eChapters

5.1 Introduction

The water quality modeling methodologies are started from conceptual models such as defining the problem in a particular region of interest like fresh water ecosystem, coastal ecosystems, ocean ecosystems, the following methodology can be studied carefully for water quality modeling.

Identification of problems in the region of interest

Monitoring of field data using standard methods like APHA, USGS, BIS etc.

Evaluation of primary data for the toxins, higher amount of concentration from the ambient conditions

Processing of primary data to secondary data

Based on the primary data and secondary data, suitable modeling software can be used. If the temperature of the region is higher than the ambient, it should be used Qual2E, MIKE21 etc.

Modeling results can be compared with field data for calibration and validation.

4.1 Introduction

The developed or commercially available models can be applied for any water bodies such as fresh water lakes, ponds, rivers, estuaries and marine ecosystems. The predicted results can be compared with proved with field data and existing approved models and applies to the other such ecosystems. In this chapter, we can discuss about modeling of water bodies, water quality model, spatial discretizafion, modeling pollutants and toxicants, concentration modeling, hydrodynamic mixing zone analysis.

4.2 Modeling of Water bodies

The need for predictive water quality modeling has arisen largely as a result of increased eutrophication of lakes throughout the world (Forsberg, 1987; Canfield and Hoyer, 1988). The most common modelling approach is exemplified by the development and application of steady state, input-output models. Generally, nutrient concentrations are calculated from net inputs and chlorophyll a concentration is predicted by correlation with the limiting nutrient, most often phosphorus (Dillon and Rigler, 1975; Canfield and Bachmann, 1981; OECD, 1982).

Factors that can also influence phytoplankton biomass, such as light, climate, biological interactions and internal loading of nutrients, are not considered. Further more, the assumption that a lake is a continuously mixed system is very restrictive and only applicable at discrete times of the year. As a result, the shortcomings of such approaches include an inability to make predictions in the face of varying physical and biological conditions, and a failure to offer insights into the determinants of changing water quality.

3.1 Introduction

By the end of the twentieth century one of our most important scientific accomplishments has been the explicit realization that the human population is changing the earth system. Some of these changes are occurring at a remarkable rate. We know, with certainty, that human activities are changing land use, habitats, the chemistry of the Earth’s atmosphere and water, rates and balance of biogeochemical processes, and diversity of life on the planet (Vitousek et al. 1997). One prominent mode of human disturbance has resulted from activities that mobilize the nutrient elements nitrogen and phosphorus through land clearing, production and applications of fertilizer, discharge of human waste, animal production, and combustion of fossil fuels (Nixon 1995).

As a result of these activities, surface waters and ground waters throughout the world now have elevated concentrations of N and P compared to concentrations even in the middle of the 20th century. Our mobilization of N and P has accelerated the fluxes of these elements to coastal waters, and fertilization of coastal ecosystems is now a serious environmental problem because it stimulates plant growth and disrupts the balance between the production and metabolism of organic matter in the coastal zone. Coastal eutrophication is a recently recognized phenomenon (Nixon 1995), and scientific investigation of this human disturbance has progressed for only a few decades, so our conceptual model of the problem is evolving rapidly. Here, I describe 2 phases in the evolution of our conceptual model of how nutrient enrichment disrupts coastal ecosystems, and then finish with a view to the future, suggesting critical questions that must be answered as we work to advance and broaden our understanding of this complex environmental problem. This examination of conceptual models is designed as a complement to the excellent general reviews of coastal eutrophication (Vollenweider 1992, Heip 1995, Nixon 1995, Jørgensen & Richardson 1996, National Research Council 2000).

2.1 Historical Development

We have seen in Chapter 1 that modeling is about establishing cause effect relationship. Perhaps one of the earliest attempts in this direction is made as early as 1848 in Germany where it was tried to establish a relation between purity and pollution to the occurrence of certain biological organism. But as far as water quality modeling is concerned the first major breakthrough in this direction is the effort of Streetor and Phelps (1925) in oxygen sag curve. They developed model for estimating DO and BOD in Ohio River. The work of O’Conner (1962) for bacteria models are major milestone in pre-computer era modeling.

With the advent of computer during 1960s complicated kinetics and time variable simulation came into being. Most of the workers presented their efforts in terms of linear programming based water management models concerning waste discharge. Thomann(1963) has formulated linear programming based models for dissolved oxygen in an estuary. So a stage is set for study of eutrophication through modeling, but the problem is determination of values of various parameters in these equations.

During 1970s models expanded in terms of complexities mainly because of enhanced computational facilities. Two dimensional and dynamic framework has started replacing one dimensional steady state configurations. In the same year, Di Toro presented an analysis of the steady state two dimensional concentration distribution that results in the horizontal plane from the continuous discharge of a non-conservative substances (DO and BOD) into an infinite body of water.

A model is something that mimics the behavior of some real system of interest. Our interest here will be in water quality models, which are usually equations, and which predict some result based on factors that influence that result. A water quality model is a representation of a real system. The essence of a good water quality model is that it is simple in design and exhibits the basic properties of the real system that we are attempting to understand. The model should be testable against empirical data. The comparisons of the model to the real system should ideally lead to improved mathematical models. The model may suggest improved experiments to highlight a particular aspect of the problem, which in turn may improve the collection of data. Thus, modeling itself is an evolutionary process, which continues toward learning more about certain processes rather than finding an absolute reality.

Water pollution is a large set of adverse effects upon water bodies such as lakes, rivers, oceans, groundwater caused by human activities. Although natural phenomena such as volcanoes, storms, earthquakes etc. also cause major changes in water quality and the ecological status of water while these are not deemed to be pollution. Water pollution has many causes and characteristics. Increases in nutrient loading may lead to eutrophication. Organic wastes such as domestic sewage and farm waste impose high oxygen demands on the receiving water leading to oxygen depletion with potentially severe impacts on the whole ecosystem. Industrial discharge a variety of pollutants in their wastewater including heavy metals, organic toxins, oils, nutrients, and solids. Discharges can also have thermal effects, especially those from thermal and nuclear power stations, and these too reduce the available oxygen. Siltbearing runoff from many activities including construction sites, forestry and farms can inhibit the penetration of sunlight through the water column restricting photosynthesis and causing blanketing of the lake or river bed which in turns damages the ecosystems the process is called as eutrophication.

Pollutants in water include a wide spectrum of chemicals, pathogens, and physical chemistry or sensory changes. Many of the chemical substances are toxic or even carcinogenic. Pathogens can obviously produce waterborne diseases in either human or animal hosts. Alteration of water’s physical chemistry include acidity, conductivity, temperature, and excessive nutrient loading. Even many of the municipal water supplies in developing countries can present health risks leads to many diseases.

Molecular diagnostics has witnessed groundbreaking technological advances in recent times, starting from automated sample preparation to real time amplification technology. Possibility to develop and run assays for ever increasing number of clinical queries has become effortless due to the technological advances. However, the state of the art in quality assurance and quality control practices for molecular diagnostics has seldom been up to the expectations if one considers accuracy for once in a lifetime genetic tests or new genetic test targets appearing almost every single day. In the face of such issues, clinical laboratories are struggling to develop appropriate quality assurance programs for the molecular diagnostic tests they conduct. In addition, legislation and government policies threaten to increase oversight of genetic tests to a level not seen before in laboratory medicine, for example, FDA’s guidance on in vitro diagnostic multivariate index assays (IVDMIA).

To relate patient results to previous test results or to absolute values in clinical practice guidelines, those results need to be comparable across time and methods. This may either be achieved by designing the identical value across methods and test versions or by using reliable and stable conversions. Therefore, the establishment of international standards and reference materials is of paramount importance. Monitoring molecular test system outputs and statistical analysis might provide a good way to obtain such standards; however, such traditional QC (Quality Control) strategies can be slow to take root in molecular diagnostics.This chapter highlights general and specific issues relevant for quality assurance and quality control in the routine molecular diagnostics laboratory and guidelines for designing quality manuals for a molecular diagnostic laboratory.

12.1 Assays for molecular diagnosis of Acute Myeloid Leukaemia (AML)

Acute Myeloid Leukaemia (AML), also known as Acute Myelogenous Leukaemia or Acute Myeloblastic Leukaemia or Acute Granulocytic Leukaemia or Acute non Lymphocytic Leukaemia is an aggressive type of cancer which affects blood and bone marrow. AML is a heterogeneous disorder if one considers its clinical status, therapeutic responses and overall prognosis.¹ This disease called acute because it progresses very fast and myeloid as it originates from myeloid cell line in the bone marrow.

In bone marrow blood cells are made in a controlled way. When AML occurs excess numbers of immature leukaemia cells are produced. Overproduction of leukaemia cells in bone marrow disables bone marrow to make mature white blood cells. These accumulated immature cells are unable to function properly (Inability to fight infection).

Diagnosis: Correct diagnosis is important for a successive treatment for AML. There are several tests available to diagnose AML but not all tests will be used for each person. The following tests may be used to diagnose AML.

11.1 Principle

In situ hybridization techniques involve detection of specific nucleic acid sequences to in morphologically preserved chromosomes, cells or tissue sections. Along with immunocytochemistry, in situ hybridization can correlate microscopic topological information to gene activity at the level of DNA, mRNA or protein. The FISH protocol involves 1) denaturation and hybridisation performed on Day 1 and 2) washing and detection performed on Day 2. DNA of the chromosomes and the probes are denatured and allowed to hybridize overnight on the first day. On day 2, slides are washed to remove unbound DNA sequences followed by detection, counterstaining and mounting of the slides.

10.1 Purpose

To lay down a standard protocol to perform qPCR for quantitative analysis of target genomic sequence.

10.2 Principle

qPCR or quantitative polymerase chain reaction or real-time polymerase chain reaction, is a molecular biology technique to amplify and at a time quantify a targeted DNA molecule and based on the polymerase chain reaction (PCR). It is called real time as the amplified DNA is detected as the reaction progresses and holds an advantage over standard PCR where the reaction is detected at its end. There are two common methods in quantitative PCR to detect the products i) non-specific fluorescent dyes which intercalates with any double stranded DNA ii) sequence-specific DNA probes labeled with a fluorescent reporter consisting oligonucleotides. This reporters helps in detection of the complementary hybridization of the probe and quantifies amount of DNA in cells or tissues.

9.1 Purpose

To lay down a standard protocol to perform RT-PCR for quantitative analysis of target RNA.

9.2 Principle

RT-PCR technology is used to amplify a specific RNA sequence (target sequence) to measure its expression inside the cell. RT-PCR follows the same principle as of normal PCR, but instead of DNA here cDNA is used as template for amplification. Extracted RNA is reverse transcribed to cDNA with the help of reverse transcription enzyme. The cDNA is then subjected for PCR amplification with the help of DNA polymerase, target specific primers, nucleotides and reaction buffer. In molecular diagnosis, RT-PCR is used to detect the expression of oncogenes at the time of diagnosis. It is also used to detect minimal residual disease during treatment

For RT-PCR, the extracted total RNA is first reverse transcribed to cDNA using reverse transcriptase enzyme. Following are the protocols for cDNA sysnthesis and RT-PCR.

Note: cDNA synthesis and RT-PCR can be performed according to the manufacturer protocol from where the specific reagents for the above methodologies are purchased.

8.1 Purpose

To lay down a uniform protocol for the synthesis of c-DNA from total RNA

8.2 Scope

The scope of this Standard Operating Procedure is to lay down a standard procedure for the synthesis of c-DNA from total RNA

7.1 Basic concept

What is DNA sequencing?

The genome of any biological organism is a sequence of nucleotides arranged in a specific manner. The nucleotides are chemically a base which usually exists in 4 different forms; Purine – Adenine (A) and Guanine (G) and Pyramidine – Cytosine (C) and Thymine (T). These four nucleotides make up an entire sequence of Deoxyribose Nucleic Acid (DNA) which is encodes the information of any cell in the form of a gene. The genome, therefore, is the complete set of all genes that is required to build and maintain that organism. DNA sequencing is the process wherein the precise order of these nucleotides along the gene is detected and analysed which includes any method or technology that assists in determining the sequence.

6.1 Designing primers

Designing correct primers are very important to get the expected result in PCR experiment. There are two primers (Forward & Reverse) required for the amplification of the desired DNA fragment. One primer should anneal to the sense strand (oriented to the 5'→3' direction) and another primer should complement the antisense strand (oriented in the 5'→3' direction).

There are various characteristics to be considered to design a good primer including Tm, length, GC content, secondary structure and specificity.

There are commercially available softwares besides free online tools at NCBI (primer blast) for designing PCR primers. In addition, primer sequences published in peer reviewed literature can also be used.

5.1 Purpose

To employ a standard protocol to perform agarose gel electrophoresis.

5.2 Principle

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb. Migration rate of DNA molecule depends on various factors like 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under UV light.

Nucleic acid extraction from clinical samples is the first step to be followed in molecular detection of cancer. Nucleic acids are the starting material for all downstream molecular diagnostic tools. Quality of test results largely depends upon the quality of starting material. Thus utmost importance should be given to the extraction protocols to isolate good quantity and good quality nucleic acids from patient samples.

Basic principle: The basic principle of nucleic acid extraction is to disrupt cell membrane and nuclear membrane to release and precipitate nucleic acid in the solution. Following precipitation,removal of other cellular contaminates such as protein, lipids, polysaccharides etc is performed to obtain a good quantity and quality of nucleic acid.

Molecular diagnostic laboratory set-up has basic requirements of space, laboratory benches and equipments. In terms of laboratory space, minimum four chambers, one each for sample preparation and nucleic acid extraction, PCR reaction mixture preparation, thermal cycling and gel analysis are required. In addition there should be sufficient space for storage of consumables and laboratory wares. In addition, there are some laboratory equipments which are needed in a molecular diagnostic laboratory. In the following section the equipments of a molecular diagnostic laboratory are discussed. The pictures are taken from the instruments present in the laboratory of the author. The purpose of this chapter is to introduce the reader to a molecular diagnostic laboratory. None of the pictures below are meant for promotion of any particular brand or manufacturer.

3.1 UV-VIS spectrophotometer

A spectrophotometer is required for determining the quality and quantity of nucleic acids extracted from a sample. Photometric research applications such as DNA, RNA and protein analysis can be carried out in a UV-Vis Spectrophotometer. There are various units that feature a broad wavelength range (including UV area), path length correction and a fast reading speed. Various instruments also provide an interface that allows quick measurements directly from the instrument or comprehensive easy-to use software for demanding assays.

In any organism and biomolecules (enzyme, proteins, etc.), most biological activities could be seen only within a narrow environmental conditions. Therefore in order to carry out a successful experiment, from cell culturing to DNA sequencing or assessing an enzyme’s activity, one has to pay utmost attention in calculating correct reaction components.

A solution is defined as a homogenous mixture of solute and solvent. In this case the amount solute is less as compared to the solvent. It is not always necessary that solvent is liquid and solute is solid. There are several examples where solute and solvents are found in other physical states such as gas or solids. For example, carbonated water CO₂ is solute and water is solvent; and smoke is solution of different smoke particles (solute) in air (solvent). The concentration of solution is described as amount of solute in a given volume of solvent. Several ways are there to express the concentration of a solution, such as molarity, normality, molality, and ppm. In this chapter we would discuss the general terms used in making solutions and a brief introduction about buffer solutions.

Molecular biology is a branch of science that deals with understanding the biological activities at the molecular level. Molecular biologists are involved in understanding the concepts behind various intra and intercellular interaction of molecules, contributing to the knowledge about interrelationship of DNA, RNA and protein synthesis, i.e., how genes are transcribed into RNAs and how RNA is translated into protein, the phenomenon which is commonly known as “Central Dogma”stated by Francis Crick in 1956.

“The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid”-Francis Crick.

Once a pest, pathogen or a weed has been detected in the introduced planting material, quarantine officials must make all efforts to disinfect/decontaminate the material and make it available for further exploitation in the country without undue delay. However, it may be kept in mind that treatments, which only reduce the inoculum, may be acceptable for general agricultural practices, but they are not acceptable in plant quarantine. For quarantine purposes, tolerances are zero and, therefore, no residual inoculum of exotic pests/pathogens must remain. Fullproof eradicative treatments are required to be employed before release of the planting material from quarantine.

16.1. Fumigation

Fumigation of the material under atmospheric or under reduced pressure has been found acceptable as a quarantine treatment against insects and mites. Fumigants like methyl bromide, HCN, phosphine and EDCT (ethylene dichloride + carbon tetrachloride mixture) are commonly used.

In general, fumigation with Methyl bromide at 48g/cubic metre for 24 hours at 21ºC or above or 32g/cubic metre for 2 hours at 21ºC or above is used based on the kind of infected material and the pest to be salvaged.

15.1. Cereals

15.1.1. Oat (Avena sativa)

The Export-Import (EXIM) Committee was constituted in the Seeds Division to deal with application for exports/imports of seeds and planting materials in accordance with the New Policy on Seed Development and EXIM regulation.

The Policy reiterated that all imports of seeds and planting material would be regulated under the Plant Quarantine Order 2003 and amendments made their under, Import licences would be granted by DGFT/PPA on the recommendations of DAC.

The composition of the EXIM Committee is as under: (i) Secretary (A&C) - Chairperson (ii) Agriculture Commissioner (iii) DDG (CS), ICAR (iv) DDG (Hort.), ICAR (v) JS (IC) (vi) JS (PP) (vii) Horticulture Commissioner (viii) Animal Husbandry Commissioner, Deptt. of Animal Husbandry & Dairying (proposed to incorporate by the 94th Exim Committee) (ix) Director, National Bureau of Plant Genetic Resources (NBPGR) (x) Plant Protection Adviser (xi) Economics and Statistical Adviser (xii) JS (Seeds) - Member Secretary

A small quantity of seeds sought to be imported would be given to ICAR, or farms accredited by ICAR, for trial and evaluation for one crop season. On receipt of applications for commercial import, DAC would consider the trial/ evaluation report on the performance of the seed and their resistance to seed/ soil borne diseases. DAC is required to either reject or recommend the application to DGFT for grant of import licence within 30 days of receipt.

13.1. Quarantine Inspection and Certification

13.1.1. Scope/Purpose

Provides guidance and describes the standard operating procedures for certification of facilities for growing imported plants/plant material including transgenic plant material and other regulated articles such as biological control agents/beneficial organisms and living modified organisms under post-entry quarantine and inspecting the same to ensure free from quarantine pests and other regulated non-quarantine pests.

The purpose is to facilitate adoption of standard operating procedures by all the inspection authorities notified by the Ministry of Agriculture (Department of Agriculture & Cooperation)/PQOs (with PEQ responsibilities) for undertaking certification of post-entry quarantine inspection facilities as well as conducting postentry quarantine inspection of growing plants and other regulated articles under the supervision of concerned inspection authority/ PQOs (with PEQ responsibilities) in accordance with phytosanitary requirements specified under the Plant Quarantine (Regulation of Import into India) Order, 2003 and amendments issued there under to prevent the introduction and spread of destructive pests that affects plants and other regulated articles such as biological control agents and beneficial organisms.

12.1. Introduction

The protocols provides guidance on the structure and content of the International Plant Protection Convention (IPPC) diagnostic protocols for regulated pests. The protocols describe procedures and methods for the official diagnosis of regulated pests that are relevant for international trade. They provide at least the minimum requirements for reliable diagnosis of regulated pests.

This standard sets the framework for the content of diagnostic protocols, their purpose and use, their publication and their development. Diagnostic protocols for specific regulated pests are included as annexes to this standard. Information relevant for diagnosis is provided in the diagnostic protocol on the specified regulated pest, its taxonomic position, and the methods to detect and identify it. Diagnostic protocols contain the minimum requirements for reliable diagnosis of the specified regulated pests and provide flexibility to ensure that methods are appropriate for use in the full range of circumstances.

The methods included in diagnostic protocols are selected on the basis of their sensitivity, specificity and reproducibility, and information related to these factors is provided for each of these methods. Detailed information and guidance for the detection of pests is provided on, for example, signs and/or symptoms associated with the pest, illustrations (where appropriate), developmental stages of the pest, and methods for detecting the pest in a commodity, as well as methods for extracting, recovering and collecting the pests from plants.

11.1. History of Plant Quarantine in India

The first recorded plant quarantine measure in India dates back to 1906, when perceiving the danger of introducing the Mexican boll weevil, the Government of India directed that all cotton imported from the New World should only be admitted to India after fumigation with carbon disulphide at the port of entry.

In India two categories of regulatory measures are in operation for controlling pests, diseases and weeds. In the first category regulatory measures are aimed to prevent the introduction of exotic pests and diseases into the country or their spread from one State or Union Territory to another (Plant Quarantine). The second pertains to suppression or prevention of spread of pests and diseases in localized areas within a State or Union Territory.

The former derives its authority from the Destructive Insects and Pests (DIP) Act 1914 of the Central Government and the latter from Agricultural Pests and Diseases Acts of the various States. The legislative measures against crop pests and diseases were initiated under the DIP Act of 1914 which was passed by the then Governor General of India in Council on 3 February 1914.

Prior to the establishment of the Directorate of Plant Protection, Quarantine and Storage in 1946, under the Ministry of Food and Agriculture, the various rules and regulations of the DIP Act were enforced by the customs department. The quarantine regulations are operative through The Destructive Insects and Pests Act, 1914 (which has been revised 8 times from 1930 to 1956 and amended in 1967 and 1992).

The IPPC Secretariat provides support for the International Plant Protection Convention (IPPC) and coordinates the annual work programme put in place by the Interim Commission on Phytosanitary Measures. The three key activities of the Secretariat are: standard setting, technical assistance and information exchange. To facilitate the information exchange obligations laid out in the IPPC, the Secretariat adapted an existing Web-based environment to allow users to be able to both deposit and retrieve data from various sources. This Web site was named the “International Phytosanitary Portal” (IPP). As the IPP continues to evolve every effort are being made to ensure that specific issues necessary for the management of invasive alien species are addressed.

Classical biological control is one of the important tools for the management of invasive species. This involves the introduction and release of natural enemies, usually from the invaders’ area of origin. During the past decade, increasing concerns have been raised about the potential negative impact of introduced biological control agents on non-target organisms. This has highlighted the need to examine and guide the process of importation and release of natural enemies. The third international standard for phytosanitary measures, ISPM 3: Code of conduct for the import and release of exotic biological control agents, is specifically concerned with this process. ISPM 3 was endorsed by members of the Food and Agriculture Organization of the United Nations in 1995.

There is a growing demand and need for biological control across the globe. This has been fuelled not only by the increasing spate of invasive species but also by the need to develop integrated pest management approaches as well as the increased interest in organic production. Classical biological control of arthropod pests and weeds has been carried out successfully for more than a century (Greathead and Greathead, 1992; Julien and Griffiths, 1998). However, over the years, practitioners have become increasingly aware that introduced biological control agents may have undesirable side-effects (Thomas and Willis, 1998; Howarth, 2000; Follet and Duan, 2000; Lynch and Thomas, 2000; Wajnberg, Scott and Quimby, 2000; Henneman and Memmott, 2001). Initially, this concern was limited to the possible impact of these introduced agents on economically important plants and insects (notably, honey bees, silk moths and weed biological control agents). More recently, increased environmental awareness has drawn attention to the potential danger to all indigenous fauna and flora, particularly rare and endangered species.

To address these concerns, a code of conduct for the import and release of exotic biological control agents was developed with a view to fostering safe importation and release of biological control agents (Greathead, 1997). It was developed over a period of six years and was finally endorsed by FAO member countries at the end of 1995. The code of conduct, the third in a series of international standards for phytosanitary measures developed by the International Plant Protection Convention, was formally published in 1996 as ISPM 3: Code of conduct for the import and release of exotic biological control agents and is available, with other ISPMs

8.1. Phytosanitary Capacity Evaluation (PCE): The Tool, and Its Relation to Invasive Alien Species

Phytosanitary Capacity Evaluation (PCE) is a diagnostic tool enabling a country to assess the weaknesses and strengths of its phytosanitary system in relation to its ability to fully implement the International Plant Protection Convention and other international phytosanitary obligations. PCE has also been applied as a cross-disciplinary tool among the sanitary, phytosanitary and food safety areas in the Andean subregion. Since “quarantine pests”, as defined by the convention, constitute a subset of invasive alien species, PCE results are already useful in relation to invasive alien species. PCE methodology has the potential to be further developed to cover a country’s needs in implementing Article 8(h) of the Convention on Biological Diversity.

Article XX of the International Plant Protection Convention establishes the agreement by contracting parties to promote the provision of technical assistance to facilitate implementation of the IPPC. Phytosanitary Capacity Evaluation (PCE) is the first tool approved by the Interim Commission of Phytosanitary Measures to address that commitment, assisting contracting parties to perform a needs assessment and identification of their constraints for achieving full implementation of the IPPC at the national level.

7.1. BioNET International

7.1.1. What is BioNet International

BioNET-International, is the Global Network for Taxonomy, and is dedicated to creating sustainable mechanisms to assist developing countries to overcome the Taxonomic Impediment by becoming self-reliant in taxonomy i.e. self-reliant in the skills, infrastructure (collections etc.) and technologies needed to discover, identify, name and classify and to understand the relationships of all organisms on this planet.

It is concerned with helping developing countries to recognise and know the organisms that constitute and threaten their biodiversity, not for taxonomy’s own sake, but rather to support national programmes for sustainable agricultural development, and conservation and sustainable use of the environment.

BioNET-International is particularly focused on helping countries implement the various environmental conventions such as the International Plant Protection Convention (IPPC; www.ippc.int) and the Convention on Biological Diversity (CBD; www.biodiv.org), especially its taxonomic capacity building compnent, the Global Taxonomy Initiative (GTI). The subregional networks of BioNET-International have been identified as appropriate structures through which much of the GTI (www.biodiv.org/programmes/cross-cutting/taxonomy/default.asp) can be effectively implemented.

6.1. Speed Detection of Pests in China for Phytosanitary Programme

Phytosanitary procedures such as pest detection and identification rely on technology. With the rapid development of science, it is necessary for national plant protection organizations to keep informed and to make diagnoses more sensitive and accurate. Previous general pest detection methods frequently have limitations for the diagnosis of quarantine pests. In the past ten years, China has conducted considerable research into how to improve its diagnostic measures and methods.

6.1.1. General Pest Detection Measures and Methods

Traditional determination of morphology by microscope is used mostly to detect fungi and adult insects. The morphological method may be used, for example, in the separate identification of wheat dwarf bunt (Tilletia controversa), wheat karnal bunt (T. indica) and wheat common bunt (T. tritici). On the other hand, it is hard to detect seed-borne pests using the morphological method.

Isolation culture is also used to detect fungi and bacteria in China. It is an effective method for detecting seed-borne disease or systemic infection. However, it takes a long time (more than 1-2 weeks). Inoculating the indicated plant (a healthy plant that is a host for the suspected pest organism) is used mainly to identify viruses. This was the principal and time-consuming detection method used before immunological and molecular biological methods were developed. Because viruses are very important kinds of quarantine pests of young plants, effective and rapid methods for detection were urgently needed.

5.1. Australia’s Experience and Approach to Pest Risk Analysis

Australia applies the principles of pest risk analysis for the identification and management of sanitary and phytosanitary risks associated with new trade proposals and, where the need is identified, to the review of sanitary and phytosanitary risks of existing trade. One such trade activity is the intentional importation of exotic plant species not yet established in Australia.

Of approximately 250 000 plant species in the world, 30 000 have been intentionally introduced to Australia since European colonization, along with an unknown number of unintentional introductions, of which about 2 700 have naturalized (Cunningham et al., 2003). Some become problematic plants of which about 300 have become serious weeds of agriculture and natural ecosystems. Clearly, the majority of plant species have yet to be introduced to Australia and some of these would become weeds if allowed into the country.

The weed risk assessment (WRA) system is a decision support tool that is employed by Australia in applying the principles of pest risk analysis to the review of sanitary and phytosanitary risks associated with the intentional importation of exotic plant species not yet established in the country. The WRA system is used specifically to assess the weed potential of such species. It generates a score for a species based on its history as a weed in other parts of the world, climatic suitability to Australia and biological attributes. The weed risk assessment (WRA) system is one means by which the assessment component of pest risk analysis is addressed. The WRA system is a question-based scoring method that can be operated using a computer or manually using paper-based forms. A Microsoft® Excel spreadsheet version of the system, including documentation, has been made available through the International Phytosanitary Portal

In Article IX of IPPC, it is stated that RPPOs shall

• Function as coordinating bodies in the areas covered by the IPPC (including information sharing)
• Cooperate with the IPPC Secretariat in achieving the objectives of the IPPC (including the development of ISPMs)
• Cooperate with other RPPOs and participate in the regular Technical Consultations for RPPOs that are convened by the IPPC Secretariat

At present, there are 10 RPPOs covering the different regions of the world. Each RPPO has its own independent statutes and conducts its own regional cooperation programme. RPPOs produce regional standards for their members. They cooperate with each other and with the IPPC Secretariat. In particular, they meet in Technical Consultations to promote the development and use of relevant ISPMs and to encourage inter-regional cooperation on phytosanitary measures for controlling quarantine pests and preventing their introduction and spread.

3.1. What is the International Plant Protection Convention (IPPC)

The International Plant Protection Convention (IPPC) is a 1951 multilateral treaty deposited with the Food and Agriculture Organization of the United Nations (FAO) that aims to secure coordinated, effective action to prevent and to control the introduction and spread of pests of plants and plant products. The Convention extends beyond the protection of cultivated plants to the protection of natural flora and plant products. It also takes into consideration both direct and indirect damage by pests including weeds.

The IPPC as an intergovernmental treaty signed by over 180 countries, aiming to protecting the world’s plant resources from the spread and introduction of pests, and promoting safe trade. The Convention introduced International Standards for Phytosanitary Measures (ISPMs) as its main tool to achieve its goals, making it the sole global standard setting organization for plant health.

The IPPC is one of the “Three Sisters” recognized by the World Trade Organization’s (WTO) Sanitary and Phytosanitary Measures (SPS) Agreement, along with the Codex Alimentarius Commission for food safety standards and the World Organization for Animal Health (OIE) for animal health standards.

2.1. Guidelines for Pest Risk Analysis

This standard describes the process of pest risk analysis for plant pests for the purpose of preparing phytosanitary regulations by National Plant Protection Organizations. Pest risk analysis (PRA) consists of three stages: initiating the process for analyzing risk, assessing pest risk, and managing pest risk.

Initiating the process involves identification of pests or pathways for which the PRA is needed. Pest risk assessment determines whether each pest identified as such, or associated with a pathway, is a quarantine pest, characterized in terms of likelihood of entry, establishment, spread and economic importance. Pest risk management involves developing, evaluating, comparing and selecting options for reducing the risk.

PRA is only meaningful in relation to a defined “PRA area” considered to be at risk. This is usually a country, but can also be an area within a country, or an area covering all or parts of several countries [e.g. the area covered by a Regional Plant Protection Organization (RPPO)].

1.1. Plant Quarantine

The literary meaning of the word quarantine is” a state, period or place of isolation in which the people or animals or plants or acquacultures that have arrived from elsewhere or been exposed to infectious or contagious disease are placed.

Plant quarantine is a technique of keeping the imported or introduced plants or planting material in isolation for detecting the exotic pests, diseases and disease pathogens and weeds which may be harmful to the importing country for its crop plants, agriculture or the ecosystem. These plants/planting material are kept in isolation for a specified period which differ from plant species to plant species depending on the type of pathogen/pests for which the material has to be quarantine. This is based on the Rules and regulations promulgated by governments to regulate the introduction of plants, planting materials, plant products, soil, living organisms, etc. with a view to prevent inadvertent introduction of exotic pests, weeds and pathogens harmful to the agriculture or the environment of a country/region, and if introduced, to prevent their establishment and further spread. Plant quarantine is thus designed as a safeguard against harmful pest /pathogens exotic to a country or a region.

Plant quarantine is a most important activity in the introduction of plants and planting material as various insects, including mites and nematodes and diseases caused by fungi, bacteria, viruses, viroids, phytoplasmas,rickettsialike organisms are known to attack various crops of economic importance to not only reduce the quantity but also spoil the quality of the produce to a considerable extent and if these pests and pathogens are introduced with the planting material in its non ecosystem areas may prove fatal to the agriculture or ecosystem

9.1 Introduction

Xeriscaping is the fine art of creating water-efficient landscapes by using plants that are appropriate to the natural environment. Xeriscaping (zer-i-skaping) is a word originally coined by a special task force of the Denver Water Department, Associated Landscape Contractors of Colorado and Colorado State University to describe landscaping with water conservation as a major objective. The derivation of the word is from the Greek “xeros,” meaning dry, and scape meaning the pattern of the landscape – thus, xeriscaping. The term xeriscaping represents a practice or philosophy with the goal to establish and maintain an attractive and healthy landscape while reducing water usage. One of the prime practices in xeriscaping is the use of drought tolerant plants, but xeriscaping is more than that. It also includes changes in the landscape design, soil improvement, efficient irrigation, mulching, and other maintenance practices which contribute towards a water-wise landscape. But xeriscapes are not dry and dull. Well-designed xeriscapes are enchanting and beautiful. The best xeriscapes use a fraction of the water needed by traditional lawn-dominated landscapes. Some xeric plants require little or no supplemental watering once they are established. And xeriscapes require far less ongoing maintenance.

8.1 Introduction

One important aspect of bio-aesthetic planning is to landscape public places on a priority basis compared to private places. For this specific reason, the railway station and the railway lines should attract attention at the very outset for landscape gardening.

8.2 Definition

Bio-aesthetic planning means the proper utilization of the available flora and fauna in the beautification of the surroundings. The concept of bio-aesthetic planning is given by concept of Prof. Lancelot Hogben.

In India, the theme of bio-aesthetic planning was propagated by Dr. M. S. Randhawa. Le Corbusier and his associates, Pierre Jeanneret, E. Maxwell Fry and Jane B. Drew had planned Chandigarh city as per the principles of bioaesthetic planning.

7.1 Introduction

Garden designing is an important and crucial step as whole aesthetic view of the garden depends upon it. A beautifully designed garden can attract plenty of viewers as well as fauna while a poorly designed garden can destroy the view of the garden as a whole. So, while designing a garden all the basic principles and elements of gardening should be kept in mind.

7.2 Steps in Preparation of Garden Design

Site identification

Generally, the site for garden development is provided by the client itself. So, in this case we should go for site analysis step directly. Site identification is always a choice of client/human. If landscape architect has liberty to identify a land for garden establishment, he should identify the site as per choice of the client, usage and special considerations of the client.

6.1 Introduction

Garden design encompasses the aesthetic beauty, artistry, knowledge of plant growth and development with basic maintenance of plants and other elements as required. Principles are the basic rules of designing a landscape. The basic principles of garden design are very simple; however, each is often referred to by more than one name. Principles of landscape garden keeps the garden lively and beautiful. The principles of gardening should be kept in mind always while designing a garden.

6.2 Axis

It is an imaginary line in landscape designs around which the garden is created striking a balance. In a formal garden the central line is the axis.

5.1 Elements of Landscape Gardens

5.1.1 Introduction

Elements of a garden are the basic units of any visual design which form its structure and convey visual messages. Elements are based on the art principles of landscaping. Process of landscape design includes concepts and elements of landscape designing. Generally, elements of a garden are divided into 2 types

4.1 Introduction

Many styles of gardens do not follow strict rules and so those are known as informal gardens. Some gardens evolved as informal garden in due course of time as per the choice of people but some gardens are informal in nature from origin. Informal gardens are:

English garden

Japanese garden

Hindu garden

Buddhist garden

3.1 Introduction

Many gardens follow strict rules. So those are known as formal gardens. Generally formal gardens include:

Italian gardens

French gardens

Persian gardens

Mughal gardens

2.1 Introduction

Generally, gardens are divided into different sections as per the rules and regulation followed in the placement of different elements and features in it. On the basis of this garden types are divided into 4 categories such as

1.1 Introduction

Irrespective of caste, creed, culture, sex, age or religion people like garden. A well-maintained garden serves as lungs of the city or locality as it is a prime source of plenty of oxygen and people enjoy the surrounding and feel happy by fresh air. In holy books of Hindu religion, the importance of plants as well as gardens are explained very beautifully. In the holy Bible it is mentioned that Adam and eve lived in garden. In Quran it is explained as the paradise on earth. So, scriptures of all religions explain about gardens. It shows gardens and plants are closely related to human from the origin of human belief.

In recent years, oilseed crops are being increasingly exploited for production of pharmaceuticals, surfactants, plasticisers, emulsifiers, detergents, lubricants, adhesives, cosmetics, oleo-chemicals, biofuels apart from their demand for their healthy vegetable oils and livestock feeds (Metzger and Bornscheuer, 2006). The increased interest resulted in an 82% expansion of oilseed crop cultivation areas and about a 240% increase in total world production over the last 30 years (Rahman and Jimenez., 2016).

Introduction

Indian oilseeds scenario has been able to surmount the crisis of prolonged stagnation with increased production in the decades of 1980s and 1990s (Prasad 1991). Nevertheless, in the face of growing demands of vegetable oil both for human consumption and industrial use, there is every need to augment the oilseed production to new heights of sustainability (Prasad 1994a).

Apart from the traditional sources of vegetable oils from annual crops like groundnut, rapeseed-mustard, sesame, sunflower, safflower, niger, linseed, castor and soybean besides cotton seed and rice bran, more than 100 species of domesticated or wild plant species of India are known to contain oil in considerable quantities (Prasad, 1994c). In addition to the production from nine traditional oilseeds mentioned above, 3 million tonnes of vegetable oil is being harnessed from secondary sources like cottonseed, rice bran, coconut, Tree Borne Oilseeds (TBOs) and Oil Palm. Subramanian et al., (2005) reported that there are over 300 different species of trees which produce oil bearing seeds. Thus, there is a significant potential for non-edible oil source from different plants for biodiesel production as an alternative to petrodiesel.

It is estimated that TBOs have the potential to contribute more than 3 million tons of oil; but only a fraction of the potential is realised currently. Seeds of many of the oil bearing trees have been used by the ethnic communities for different purposes. Apart from seed oil, the trees yield valuable by-products including cake, which have industrial applications (Hocking, 1993; Chakravarty et al., 2012).

There are many species of plants found wild or cultivated inside as well as outside the forest areas containing sizeable amount of vegetable oil having domestic and industrial utility. Out of these species.The country has enormous potential of oilseeds of tree origin like Mahua (Madhuca indica and M. longifolia ), Sal (Shorea robusta), Neem (Azadirachta indica), Simarouba (Simarouba glauca), Karanj (Pongamia pinnata), Ratanjyot /physic nut (Jatropha curcas), Jojoba (Simmondsia chinesis), Cheura (Diploknema butyracea), Kokum (Garcinia indica), wild Apricot (Prunus armeniaca), wild Walnut (Aleurites molucana), Kusum (Schleichera oleosa), Undi ( Calophyllum inophyllum), Tung (Verniciafordii) etc. which can be grown and established on the wastelands and under varied agroclimatic conditions.

Introduction

Castor plant (Ricinus communis L) is an age old crop of India which has been in use in Ayurvedic medicine since 2000 BC, when the oil was used in lamps and also in local medicine particularly as a laxative and also to cure arthritis. The seeds of the crop yield non-edible viscous oil which has a number of applications in industry apart from its medicinal properties, which are well documented in Ayurvedic, Siddha and Unani medicine. The word Ricinus in the scientific name of the castor plant has cropped due to the appearance of its seed resembling dog’s tick!

Castor is cultivated on commercial scale in an area of 1,296,855 ha in 30 countries with global castor seed production at 1,396,104 MT (FAO STAT, 2019). India is the world’s single largest producer of castor seed accounting for more than 85% followed by China with about 7% and Brazil with about 5% of world castor seed output. There has been a consistent increase in output primarily on account of rise in yield levels in India. In recent years, however, Brazil and China have experienced stagnation in castor crop. Castor is widely grown in Ethiopia too. Among oilseed crops of India, castor crop has registered positive and high growth rate along with soybean (Mohapatra 2017).

Introduction

Flax (Linum usitatissimum L.), also known as common flax or linseed, is a member of the genus Linum in the family Linaceae. Linseed is an annual oil crop that is grown either for its fibre (fibre flax) or for its oil. The area under annual cultivation is 3 million hectares, accounting for 1% of the total world production of plant oil. The five major flax-producing countries are Canada, China, India, the United States, and the European Union.Canada with 614,000 metric tonnes of flaxseed produced in the year 2013-2014, is the world’s largest producer of flax and accounts for nearly 80% of the global trade in flaxseed (Oomah 2001; Bhatty, 1995)

Flaxseed, of Mesopotamic origin, has been cultivated in Mediterranean region and India since 5000 BC, being used principally for the fabrication of cloths and papers (Soni, et al., 2016).

With the adoption of cotton as a fibre crop for cloth preparation, fibre flax production declined and the major use of flax was switched from stem fibre to seed oil. It is a food and fibre crop cultivated in cooler regions of the world. Textiles made from flax are known in the Western countries as linen, and traditionally used for bed sheets, underclothes, and table linen. Its oil is known as linseed oil. In addition to referring to the plant itself, the word “flax” may refer to the unspun fibres of the flax plant. The plant species is known only as a cultivated plant and appears to have been domesticated just once from the wild species Linum bienne, called pale flax. (Allaby et al.,2005). Fibre flax is currently grown in the cool-temperate regions of China, the Russian Federation and Western Europe while linseed cultivars are grown in Canada, India, China, the United States and Argentina (Green et al., 2008).

Introduction and History

Niger, Guizotia abyssinica (L.f.) Cass. [Asteraceae] is commonly known as nigerseed [English]; noug, guizotia oléifère [French]; verbesina da Índia, abisin, negrillo, ramtilla [Spanish]; ramtil, nigersaat [Dutch]; [Amharic];[Chinese]; Ram-til[Hindi]; Gurellu [Kannada]; Verri-nuvvulu (Telugu) Karalle[Marathi] and Jhusetil [Nepali] Niger’s other synonym is Guizotia oleifera DC., Polynya abyssinica L. f.

Niger (Guizotia abyssinica (L. f.) Cass.) is an oilseed crop cultivated in Ethiopia and India for its edible oil. Niger plant is originated in highlands of Northern Ethiopia (Weiss, 2000). The crop is reported to have been introduced into India from Ethiopia during around2000BC. The Ancient Agau people of Ethiopia had a well-developed agriculture, who traded with Egypt which facilitated the exchange by barter that included Niger too (Weiss, 2000). Currently, Niger is an important oilseed crop of Ethiopia. Ground niger seeds and chillies are the main components of the traditional stew known as wat of Ethiopia. Niger is the most important oilseed crop of Ethiopia contributing to 50% of the country’s oilseed production. Although the crop is grown throughout the country, the main production centres are Begemdir, Gojam and Welaga (Weiss, 2000). Since the Ethiopian government actively supports the oilseed industry, production was on steady increase till 1974. With the fall in the production post-civil war in 1974, most of the niger produced is consumed domestically and the exports got dwindled.

Introduction

Safflower belongs to the family Asteraceae, which is also called Compositae, the aster, daisy, or composite family of the flowering-plant order Asterales.tribe Cardueae (thistles) and subtribe Centaureinae . With more than 1,911 genera and 32,913 accepted species of herbs, shrubs, and trees distributed throughout the world, Asteraceae is one of the largest plant families. The species of the family are annuals and perennials of worldwide distribution, consisting of ornamentals, vegetables and spice or medicinal plants.

The genus Carthamus L., contains about 25 valid species distributed from Spain, North America and West Asia to India. Many are indigenous to the Mediterranean region, but only one viz., Carthamus tinctorius L. (safflower) is cultivated for oil. Safflower is a diploid species (2n=24). The probable origin of cultivated safflower is the area bounded by the Eastern Mediterranean and the Persian Gulf.

Safflower is grown as edible oil crop in pots, as strip crop, on field borders or around home-steads in the tropical Asia, Africa, Russia and China. Safflower is more drought resistant than other oilseed crops and can yield well on drylands, exploiting sub-soil moisture. (Lovelli et al., 2007). Safflower is also salt tolerant and can be grown on soils affected by some degree of salinity (Bassil and Kaffka, 2002).

The safflower plant has a history of long domestication, initially for orange red dye obtained from florets of the plant. The plant was identified as growing in Egypt in 2000 BC, introduced from Euphrates (Weiss, 2000). Safflower oil has unique variation in fatty acid composition (Knowels, 1969). In general, linoleic acid is the dominant fatty acid ranging from 70 to 78% in local types. In improved types oleic acid ranges from 70 to 75%.

Introduction

The Heliantheae are the third-largest tribe in the sunflower family (Asteraceae). With some 190 genera and nearly 2500 recognized species, only the tribes Senecioneae and Astereae are larger. The name is derived from the genus Helianthus, which is Greek for sunflower.

This is one of the large and predominantly flourishing flowering botanical groups occurring in almost all parts of the world. Except for three species in South America, all other Helianthus species are native to North America and Central America i.e., Southwest United States-Mexico area (Heiser, 1976). The common name, “sunflower”, typically refers to the popular annual species Helianthus annuus, or the common sunflower, whose round flower heads in combination with the ligules look like the sun. This and other species, notably Jerusalem artichoke (H. tuberosus), are cultivated in temperate regions and some tropical regions as food crops for humans, cattle, and poultry, and as ornamental plants.

The species H. annuus typically grows during the summer, post summer rainy season and later in post-rainy season too with the peak growth during pre-summer season with temperatures ranging from 28^oC to 35^oC in India.

Domestication of sunflower started around 4,000 years ago in Eastern North America by the native tribes of American continent (Blackman et al., 2011). The current annual oilseed yielding sunflower was cultivated originally by local inhabitant tribes (Weiss, 2000), who used the seed as a source of food. The adaptations in annual sunflower to human cultivation include a dramatic increase in apical dominance, an increase in seed size, the loss of natural seed dispersal and seed dormancy, and the loss of self-incompatibility (Wills and Burke, 2007).