eChapters

Introduction

Fish and the aquaculture products contribute a significant amount of animal protein to the diet of the people worldwide. Being highly nutritive they serve as valuable food supplement in diets lacking essential vitamins and minerals. Besides its role of food security, fish is a source of income for millions of people around the World. Though the trade is not prominent at Global level, in some countries its contribution to foreign currency earning is vital to the National Economy. India has a coastline measuring 7500 km and important aquaculture country in the World. Being the home for more than 10% of the global fish biodiversity, the country ranks third in the World in the total fish production with an annual fish production of about 6.4 million tones. Constituting over the 1% of the GDP, fisheries contributes to 5.3% of the agricultural GDP. The estimated foreign earning for the year 2006 was US$ 1365 million.

Introduction

Improvements in Information and Communication technology are revolutionizing the way people access information. These new technologies are helping to improve communication, disseminate information and facilitate sharing of knowledge and skills. Zijp (1994) notes, Information Technology is making both public and private sector agricultural information systems more accessible and more rapid in transmission. The increase in electronic information and communication technologies and in particular networked information is the most notable change to affect the working practices of information professionals in recent years. Digital technologies have led to the emergence of wide-area connectivity through the Internet, making information on agriculture available worldwide and on-demand. Information technology and electronic networking particularly can strengthen organizations by improving their knowledge base and ability to share information and experiences with partners in the field. Electronic networking not only helps in the exchange of the growing volume of information but also brings people together in partnerships and facilitates a joint programme of action on common themes.

Introduction

In this computer age software plays a vital role in speeding up the research activity. Software and databases help in storage, processing and accessing large volumes of information. Software helps to retrieve right information at the right time at the right place for the right purpose. The time of researchers is very precious. Instead of spending it in monotonous and tedious tasks, it could be used more effectively for new findings. With the advent of computer and its softwares, this problem could be overcome to a considerable extent.

Software is a set of instructions given to the computer to perform certain tasks. In this era of information technology, its essential to apply different softwares to speed up the research activity. It is therefore, utmost importance to have information about the different software already developed in the area of fisheries/aquaculture worldwide. Almost all the routine tasks which the scientists or the farmers are doing, could be automated in the areas like financial & economic analysis, development planning and project appraisal, facility design, management planning and production forecasting, facility construction, management decision support and record keeping, disease diagnosis and treatment, environmental regulation and aquaculture databases. FAO, World Fish Centre and other International Research Organisations have contributed software and database development in the area of aquaculture (Anon, 1999; ICLARM, 1998; FAO, 1999; Erist, 1998). In India also initiative to develop software and database has been taken up. Preliminary report on the availability of fishery related software and databases are available (Roy, 2000). In this communication, an attempt has been made to list softwares and databases that may be used in fisheries and aquaculture research and development/activities.

Introduction

The development of DNA technology over the last few decades has led to generation of huge amount of data from plant and animal genome. The main sources of markers are mitochondrial DNA (mt DNA), minisatellites, micro satellites and anonymous nuclear sequences assayed using highly specific PCR primers or by using the RAPD technique. A major contribution comes from molecular markers used for analyzing genetic variations. There has been the infusion of computers, softwares and online databases into the daily activities of many molecular geneticists. The identification of abundant, highly variable loci, detectable by a wide variety of techniques has led to a revolution in the way researcher view and analyses levels of variation. We will here discuss about current computer programs in this area to characterize the DNA profiles and data analysis for intra and inter population structure, phylogenetic inference and parentage determination.

Introduction

Technologies and tools that have developed in the recent information technology revolution can play a very vital role in overcoming most of the present problems related to agriculture and rural development. In order to achieve the goal of an economically sound and stable society through environmentally friendly systems of agricultural production, it is imperative to have a comprehensive data storage system. This will not only help in providing systematic and periodic information to the planners, decision-makers and developmental agencies, but also help to manage our limited natural resources efficiently. The development of a data warehouse is one of the recent tools in the field of information technology that can fulfill the demands of the information that is required in the field of agriculture research, management and education

Nanotechnology: The Next Big Thing is Really Small

Nanotechnology can be considered as a brainchild of Richard Feynman, as the conceptual underpinings of nanotechnologies were first laid out in 1959 in his historical lecture, ‘ There is plenty of room at the bottom’. The term ‘nanotechnology’ was not used until 1974, when a researcher, Norio Taniguchi, at the University of Tokyo, Japan, used it to refer to the ability to engineer materials precisely at the nanometer level. The prefix ‘nano’ is derived from the Greek word ‘drawf’. One nanometer (nm) is equal to one billionth of a meter or about the width of six carbon atoms or ten water molecules. A human hair is approximately 80,000 nm wide and a red blood cell is approximately 7000 nm wide¹. Nanotechnology can be defined as the science and engineering involved in the design, synthesis, characterization and application of materials and devices whose smallest functional organization in at least one dimension is on the nanometer scale or one billionth of a meter^2-5. It is a multidisciplinary field, which covers a vast, and diverse array of devices derived from Engineering, Physics, Chemistry and Biology and the cumulative efforts of all the disciplines is necessary for any significant outcome.

Introduction

Of the five human sensory perceptions, the feelings of sight, hearing and touch have been simulated by artificial sensors quite successfully. Electronic eyes (digital cameras), electronic ears (microphones) and touch sensitive electronic devices are quite common nowadays. In comparison to these devices, the perception of smell and taste are relatively unexplored. Sensing of smell and taste is full of uncertainty and the prevalent technology is at its infancy. Electronic noses for smell and electronic tongues for taste or a combination of both have vast prospects in the field of standardization of quality of food and agro products. In India, proper use of these instruments can revolutionize the quality of the food and agro products, thereby increase the export worthiness of these products. In this article, we have tried to discuss applicability various electronic olfaction technologies like electronic nose and electronic tongue for fish freshness determination. A report on an experiment with electronic nose on fish samples has been presented.

Introduction

The major potential areas for inland aquaculture have already been explored in India. Additional production can only be achieved through successful manipulation of available resources that influence the productivity of various aquaculture systems. This can be achieved through maintenance of adequate levels of nutrients in the pond environment. Pond management in fish culture is mainly concerned with fertilization requirements and strategies with better management practices (BMP) of pond soil and water quality. BMP could be achieved through adoption of advanced technology, computer based diognostic/decision tools, software packages for quick, accurate, authetic data management.

Introduction

India is an agrarian society where 70% of the population depends on agriculture, animal husbandry and fisheries. Fishery is an important sector, its planning and development largely depends on a sound and reliable data and information on resource, production, marketing and distribution. Generating reliable information basically needs identification, conceptualization, classification and sound scientific techniques for collection, compilation and analysis of data. Geographical Information System emerged as an efficient tool to access, organize, update and analyse the information and to utilize it in an optimal way.

A proper computer based information system is the need of day to organize such complex data in order to draw reliable conclusions which may help in drawing action programmes. This multidimensional nature of information on topography, physico-chemical parameters, socio-economics and fish production data can only be handled and processed by Geographical Information System (GIS).

Introduction

Activities to promote and monitor the growth of aquaculture inherently have a spatial component, because of the variations among biophysical and socio-economic characteristics from location to location. Biophysical characteristics may include water quality, soil type and climate. Socio-economic characteristics in aquaculture development may include administrative regulations, competing resource uses, market conditions, infrastructure support, and availability of technical expertise. Geographical Information Systems (GIS) provides the spatial information needed for decision-makers who evaluate such biophysical and socioeconomic characteristics as part of aquaculture planning efforts more effectively and timely (Kapetsky and Travaglia, 1995). GIS is potentially a powerful tool for assisting this class of decision-makers, and is already being effectively used for such purposes in some places (Carswell, 1998; Arnold et al., 2000) where advanced capabilities in terms of infrastructure and trained personnel exists. Nath et al. (2000) discussed various applications of GIS in aquaculture. In general spatial information technologies are being effectively used for sustainable management of aquaculture and inland fisheries. Some potential applications are as follows:

Introduction

Ornamental fish keeping in aquarium has emerged as the second most popular hobby next to photography. As these fishes usually are kept in aquarium, they are popularly known as ‘Aquarium Fishes’. These beautiful fishes form an important commercial component of aquaculture, providing for aesthetic requirements and upkeep of the environment. At present the market for ornamental fish in the world for public aquaria is less than 1% and over 99% of the market is still confined to hobbyist. In India the hobby of ornamental fish keeping is nearly 70 years old. The brilliant, flamboyant color and exotic appearance of fish appeal almost for every one, children and aged alike. According to psychiatrists, placing aquaria with ornamental fishes in the patient’s house could treat certain type of mentally disordered problems. The relatively minimum requirement of space or attention compared to other pet animals is the reason of growing interest in keeping aquaria all over.

The term ‘Ecology’ deals with the study of organisms from all sources and their interaction with surrounding environments. The aim of ecology is, therefore, to understand and also to explain the relationships of all organisms to their environment. In this respect, the duty of the ecologist is to study a particular environment, estimate the population of each species, recognize the communities, and determine their activities and their interactions with both related species, the rest of the community, and their environment. Macroecological studies always initiate by defining the species composition and then proceed to draw certain conclusions on the role of these species in the ecosystem. On the other hand microbial, especially bacterial classical taxonomy (based on isolation techniques and determination of morphology and in vitro biochemical characteristics of isolates) for determination of each species of aquatic bacteria is almost impossible, except in a few cases. Consequently, the microbial ecologist has to depend upon certain methods that can measure the biomass or activity of a very large conglomerate of coexisting microbial taxa in an aquatic environment. Probably, this has caused the very slow development of microbial ecology concepts and application of a general ecological theory to the microbial ecology.

Introduction

Global diversity in domestic animals and aquatic organisms is considered to be under threat worldwide. Worldwide 11 % birds, 25 % mammals and 34 % of fish species are threatened (Lovell-Badge, 2001; Vemuganti and Balasubramanian, 2002) and aquatic ecosystem is becoming more vulnerable to disasters due to run off from agriculture and industrial sources, oil spills or sudden environmental changes leading to total elimination of stocks from different ecosystems. The multifarious human activities in open waters have threatened the fish diversity all round the world. Fish worldwide are in crisis. The effective population sizes in fish hatcheries are getting smaller and smaller that causes loss to farmers worldwide. The World Resources Institute has reported that nearly 70 percent of the world’s marine fish stocks are over fished or are being fished at their biological limit. Apart from fish, across all live stock species there is a shrinking pool of genetic diversity. For instance, the effective population size for all dairy cattle breeds is less than 60 animals. To preserve the gene pool of unique populations by protecting them from extinction, loss of genetic variability (inbreeding) and dilution due to inter breeding with unrelated populations (hybridization) gene banks or germplasm repository can play a vital role. Germplasm repositories in fisheries could be used for: 1) restoration of threatened species, 2) brood stock improvement through genetic modification of a targeted population, and 4) information and technology development including gene pool database management.

Introduction

Majority of the commercially important freshwater prawns belongs to the genus Macrobrachium of family Palaemonidae. Among the commercially important freshwater prawns of India the most important cultivable species at present is the giant freshwater prawn Macrobrachium rosenbergii due to its superior cultivable attributes such as fast growth rate, large size, wide range of salinity tolerance, hardiness and compatibly to grow with carps. The species enjoys good consumer preference and domestic as well as export market demand. Freshwater prawns are cultured in freshwater or low saline brackish water (salinity <10 ppt) and can be cultured either alone (monoculture) or in combination with fishes such as carps, tilapia and milkfish (polyculture). Freshwater prawn culture can be carried out in earthen ponds, cement cisterns, in pens or in cages. However, most of the operations are being carried out in earthen ponds.

Introduction

Indian major carps viz. Catla catla, Labeo rohita and Cirrhinus mrigala are the fast growing, consumer preferred and the stay component species in Indian pond aquaculture system. These carps breed spontaneously in natural water viz. river and bundh type tanks where fluviatile condition prevails (Hora, 1945; David 1959; Quasim and Qayyam, 1962; Natarajan, 1971). Above three species under culture condition attain sexual maturity but do not spawn in confined water (Chaudhuri, 1960; Chaudhuri and Singh, 1984). Khan and Jhingran (1975) in their review described several factors viz. temperature, run off water, photoperiod, turbidity and water depth that are playing important roles in initiating natural spawning in ‘bundhs’ and rivers. They further described that no single factor can be considered responsible for spawning separately. The act spawning involves a chain of interrelated conditions as prerequisite to spawn. Monsoon, flood forms the spawning ground and initiates natural spawning. Although fish bred in its natural environment, it was difficult to understand why some species do not breed in confined water where as other species in the same environment breed somoto.

The initial attempt to induce breed IMC (mrigal) was made during 1937. Khan (1938) was able to induce ovulation in Cirrhinus mrigala by administration of mammalian pituitary extract but eggs were not fertilized. No remarkable success on induced breeding of Indian major carps was made till 1957. Indian major carps were induced to breed for the first time on 10th July, 1957 by the injection of aqueous carp pituitary extract at Govt. Fish Farm, Angul of Orissa state by the scientific team from pond culture substation, Cuttack (Chaudhuri and Alikunhi 1957). Eversince 1957, the induced breeding of carps have been tried by many permutation and combination, addition and alteration of inducing agents.

Introduction

Brood stock management is an essential component of fish farming since the success of aquaculture industry mainly depends on quality of brood stock in order to ensure the production of top quality offspring. Their health condition is also important from culture point of view, which in turn increases the fish production. Unfortunately, in India, less attention is given to the brood stock management during non-breeding seasons. The pond aquaculture is also becoming over utilized due to high stocking beyond the carrying capacity, addition of huge quantities of chemicals, drugs, fertilizers and supplementary feeds etc. Physical injury due to rough handling, temperature fluctuations, extremes in oxygen levels can also work in a cumulative way and produce stress and make the fish susceptible to variety of diseases. Environmental deterioration, which occurs due to dumping of pesticides and chemicals alongwith metabolic waste products, left out feed materials and organic load of the pond bottom regularly come in contact with certain vital organs and tissues of fish. All such factors can cause deterioration of fish health and magnify the risk of outbreak of diseases. Disease outbreaks are one of the stumbling blocks in the development of aquaculture industry affecting both the economic development and socio-economic revenue from this sector. Today, there is no availability of exact figure on loss due to diseases in fish farming. The phenomenon is more common in carp Industry, and mortalities due to disease outbreaks cause major management problems and economic loss every year.

Introduction

Fish production in aquaculture has increased dramatically over the last 20 years with an increment of 9-10% per year over the last decade. Microbial disease problems are prevalent in aquaculture as in any other intensive animal or plant production sector. Vaccines are used as disease prevention and can be very effective, however, they do not work at all developmental stages of fish or in all species. Therefore, antibiotics play a major role in control of fish bacterial diseases, although serious concerns have been raised with respect to development of antibiotic resistance and its transfer to human pathogenic bacteria. Also, new EU regulations call for specific license for antibiotic use in aquaculture and this is too costly even for fish farmers.

The urgent need for development and application of non-antibiotic disease control measures has led to research in probiotic organisms. Probiotics are “live microorganisms which when administered in adequate amount, confer a health benefit on the host (FAO/WHO 2001)” and the principle is most widely known from the belief that ingestion of high numbers of lactic acid bacteria (fermented foods) can control human pathogenic organisms in the intestine. Fish pathogenic agents, however, can invade via skin and gills and probiotic organisms may therefore be as efficient if applied to the outer environment of the fish.

Introduction

The United Nations’ Food and Agricultural Organisation reported that global aquaculture is increasing by 11 percent per year and is the world’s fastest growing food-producing sector. More than 38 million people are employed in aquaculture and associated industries worldwide, and 131 aquatic species are currently being commercially cultured. In 2002, Asia led the world in the aquaculture production, with about 12.4 million tonnes, while Europe and America together produced 1.2 million tonnes.

Among the Asian countries, India ranks second in aquaculture and third in capture fisheries. Freshwater aquaculture in India is mainly based on Indian major carps (Labeo rohita, Catla catla and Cirrhinus mrigala) with an annual production of 1.8 million tonnes, and exotic carps, which together contribute to over 87% of the total aquaculture production of 2.2 million tonnes. Disease problems represent important constraint to the aquaculture industry. The need to control endemic diseases imposes severe year-on-year costs on producers. The advances made in the development of vaccines for diseases of Indian major carps are very meager.

Introduction

Recent advances in bioinformatics such as microarray analysis are bringing about a revolution in our understanding of the molecular mechanisms underlying normal and dysfunctional biological processes. With the help of microarray technologies, biologists are currently capable of observing the abundance of transcripts from tens of thousands genes in biological samples, enabling the exploration of the dynamics of transcription and interaction between genes on a genome-wide scale. With the accumulation of gene expression dataset, the challenging task of all microarray experiments is how to extract meaningful and trustworthy information out of thousands of genes that do not contribute in the designed experiments. To achieve this goal, many rigorous mathematical tools and computational software were introduced to the field, like statistical techniques for data normalization, clustering algorithms, class prediction methods, ANOVA, and gene-gene interaction studies. Microarray technology has been used widely in various areas of agriculture and allied field. Application of statistics in microarray is limited particularly in experiments involving fishes. In this chapter it is attempted to present various statistical methods applied to accessory microarray experiments with illustrated example of fish microarray data.

Introduction

Nucleotide and protein sequences construct the core of Bioiformatics. These biological sequences form complex and very large datasets. Various Statistical techniques have been used for analysis and extraction of precise information form small as well as large biological datasets. Evolution and natural selection makes biological sequences redundant and statistically biased. Once the mechanisms involved in such biases have been characterized, their analysis and systematic investigation become valuable tools for use in predicting the properties of other biological sequences. This biased nature results in relative codon usage value among the synonymous codons or Relative Synonymous Codon Usage (RSCU) value. Codon usage variation within a single genome can be an important source of information about gene expression levels and events of horizontal gene transfer (Medigue et al., 1991). The analysis of codon usage patterns can be traced back to when first molecular sequence databases were being colleted (Grantham et al., 1981). In order to evaluate the codon and amino acid usage variation, multivariate analysis options like Correspondence Analysis, Principal Component Analysis, Cluster Analysis, Factor Analysis, Multidimensional Scaling and Eigenanalysis Ordination are available (Morrison et al., 1994). It is well established that codon usage by its nature is multivariate. These methods provide a low dimensional point representation of genes, where the proximity of gene specific points indicates (CoA) a similar codon usage of associated genes. Correspondence Analysis is an exploratory graphical approach that requires contingency tables and generates results in the form of tables, scattered plots and graphs. CoA can identify the major sources of variation in the dataset. The output from a CoA can be used to evaluate other aspects of genes, such as base composition, expressivity, aromaticity and location on the genome (Thiouse et al. 1997).