eChapters

1. INTRODUCTION

Motifs are patterns in biological sequences which can indicate the presence of certain biological characteristics and function. In general, these could represent patterns in any kind of biological sequences such as DNA sequences, RNA sequences and protein sequences. Evolutionary conserved regions (ECRs) are sequences with atleast 100 bp length alongwith minimum 70% identity, which includes most of the protein-coding exons, promoters, enhancers and repressors. ECRs are the preliminary step for finding TFBSs (Transcription factor binding sites) within the raw genome sequences of higher eukaryotes (large sizes of the genomes). DNA sequence motifs are short length, recurring patterns in DNA and are known to be associated with a biological function. These motifs sometimes indicate sequence specific binding sites for proteins such as nucleases and transcription factors (TF). Some sequence motifs are involved in biological processes at RNA level, such as ribosome binding, mRNA processing (splicing, editing, polyadenylation) and transcription termination. Motif identification is important at protein level for biological processes such as protein-subcellular localization, protein membrane, protein-protein interactions, identification of active site of enzyme(s) and post-translational modifications. Motif search is useful in understanding gene function, human disease, drug design, etc. Regulation of splicing in eukaryotes occurs through the coordinated action of multiple splicing factors. Sequence motifs are also useful in the study of genetic regulatory networks and regulatory program of individual genes.

INTRODUCTION

Soil is a very important component of the earth’s biosphere. It is the basis of agricultural production and also in the maintenance of local, regional and global environmental quality (Glanz 1995). The thin layer of soil covering the surface of the earth represents the difference between survival and extinction for most land-based life (Doran and Parkin 1996). Analysis of soil productive capacity point out human-induced degradation on nearly 40% of the world’s agricultural land as a result of soil erosion, atmospheric pollution, widespread soil cultivation, over-grazing, land clearing, salinization and desertification (Oldeman 1994). Degradation and loss of productive agricultural land is definitely one of our most pressing ecological concerns, similar to the other human caused environmental problems like global climate change, depletion of the protective ozone layer and serious reduction in biodiversity (Lal 1998).

INTRODUCTION

The field of virology is still not explored extensively. The use of bacterial and algal viruses till date are mostly restricted to areas like phage therapy (Sanmukh et al., 2012), whole genome sequencing, isolation and characterization of lytic enzymes (Paunikar et al., 2011), control of pathogenic multi drug resistant micro-organisms, structure elucidation through electron microscopy as well as NMR spectroscopic methods. Bioinformatics approach is also well explored for the gene annotation, sub cellular localization as well as structure prediction of various unknown as well as unclassified proteins in different viruses (Sanmukh et al., 2010). Our main concern while dealing with most viruses is limited to its classification and characterization but, we forget to reveal its true nature by exploring various budding applications which they may suffice. Moreover, very few viruses are sequenced and their genome is made available at ICTV (International Committee for Taxonomy of Viruses) which makes their information more unclear. Considering all above scenario, we can feel the urgent need for entering into a new area of “Applied Virology”. Due to various limitations with respect to funding and possible facility requirements, researchers are not yet optimizing on the applications of viruses for potential molecular biology applications as well as its industrial implementation in cost effective, time efficient and for commercial gain.

1. INTRODUCTION

Dielectric-barrier discharges (DBDs) also referred to as barrier discharges or silent discharges. DBDs have for a long time been regarded as the ozonizer discharge. In 1932 Buss observed that in a plane parallel gap with insulated electrodes air breakdown occurs in a number of individual tiny breakdown channels.^1,2 Recently, it was realised that plasma can be influenced, modelled and optimised for a given application through microdischarges. The most important characteristic of dielectric-barrier discharges is that non-equilibrium plasma conditions can be provided in a much simpler way than with other alternatives like low pressure discharges, fast pulsed high pressure discharges or electron beam injection. Moreover, the DBDs can breakdown most of the gases at about atmospheric pressure in a large number of independent current filaments or microdischarges. The dielectric barrier limits the amount of charge and energy deposited in a microdischarge and distributes the microdischarges over the entire electrode surface. When a dielectric-barrier discharge is operated in rare gases or a rare gas halogen mixture plasma conditions in a microdischarge channel are similar to those in pulsed excimer lasers. Consequently, each microdischarge can act as an intense source of ultraviolet (UV) or vacuum ultraviolet (VUV) radiation. The absorption coefficient of most substances increases at shorter wavelengths. So, in many cases the UV radiation is absorbed in a very thin surface layer. The xenon excimer lamp can induce photo-cleavage of water and oxygen.²

INTRODUCTION

Scientists have known that certain animals can regenerate missing parts of their bodies. But we can not replace a missing leg or a finger; our bodies are constantly regenerating blood, skin and other tissues. The identity of the powerful cells that allow us to regenerate some tissues was first revealed when experiments with bone marrow in the 1950’s established the existence of stem cells in our bodies and led to the development of bone marrow transplantation, a therapy now widely used in medicine. Stem cell therapies are one of the most promising areas of medicine, and many such therapies are now in development by industrial and academic groups. The first successful allogenic stem cell graft in humans using donor bone marrow was undertaken in the USA in 1968 and bone marrow transplantation continues to provide the best example of the clinical use of adult stem cells. Currently, cell therapies are regulated under the US Food and Drug Administration’s (FDA’s) Good Tissue Practices Final Rule, which uses a tiered system based on the level of risk associated with the cell product. Scientists were able to extract embryonic stem cells from mice in the 1980s, but it wasn’t until 1998 that a team of scientists from the University of Wisconsin–Madison became the first group to isolate human embryonic stem cells and keep them.

Every aspect of the living organism is the sum total result of the metabolism carried out within its cells and in other organisms. Metabolism is the sum total of the chemical reactions occurring in the cell or organism. Metabolism is of two kinds:

1. Anabolism- It is also known as constructive metabolism as it involves synthesis of complex substances from the simpler ones, which are required for growth, maintenance and storage in the organism. Example: Formation of starch from glucose.
2. Catabolism- It is also known as destructive metabolism as it involves breaking of the complex substances into simpler ones, leading to release of the energy required for performing various activities of living beings. Example: Respiration.

Metabolite is the end product or the intermediate product of a biological pathway. Metabolite can be classified into two types mainly:

ABSTRACT

During the efficient genetic transformation of plants with the gene of interest, some selectable marker genes are also used in order to identify the transgenic plant cells or tissues. Antibiotic and herbicide selective agents and their resistance gene are commonly used to introduce economically valuable genes into crop plants. According to the biosafety authority and consumer view points, the presence of selectable marker genes in released transgenic crops may be transferred to weeds or pathogenic microorganism in the gastrointestinal tract or soil, and will make them resistant to treatment with herbicides or antibiotics, respectively. Sexual crossing also raises the problem of transgene expression because redundancy of transgenes in the genome may trigger homology-dependent gene silencing. The future potential of transgenic technologies for crop improvement depends greatly on our abilities to engineer stable expression of multiple transgenic traits in a predictable fashion and to prevent the transfer of undesirable transgenic material to non-transgenic crops and related species. Therefore the development of efficient marker free transgenic plants system is very essential. That is why many technologies and various approaches designed to timely elimination of transgenes when their function is no longer needed. Due to the limited number of available selectable marker genes, in future the stacking of transgenes will be increasingly desirable. The production of marker-free transgenic plants is now a critical requisite for their commercial deployment and also for engineering multiple and complex trait. Here we describe the current technologies to eliminate the selectable marker genes (SMG) in order to develop marker-free transgenic plants and also discuss the regulation and biosafety concern of genetically modified (GM) crops.

INTRODUCTION

Plants are rich source of nutrients for most of the organisms including microbes' arthropods and vertebrates. There are various biotic viz. insects, weeds and pathogens and abiotic factors viz. temperature, humidity, salinity etc. that causes harm to plants. For yield loss due to pest EIL (Economic injury levels) calculation is important (Stern et al, 1959). EIL calculation will define economic damage (yield losses equal to management costs) in calculable terms. Since plants are sessile they cannot move to avoid the menace of these factors, but they have developed a unique way of structural, chemical, and protein-based defences which are specifically designed to detect and inhibit invading organisms before they are able to cause extensive damage. In response to the incitations by the pathogens some genes are activated which in turn codes for defence proteins (Grennan, 2006). Understanding how plants defend themselves from pathogens and herbivores is essential in order to protect our livelihood and nutritional security. In addition to proteins, plant anatomy and some of the ecological relationship also plays an important role in plant defense mechanism. Induction of plant resistance against fungi and bacteria was reported in 1900.

ABSTRACT

Genomics is a relatively new scientific discipline, having DNA sequencing as its core technology. As technology has improved the cost and scale of genome characterization over sequencing’s 40-year history, the scope of investigation has commensurately broadened. Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalyzed the development of next-generation sequencing (NGS) technology. Over the past few years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. These new technologies are rapidly evolving, and near-term challenges include the development of strong protocols for generating sequencing libraries, building effective new approaches to data-analysis, and often a rethinking of experimental design. Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts. This article explains the methods, advantages and disadvantages of methods and softwares of Next Generation Sequencing with its impact and applications on genomics and other related field of biology.

INTRODUCTION

DNA sequencing is a process of deciphering the complete order of nucleotide in the DNA molecule with precision. Over the past few years, there has been a shifting from the automated Sanger’s method of sequencing to next generation technologies. There was a milestone in the year 2003 for the researchers when fine sequence of human genome project was declared complete. The project was completed in 13 years with nearly $3 billion expenditure and more than 20,000 researchers and technicians took part in it all over the Globe. DNA sequence determination is performed using dideoxy chain termination technology (Ronaghi, 2001). The dideoxy sequencing method was developed by Frederick Sanger and his colleagues (Sanger et al., 1977) and is called as First-generation sequencing technology. Since early 2000s, there became drastic improvements in the sequencing technologies from Sanger’s method used for Human genome project to Next Generation Sequencing (NGS) technologies used these days. The change in technologies not only reduced the expenditure to the minimal but also involved minimum use of human resource and time. High –throughput sequencing technologies are increasingly being used to address varied range of biological objectives. It provides a promising approach to increase the scale, robustness and efficiency of the results of whole genome within few hours and minimum expense. Key players in the field of NGS are 454 GX Flex Roche, Solexa Illumina, SOLiD ABI (Applied Biosystems), ViSiGen biotechnologies, Helicose Biosciences and Polonater systems.

INTRODUCTION

Massively Parallel DNA sequencing also known as next-generation sequencing, revolutionize the genomics and transcriptomics research as their effects are increasingly widespread. A new generation of non-Sanger-based sequencing technologies has delivered on its promise of sequencing DNA at unprecedented speed, thereby enabling impressive scientific achievements and novel biological applications. Before the next generation sequencing, the Sanger’s enzymatic di-deoxy chain termination was used for nucleotide sequencing from last 30 years with various original improvements. Sanger enzymatic di-deoxy chain termination technique first described in 1977 and the Maxam and Gilbert chemical degradation method described in the same year, which was used in sequence cases which could not easily be resolved with the Sanger technique. The two laboratories where the first automated DNA sequencers were produced, simultaneously, were those of Leroy Hood at Caltech, commercialized by Applied Biosystems, and Wilhelm Ansorge at the European Molecular Biology Laboratory EMBL and commercialized by Pharmacia-Amersham, later General Electric (GE) Healthcare. The Sanger method was used in the first automated fluorescent project for sequencing of a genome region, in which sequence determination of the complete gene locus for the HPRT gene was performed using the EMBL technique; in that project the important concept of paired-end sequencing was also introduced for the first time.

1. INTRODUCTION

The key global challenges facing the mankind in the 21st century are food, water, energy security, environment, combating cancer, and infectious diseases. Solving these challenges requires concerted efforts using modern scientific and technological advances in multiple disciplines. One such technology that has revolutionized life science research is “next-generation sequencing”. The NGS technology has brought an enormous technological shift in DNA sequencing through dramatic high-throughput and a precipitously dropping cost of raw sequence data. NGS technologies changed the dynamics and pace of genomic research in humans, animals, plants and microbes largely due to their rapid, inexpensive and highly accurate sequencing capabilities. The capillary electrophoresis based sequencing technology pioneered by Sanger and Coulson.

1. INTRODUCTION

Increasingly, in recent years, we hear of new technologies for the production of clean energy or, as they say now in common usage, from renewable energy sources, there are many sources of renewable energy, but certainly the ones that deserve special attention are those derived from algae. Today, thanks to innovative systems called photobioreactors, you have a way to start producing, though unfortunately still a small part, the amount of clean energy from algae and various biological processes that develop. The photobioreactor is one of the most innovative systems of the 21st century, and is paving the way for a new concept of energy utilization , although the fossil fuel (oil of course) continues to lead the way, even if you are aware of the drastic and continuous decrease the world’s resources. Although still under investigation, but there are many aspects that allow, thanks to special engineering studies , already now create systems suitable for the production of energy directly from algae , while biofuels obtained from the latter, there are several studies and tests , which aim to further lower production costs, in order to bring them at par or even below the threshold of current fossil fuels. In addition, these photo bioreactors, allow to produce, under controlled conditions, products and raw materials from the algae for food and non-food market, often providing a viable substitute, nutritious and natural, to all those raw materials that are harmful to human health and animals, especially in the food and health sectors.

Large number of edible fruits exists in tropics and subtropics of world. Many of such fruit species are identified, domesticated and are being utilized for various purposes, though their full potential has not been exploited. There is yet another group of plants producing edible fruits with great potential in different parts of world, which are not at all being grown and utilized by people other than in a very localized manner. Such under and un-utilized fruits are made the subject for detailed study. They are evaluated for their nutritive value, potential uses for other purposes, for possibilities of commercial cultivation in suitable areas and chances for marketing. Since all of them may not be acceptable for fresh consumption as table fruit, product diversification should be thoroughly evaluated to gain popularity for such plants. Practices and techniques employed for utilizing these fruits by local people where these plant species are seen at present can be scientifically and systematically refined for commercial exploitation.

Broad spectrum of agro climatic conditions and diversity in people’s preference for taste offer great chances to identify right fruit to a particular region for commercial cultivation in India. In this context, significance of under and un-utilized fruits for exploiting potentials become more clear. Identification of such plant species in different regions, extend and method of present utilization, nutritive value and pomological significance of the products, specific climatic and cultural requirements for successful growth and development should be documented as first step for exploitation of lesser known fruit species. Some of the under and un-exploited fruit species prevalent in tropical and subtropical conditions are discussed. In addition to this, attempt is made to incorporate an exhaustive list of plant species, which have potential for utilization as fruits and are rarely exploited at present. These are confined to only limited localities where people use produces for various purposes and are in most cases little known to other parts of world.

AONLA

Emblica officinalis Gaertn

F: Euphorbiaceae

Aonla is one of the most important minor fruits of Indian origin, which is predicted to be the ‘fruit of the 21^st century’ even though it existed from time immemorial. It is also called as ‘Indian gooseberry’, ‘amla’, ‘nelli’, ‘amlaki’, ‘amali’, ‘ambala’ and ‘amalakamu’ in different parts of India. This species is indigenous to tropical SouthEastern Asia precisely the Central and Southern India. The crop is seen in Sri Lanka, Malaysia and China. In India, aonla is being cultivated on a commercial scale in northern parts comprising Uttar Pradesh, Maharashtra and Gujarat.

AVOCADO

Persea americana Mill.

F: Lauraceae

Avocado, also known as butter fruit gained importance over years as one of the most nutritive fruits. Demand for this fruit increased over the past few years and now it has become an important fruit in international trade.

Original home of Avocado is Mexico in Central America and grows wild all over South America. The Spanish explorers took this fruit to Spain during 1601. It was introduced to Jamaica in about 1650. Avocado was first reported in Mauritius in 1780, Florida in 1833, California in 1856 and Zanzibar in 1892, but its cultivation started extensively in these areas during 1900 (Purseglove, 1974). It was introduced to South and West Coasts of India about 100 years ago from Ceylon. Avocado is now growing in most of tropical and sub tropical countries.

Avocado is grown commercially in USA, Israel, South Africa and Australia. USA, Israel, and South Africa are main exporters. In India, it is mainly grown in South where it is centred on hill slopes of Tamil Nadu, Kerala, Coorg and in selected regions of Karnataka and Maharashtra.

BANANA

Musa paradisiaca L

F. Musaceae

Banana, an antique food crop of the world is known as the ‘Apple of the Paradise’ and botanically named as Musa paradisiaca. Plants of the Musaceae family as a whole are strictly old world plants which are believed to be originated in the hot, tropical regions of S. E. Asia (Simmonds, 1962). Malaysia is considered as the primary centre of origin of M. acuminata (AA and AAA cultivars) and from there, it spread to India and Burma where M. balbisiana is the native. In the IndoBurman peripheral area, natural hybridization of acuminata and balbisiana types occurred and thus India is regarded as a major centre of origin for more the 300 types (AB, AAB and ABB cultivars) out of the 600 types of Musa germplasm. Mention of plantain in Ramayana (2000 BC), Arthsastra (250 BC) and in Chilappathikaram (500 AD) suggests the antiquity and long period of domestication of banana fruit in India. Present day type/cultivars were originated through natural hybridization, mutation and polyploidy breeding and perpetuated through vegetative propagation.

It was introduced to East Africa even before Christ and to the Mediterranean region about 650 AD. It reached the New World in 1516 AD and its cultivation is distributed throughout the warmer countries situated in the region between 30⁰ N and 30⁰ S of the equator. Now banana is grown widely in 130 countries like Brazil, China, India, Ecuador, Columbia, Venezuela, Florida, Panama, Cuba, Uganda, Tanzania, Zaire, Ivory Coast, Kenya, Honduras, Nigeria, Fiji, India, Philippines, Thailand, Indonesia, Sri Lanka, Australia etc. and total (world) area is 88.5 lakh ha with a production of 97.2 million tonnes. Fifty per cent of the global production is from India, Ecuador, Brazil and China.

Fruit crops can be classified into many groups or categories based on certain criteria, which may vary according to climatic and soil requirements, growth habits and of late with consumer rating. Horticultural and botanical classifications are two important types of classification followed in fruit plants. Classification often helps to identify the names and to group the plants. It also gives an account about relatedness among them which further suggest the breeding possibility and grafting compatibility. Different types of classifications followed are discussed here:

CLASSIFICATION BASED ON CLIMATIC REQUIREMENT

Fruit plants are classified based on their climatic adaptability and it is also known as ecological classification. In horticultural point of view, this classification has got much significance. Fruit growers can select crops suited to a particular region by following the demarcations given here. Fruit plants are categorized into the following groups in this classification.

Temperate fruits

Fruit crops need exact climatic requirements for their growth and development, flowering and fruiting. These plants are grown only in places where winter is distinctly cold, they are deciduous and become dormant during this season. Plants should be exposed to specific chilling temperature for certain period for flower induction. These plants are suitable to higher elevations and they can withstand frost. eg. Apple, plum, peach, pear, almond, walnut.

Orchard is a long-term investment and careful planning and resource analysis prior to establishment is essential. Lack of attention and care in the initial stages of orchard development results in irreversible damages. Essential resources for successful orcharding can be broadly grouped into two categories as biophysical and socioeconomical. Biophysical resources include land, soil, agrochemicals, planting materials, irrigation and manpower, while socioeconomic factors are finance, security, market, technical knowledge, transport, storage and social amenities.

Selection of crops and varieties should be done carefully, the most important factor being market demand. Popular fruit crops, which have demand in local markets, can definitely be a good choice. Previous experience and expertise of growers of selected locality can be made use before finalizing plans.

SITE SELECTION

Factors like climate, soil, availability of water, trained labour and inputs like fertilizers and plant protection chemicals should be considered. Accessibility to market, railway station, transport, nearness to road, storage facilities and processing units which facilitate expeditious disposal of perishable fruits, help in getting good returns from orchards. Successful fruit growing in a particular locality depends to a great extent on the natural factors especially climate and soil.

‘FRUIT’, “a food, drink and medicine, neatly packed by nature in attractive, handy and easy-to-open containers”, is a sensible definition indicating significance of fruits in human life. In botanical terms, fruit is a ripened ovary and in horticultural science it is the plant product, which is edible on ripening. From the nomadic age to present day civilized life, man has used fruits as food. Human civilization is irrevocably linked with the culture of fruit plants and trees. References of larges number of fruits in the very ancient literature of different languages throw light to this fact.

Fruits exhibit vast diversity in various forms, shapes and aspects. According to climatic requirements, they are temperate, tropical and subtropical crops. Major tropical and subtropical fruits include mango, banana, citrus, grapes, litchi, pineapple, papaya, sapota, guava, mangosteen, avocado, jack, ber, passion fruit etc. Fruits can be grown in very rich and favourable climatic conditions, but some fruits are adapted to adverse conditions of dessert (date palm), moisture-stress arid zones (aonla, ber, custard apple) and saline regions. Fruit plants vary in morphological traits such as plant size and shape. They may be herbaceous as banana and pineapple, shrubs as cherries and phalsa, small trees as ber and limes, big trees as mango and jack and vines as passion fruit and grapes. Fruits are of different sizes and shapes also. The range is from very small berries of phalsa to very big fruits of durian and jack. Taste wise variation is also very clear in fruits. We have very sweet fruits (litchi, sapota, dates and banana) acidic/sour ones (aonla, tamarind, bilimbi) and fruits with specific sugar/acid blend (varieties of mango, grapes, oranges).