eChapters

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.

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).

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.

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.

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.

15.1. Cereals

15.1.1. Oat (Avena sativa)

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.

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.

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 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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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).

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.

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.

6.1. Introduction

A river is a large natural waterway. The source of a river may be a lake, a spring, or a collection of small streams, known as headwaters. From their source, all rivers flow downhill, typically terminating in the ocean. The mouth, or lower end, of a river is known as its base level.

A river water is confined to a channel, made up of a stream bed between banks. Most rainfall on land passes through a river on its way to the ocean. Smaller side streams that join a river are tributaries. The scientific term for any flowing natural waterway is a stream; so in technical language, the term river is just a shorthand way to refer to a large stream. Rivers throughout history have been the source and support for civilization, and many major cities today are near a river of some sort (Fig. 6.1).

6.1.1 Topography

A river conducts water by constantly flowing from a higher to a lower elevation, thereby converting the potential energy of the water into kinetic energy. It starts to form loops and snakes through the plain by eroding the river banks. Sometimes the river will cut off a loop, shortening the channel and forming an oxbow lake from the cut off section. Rivers that carry large amounts of sediment may develop conspicuous deltas at their mouths, if conditions permit. Rivers, whose mouths are in saline tidal waters, may form estuaries. River mouths may also be rias.

7.1 Introduction

The coast is one of the most important boundaries in the world. It separates the marine part of the world from the continents. It separates the salt-water communities from fresh water communities; it separates land life from water borne life but amphibians living both environments (Fig. 7.1).

Some of the marine organisms move towards estuary for reproduction with less water salinity. The coastline as such is not a stable. It fluctuates in place over considerable distances due to erosion and sedimentation, but also due to the relative change of sea level with respect to land. The coastal zone is thus a very mobile part of the earth from a geographical point of view. Due to its specific geophysical properties, the coast is also a very important area for the development of flora and fauna. There is hardly any other part of the world that houses such a variety of species, both in flora and fauna.

The abundance of opportunities along the coast has also attracted a lot of human activities. The coastal zone has become an indispensable resource for mankind. It provides excellent opportunities for fisheries, housing, recreation, transport, defense purpose, industrial activities and many others. The influx of man with their social and economic activities, their needs for safe housing, food, drinking water, and with the tremendous quantities of waste they are producing poses at the same time a serious threat to the unique features of the coastal zone. It is therefore necessary to study this valuable region so as to prevent that competing activities are gradually causing depletion of the resources in the coastline. The following figures (Fig. 7.1and 7.2) show the typical coastal area of rocky coast and sandy coast.

8.1 Introduction

A lake is a body of water or other liquid of considerable size surrounded entirely by land (Fig. 8.1). A vast majority of lakes on Earth are fresh water, and most lie in the Northern Hemisphere at higher latitudes. In ecology, the environment of a lake is referred to as lacustrine.

Fig 8.1 A Typical Lakes

Large lakes are occasionally referred to as “inland seas” and small seas are occasionally referred to as lakes. Smaller lakes tend to put the word “lake” after the name, as in Green Lake, while larger lakes often invert the word order, as in Lake Ontario, at least in North America. The term lake is also used to describe a feature such as Lake Dal, which is a wet basin most of the time but may become filled under seasonal conditions of heavy rainfall and snowfall. Many lakes are artificial and are constructed for hydro electric power supply, recreational purposes, industrial use, agricultural use, or domestic water supply.

9.1. Introduction

Oceans (from Okeanos in Greek) are saline waters that cover almost three quarters (71%) of the surface of the Earth. The area of the oceans is 361 million sq. km., and nearly half of the world’s marine waters are over 3,000 meters deep.

Though somewhat arbitrarily divided into several “separate” oceans, these oceans are in fact one global, interconnected body of salt water, often called the World Ocean. The major divisions are defined in part by the continents and a variety of archipelagos, and are labeled the Pacific Ocean, the Atlantic Ocean, the Indian Ocean, the Southern Ocean, and the Arctic Ocean. Smaller regions of the oceans are called seas, gulfs and straits.

There are a some smaller bodies of salt water that are not interconnected with the World Ocean. These are not considered to be oceans or parts of oceans, though some of them have been given the name, sea.

Geologically, an ocean is an area of oceanic crust covered by water. Oceanic crust is the thin layer of solidified volcanic basalt that covers the Earth’s mantle where there are no continents. From this point of view, there are three “oceans” today: the World Ocean, and the Black and Caspian Seas that were formed by the collision of Cimmeria with Laurasia. The Mediterranean Sea is very nearly its own “ocean”, being connected to the World Ocean through the Strait of Gibraltar, and indeed several times over the last few million years movement of the African Continent has closed the strait off entirely, making the Mediterranean a fourth “ocean”.

10.1 Introduction

Biochemical Oxygen Demand (BOD) is a chemical procedure for determining how fast biological organisms use up oxygen in a body of water. It is usually performed over a 5 day period at 20 C. It is used in water quality management and assessment, ecology and environmental science. BOD is not an accurate quantitative test, although it could be considered as an indication of the quality of a water source.

10.2 Typical BOD values

Most pristine rivers will have a 5-day BOD of less than 1 mg/l. Moderately polluted rivers may have a BOD value in the range of 2 to 8 mg/l. Municipal sewage that is efficiently treated by a three stage process would have a value of about 20 mg/l. Untreated sewage varies, but averages around 600 mg/l in India and as low as 200 mg/l in the U.S., or where there is severe groundwater or surface water infiltration. Slurry from dairy farms is around 8000 mg/l and silage liquor around 60000 mg/l.

11.1 Introduction

Salinity is the saltiness or dissolved salt content of a body of water. The technical term for saltiness in the ocean is halinity, from the fact that halides, chloride specifically are the most abundant anions in the mix of dissolved elements. In oceanography, it has been traditional to express halinity not as percent, but as parts per thousand (ppt ), which is approximately grams of salt per liter of solution. In other disciplines chemical analyses of solutions, and thus salinity is frequently reported in mg/L or ppm (parts per million). Prior to 1978, salinity or halinity was expressed as % usually based on the electrical conductivity ratio of the sample to “Copenhagen water”, an artificial sea water manufactured to serve as a world “standard”(Lewis, E.L 1980). In 1978, oceanographers redefined salinity in Practical Salinity Units (psu): the conductivity ratio of a sea water sample to a standard KCl solution (UNESCO, 1981a) (UNESCO, 1981b). Ratios have no units, so it is not the case that 35 psu exactly equals 35 grams of salt per litre of solution (UNESCO, 1985).

These seemingly esoteric approaches to measuring and reporting salt concentrations may appear to obscure their practical use; but it must be remembered that salinity is the sum weight of many different elements within a given volume of water. It has always been the case that to get a precise salinity as a concentration and convert this to an amount of substance required knowing much more about the sample and the measurement than just the weight of the solids upon evaporation. For example, volume is influenced by water temperature; and the composition of the salts is not a constant. Saline waters from inland seas can have a composition that differs from that of the ocean. For the latter reason, these waters are termed saline as differentiated from ocean waters, where the term haline applies.

12.1 Introduction-Nitrogen

Nitrogen is a chemical element which has the symbol N and atomic number 7. Elemental nitrogen is a colourless, odourless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78.1% by volume of Earth’s atmosphere. Nitrogen is a constituent element of all living tissues and amino acids. Many industrial important compounds, such as ammonia, nitric acid, and cyanides are made up of nitrogen.

12.1.1 History

Nitrogen (Latin nitrogenium, where nitrum (from Greek nitron) means “native soda”and genes means “forming”) is formally considered to have been discovered by Daniel Rutherford in 1772, who called it noxious air or fixed air. That there is a fraction of air that did not support combustion is well known to the late 18th century.

Argon was discovered when it is noticed that nitrogen from air is not identical to nitrogen from chemical reactions. Compounds of nitrogen were known in the Middle Ages. The alchemists knew nitric acid as aqua fortis (strong water). The mixture of nitric and hydrochloric acids is known as aqua regia (royal water), celebrated for its ability to dissolve gold (the king of metals). The earliest industrial and agricultural applications of nitrogen compounds involved uses in the form of saltpeter (sodium- or potassium nitrate), notably in gunpowder, and much later, as fertilizer, and later still, as a chemical feedstock.

13.1 Introduction

Eutrophication, means an increase in chemical nutrients — typically compounds containing nitrogen and phosphorus in an ecosystem. It may occur on land or in water. The term is however often used to mean the resultant increase in the ecosystem’s primary productivity (Fig. 13.1), in other words excessive plant growth and decay and even further impacts, including lack of oxygen and severe reductions in water quality and in fish and other animal populations.

14.1 Introduction

An oil spill (or slick) is the intentional or unintentional release of oil into the natural environment as a result of human activity. The term often refers to marine oil spills where oil is released into the ocean or coastal waters (Fig. 14.1).

Oil can refer to many different materials, including crude oil, refined petroleum products or by-products, oily refuse, oil mixed in waste, or oily ballast. Oil is also released into the environment from natural geologic seeps on the seafloor, as along the coastline. The fate, behavior, and environmental effects of spilled oil can vary depending upon the type and amount of material spilled. In general, lighter refined petroleum products such as diesel and gasoline are more likely to mix in the water column and are more toxic to marine life, but tend to evaporate relatively quickly and do not persist long in the environment. Heavier crude or fuel oil, while of less immediate toxicity, can remain on the water surface or stranded on the shoreline for much longer. Oil from the Exxon Valdez and Gulf War oil spills, while weathering over time, has persisted along the shoreline for years after the spill.

15.1 Introduction

A tsunami is a series of waves created when a body of water, such as an ocean, is rapidly displaced. Earthquakes, mass movements above or below water, volcanic eruptions and other underwater explosions, landslides, large meteorite impacts and testing with nuclear weapons at sea all have the potential to generate a tsunami. The effects of a tsunami can range from unnoticeable to devastating. The term tsunami comes from the Japanese words meaning harbor (“tsu”,) and wave (“nami”,). The term is created by fishermen who returned to port to find the area surrounding their harbor devastated, although they had not been aware of any wave in the open water. Tsunamis are common throughout Japanese history; approximately 195 events in Japan have been recorded.

A tsunami has a much smaller amplitude offshore, and a very long wavelength (often hundreds of kilometers long), which is why they generally pass unnoticed at sea, forming only a passing “hump” in the ocean (Fig. 15.1). Tsunami have been historically referred to as tidal waves because as they approach land, they take on the characteristics of a violent onrushing tide rather than the sort of cresting waves that are formed by wind action upon the ocean (Iwan, W.D., 2006).

16.1 Introduction

Littoral drift is a geological process by which sediments such as sand or other materials, move along a beach shore.Long Shore Drift is the movement of eroded material, in a zig zag way, along the coast. The process arises when waves approach the shore obliquely. That is to say, at an angle other than 90°. The effect of this is determined by factors such as the direction and fetch of the present wind and, in the long term, of the prevailing wind.

Waves striking the shore at an angle as opposed to straight on will cause the wave swash to move up the beach at an angle. The swash moves the sediment particles up the beach at this angle, while the backwash brings them, solely under the influence of gravity, directly down the beach. Some geologists consider a beach to be merely a shoreline feature of deposited material, but William Bascom (1980) has argued that a beach is the entire system of sand set in motion by waves to a depth of ten meters or more off ocean coasts. Submerged, longshore bars are therefore also part of the beach, and thus beaches can be viewed as either:

17.1. Introduction

Throughout human history, the coastal plains and Lowland River valleys have usually been the most populated areas over the world (Wolanski et al., 2004). At present, about 60% of the world’s population live along the estuaries and the coast (Lindeboom, 2002). This is degrading estuarine and coastal waters through pollution, eutrophication, increased turbidity, overfishing and habitat destruction. The pollutant supply does not just include nutrients; it also includes mud from eroded soil, heavy metals, radionuclides, hydrocarbons, and a number of chemicals including new synthetic products.

The impact on estuaries is commonly still ignored when dams and irrigation farming are proposed on rivers. In addition, estuaries are often regarded as sites for future development and expansion, and have been increasingly canalized and dyked for flood protection, and their wetlands infilled for residential areas.

All these factors impact on the biodiversity and productivity and hence, the overall health of estuaries and the ecosystem services they provide to humans. They increasingly lead humans away from the possibility of ecologically sustainable development of the coastal zone. Integrated coastal zone management plans are drawn up worldwide but, in the presence of significant river input, most are bound to fail because they commonly deal only with local, coastal issues, and do not consider the whole river catchment as the fundamental planning unit. It is as if the land, the river, the estuary, and the sea were not part of the same system. When dealing with estuaries and coastal waters, in most countries land-use managers, water-resources managers, and coastal and fisheries managers do not cooperate effectively due to administrative, economic and political constraints, and the absence of a forum where their ideas and approaches are shared and discussed (Wolanski et al., 2004). 

18.1 Introduction

The commercially available water quality simulation models with various dimensions (1D, 2D and 3D) and database software designed to quantify movement and concentration of contaminants in lakes, streams, estuaries, and marine environments. The following water quality models were described below (Table 18.1).

18.2 Environmental Fluid Dynamics Code

The Environmental Fluid Dynamics Code (EFDC) is a multifunctional surface water modeling system, which includes hydrodynamic, sediment-contaminant, and eutrophication components. It has been applied to over 100 water bodies including rivers, lakes, reservoirs, wetlands, estuaries, and coastal ocean regions in support of environmental assessment and management and regulatory requirements. IT is a state-of-the-art hydrodynamic model that can be used to simulate aquatic systems in one, two, and three dimensions. It has evolved over the past two decades to become one of the most widely used and technically defensible hydrodynamic models in the world. It uses stretched or sigma vertical coordinates and Cartesian or curvilinear, orthogonal horizontal coordinates to represent the physical characteristics of a waterbody. It solves three-dimensional, vertically hydrostatic, free surface, turbulent averaged equations of motion for a variable-density fluid. Dynamically-coupled transport equations for turbulent kinetic energy, turbulent length scale, salinity and temperature are also solved. The model allows for drying and wetting in shallow areas by a mass conservation scheme.

The homoeopathic system of medicine is one of the finest systems of cure available in the world. It achieves in totality the ideal laid down by its founder, Dr. Samuel Hahnemann:

"The highest ideal of cure is rapid, gentle and permanent restoration of the health, or removal and annihilation oftlie disease in its whole extent, in the shortest, most reliable, and most harmless way, on easily compreltensible principles".

In homoeopathy, not a single drug is used without knowing its effect on healthy human beings. Hence there is no shooting in the dark. The system operates, by and large, without laboratory tests and other expensive means of diagnosis, which are being used when not needed and that too, unfortunately on patients who can hardly afford the expenses.

Cost wise, there is no medical system in tlie world, which is as inexpensive as homoeopathy. No patient who requires a speedy cure without side effects can ignore homoeopathy; no doctor who has nothing but the good of his patient at heart can overlook the utility and effectiveness of homoeopathy and no Government which has to balance its budget can afford not to use homoeopathy in hospitals and other institutions run for the health and care of the sick and thus it is the most cost effective treatment

The discovery of homoeopathic system of medicine makes a fascinating story.

Dr. Samuel Hahnemann laid down the fundamentals of the then new doctrine of homoeopathy in organon of medicine. As observed by him in the 'Introduction⁷ to this work, till then no one had ever taught this homoeopathic mode of cure, no one had carried it out in practice.

Dr. Hahnemann was of the view that the art of the medical practice "should. Rapidly and mildly, effect an unalloyed and permanent cure, and restore to health by means of the smallest doses of a few simple medicines carefully selected according to their proved effect, by the only therapeutic law comfortable to nature, that is Similia Similibus Curentur".

Homoeopathy is based on the following principles:

"The physicians high and only mission is to restore the sick to health, to cure, as it is termed"

The highest ideal of cure is rapid, gentle and permanent restoration of health or removal and annihilation of the disease in its whole extent in the shortest, most reliable and most harmless way on easily comprehensible principles.

Unprejudiced observer of a sick person takes note of nothing in every individuars disease except the changes in the health of the body and of the mind, which can be perceived externally by means of the senses. "All these perceptible signs represent the disease in its whole extent, that is, together they form the true and only conceivable portrait of the disease"

This individualizing examination of a case of disease, for which Dr. Hahnemann give general directions, of which the practitioner will bear in mind only what is applicable for each individual case, demands of the physician nothing but freedom from prejudice and sound senses, attention in observing and fidelity in tracing the picture of the disease.

The patient details the history of his sufferings; those about him tell what they heard him complain of, how he has behaved and what they have noticed in him; the physician sees, hears, and remarks by his other senses what there is of an altered or unusual character about him. He writes down accurately all that the patient and his friends have told him in the very expressions used by them. Keeping silence himself, he allows them to say all they have to say, and refrains from interrupting them (every interruption breaks the train of thought of the narrators, and all they would have said at first does not again occur to them in precisely the same manner after that.) unless they wander off to other matters. The physician advises them at the beginning of the examination to speak slowly, in order that he may take down in writing the important parts of what the speaker says.

He begins a fresh line with every new circumstance mentioned by the patient or his friends, so that the symptoms shall be all ranged separately one below the other. He can thus add to any one that may at first have been related in too vague a manner but subsequently more explicitly explained.