproduction. Prolonged drought, intense raining, frequent floods, cold waves high and low temperatures are the predicted abiotic stresses in the future due to climate changes. Water stress is one of the important growth limiting factor which decreases plant growth during vegetative stage. Crops grown under rain-fed conditions are the most affected by seasonal variations in rainfall. Therefore failure of monsoon, high temperature and salinity usually result in water stress. In addition, it causes serious negative impacts on crop growth and yields. A greater stress tolerance capacity could also be largely attributed to the plants by the symbiotically associating microorganisms capable of modulating stress factors. The microorganisms having close association with plants are referred as plant associated bacteria (PAB), which can be grouped into rhizospheric (in vicinity of root) and rhizoplanic (on surface of root), endophytic (inside the plant tissue)  and phyllospheric (on the leaf surface ) bacteria. Among the PAB, pink pigmented facultative methylotrophic (PPFM) bacteria belonging to the  genus Methylobacterium are well known for their intimate ubiquitous occurrence in the plant.

Abstract

Current trend of global agricultural systems entails preference towards sustainable crop production through organic agriculture (ecology based) as compared to conventional (synthetic input based). In order to claim as organic, it needs to be certified as per requirements organic standard. The soil fertility management organic standard requirements of major countries are outlined. This review article compares the agricultural management practices of organic and conventional systems so as to assess its impacts on microbial biodiversity, microbial activities on soil functioning and long term fertility based on long term field studies conducted in different parts of the globe.

Introduction
Plant breeding and genetics are at the forefront of agricultural innovation, playing a crucial role in enhancing crop traits to meet the ever-growing demands for food, fiber, and fuel. This chapter delves into the scientific principles, methods, and modern advancements in plant breeding and genetics, providing a comprehensive understanding of how these disciplines contribute to global food security and environmental sustainability. The chapter begins by exploring the fundamental principles of plant breeding, including heredity, genetic variation, selection, and hybridization. These concepts form the foundation for developing new plant varieties that exhibit desirable traits such as improved yield, disease resistance, and environmental adaptability. The importance of genetic variation is emphasized as a key driver of plant improvement, with discussions on the sources of genetic variation, the role of germplasm resources, and the impact of genetic diversity on plant adaptation. As the chapter progresses, various breeding techniques and strategies are examined, including mass selection, pedigree breeding, backcrossing, and markerassisted breeding. These methods are crucial for developing new plant varieties that can withstand the challenges posed by climate change, pests, and diseases. The chapter also addresses the role of genomics in plant breeding, highlighting the significance of genomic selection, gene editing, and bioinformatics in accelerating the breeding process and enhancing crop traits. The chapter further explores the controversial topic of genetically modified organisms (GMOs), discussing the principles of genetic engineering, the rise of genetically modified crops, and the associated controversies and concerns. The importance of GMOs in addressing global food security and environmental challenges is also discussed, providing a balanced perspective on their potential benefits and risks. The chapter concludes by emphasizing the critical role of plant breeding and genetics in ensuring food security and combating global warming. By developing climate-resilient crop varieties, improving water efficiency, and enhancing disease and pest resistance, plant breeding and genetics can contribute to sustainable agricultural practices that reduce greenhouse gas emissions and conserve natural resources

Abstract

The concern of global food security is growing day by day as the agriculturally available land is reducing each day with the expansion of industrialization and urbanization. During the course of urban and industrial development, crop production is greatly affected by global warming, contamination of hazardous materials, salinity and drought. To combat against such adversities, scientists have taken several additives measurement like development of transgenic crops, application of indigenous plant growth promoting microbes etc. for sustainable agriculture. Use of plant growth promoting microbes is getting popular day-by-day as they occupy a privilege niche with the autochthonous flora of specific environment. For the expanse of food and shelter, the microbes supply a wide range of plant regulators (e.g. auxins, cytokinins, gibberellins, ABA, phenols, NH₃ etc.), antibiotics, alkaloids, steroids, terpenoids, diterpenes, enzymes (e.g. cellulases, lipases, proteinase, esterases etc.) etc. for overall development of the plant. Apart from growth promotion, it also protects the plants against pathogenic invasion creating a competition with pathogens for nutrition and habitat. In near future, formulation of different plant growth promoting bacteria (like alpha- Azorhizobium, Azospirillum, Ancylobacter, Rhizobium, Bradyrhizobium, Sinorhizobium, Novosphingobium sp., beta- Burkholderia sp., gamma- Acinetobacter, Aeromonas, Azotobacter, Enterobacter, Klebsiella, Pantoea, Pseudomonas, Stenotrophomonas sp. Proteobacteria, Bacillus sp., Paenibacillus sp. and Actinobacteria- Microbacterium sp. etc.) and fungus (Aspergillus, Trichoderma, Penicillium etc.) may reduce the use of pesticides and chemical fertilizer to promote greener ways of crop production.

Abstract

Microbes are endowed with a high and exploitable potential of being useful associates with their surrounding environment and host in case of symbiotic relationship. Most of the microbes live alone but many of them require association of other living system for its survival. Hence, the beneficial role of microbes is always correlated with growth promotion and survivability of other associated living system. Now it is established that microbes play an important and key role in plant growth and development, even its survivability in case of symbiotic mycorrhizal association with orchids. They are nothing but potential tool protecting plants from different adverse conditions like diseased state, environmental stress like cold temperature, drought, metal contamination, salt and acidic or alkaline stress.

Plant Growth Promoting Rhizobacteria (PGPR) are root-colonizing bacteria that form symbiotic relationships with many plants. The name comes from the Greek rhiza, meaning root. Though parasitic varieties of rhizobacteria exist, the term usually refers to bacteria that form a relationship beneficial for both parties (mutualism). They are an important group of microorganisms used in biofertilizer. Biofertilization accounts for about 65% of the nitrogen supply to crops worldwide. The term PGPRs was first used by W. Kloepper in the late 1970s and has become commonly used in scientific literatures. PGPRs have different relationships with different species of host plants. The two major classes of relationships are rhizospheric and endophytic. Rhizospheric relationships consist of the PGPRs that colonize the surface of the root, or superficial intercellular spaces of the host plant, often forming root nodules. Endophytic relationships involve the PGPRs residing and growing within the host plant in the apoplastic space.Some common examples of PGPR genera exhibiting plant growth promoting activity are: Pseudomonas, Azospirillum, Azotobacter, Bacillus, Burkholdaria, Enterobacter, Rhizobium, Erwinia, Mycobacterium, Mesorhizobium, Flavobacterium, etc.An ideal PGPR should possess high rhizosphere competence, enhance plant growth capabilities, have a broad spectrum of action, be safe for the environment, be compatible with other rhizobacteria, and be tolerant to heat, UV radiation, and oxidizing agent.

Abstract

The greatest challenge facing us in the coming years is to produce adequate amounts of basic necessities of food, feed, fibre, fuel and raw materials for the rapidly shrinking per capita agricultural land. One alternative is to make a sustainable use of existing marginal lands. In many regions of the tropics and sub-tropics, the need to use marginal low-input soils with usually inadequate nutrient(s) supply permits only very low or unreliable yields to be achieved. It is frequently not possible  to supply required amounts of mineral fertilizers or chemical pesticides because of the low purchasing power of the marginal farmers. In particular, it is not possible to compensate for the deficient nutrient supply and this constitutes a yield limiting factor. The role of soil microorganisms in sustainable productivity has been well construed. In recent years, root inhabiting (rhizozosphere) bacteria (rhizobacteria) is gaining importance.