eChapters

Abstract

Cloud computing is becoming a technology mature enough for its use in genome research experiments. The use of large datasets, its highly demanding algorithms and the need for sudden computational resources, make large-scale sequencing experiments an attractive test-case for cloud computing. So far I have seen cloud computing demonstrated using R. However, it remains to be seen a rigorous comparison of its performance using a BLAST search and its ability to cope with ever-increasing databases and open source frameworks such as bioperl or bioconductor.

“Knowledge Management is the process by which an organization identifies, creates, manages and delivers information to enhance workforce performance. The purpose of knowledge management is to provide information collected from employees, best practices, clients, competitors and other sources in a format that employees can use to the productivity and quality of their work”

Before attempting to address the question of knowledge management, it’s probably appropriate to develop some perspective regarding this stuff called knowledge. Consider this observation made by Neil Fleming [1996] as a basis for thought relating to the following points.

Now days, in every walk of our life, we deal with a lot of information. It can be for personal use or family matters or for official or business matters. We store, process and retrieve variety of information. Information is basically the collection of various facts, records, statistics, formula or methods, which we use for our official work, for our research or for other use. When all these (information, we keep/ accumulate, for possible future use) are put in an organized manner, we find it convenient to use and easy to remember/ apply. Today, as it is rightly said, information is power; information is our knowledge-strength. It is thus important to organize and manage this knowledge that mostly depends on (and derived from) an information pool.

Introduction

Individual bits or “bytes” of “raw” biological data (e.g. the number of individual plants of a given species at a given location) do not by themselves inform the human mind. However, drawing various data together within an appropriate context yields information that may be useful (e.g. the distribution and abundance of the plant species at various points in space and time). In turn, this information helps foster the quality of knowing (e.g. whether the plant species is increasing or decreasing in distribution and abundance over space and time). Knowledge and experience blend to become wisdom—the power of applying these attributes critically or practically to make decisions. This quotation is from the Atlantic Canada Conservation Data Centre, a non-profit organization established in 1999.Thus, we are led to think about Data, Information, Knowledge, and Wisdom as we explore the capabilities and limitations of IT systems.

Many techniques are used in immunology to detect specific proteins (antigens) or antibodies in biological samples. These techniques are called immunotechniques. These methods are used for research and diagnostic purpose in many fields such as microbiology, biochemistry, endocrinology, hematology and in pathological laboratories. The techniques can be used to estimate proteins, drugs, hormones and toxic substances in a sample. Immunological techniques are highly specific, precise and reliable. These methods are simple and safe. Antigen and antibody reaction is highly specific in nature and this forms the base of the immunological methods. There are many immunotechniques which are used for the qualitative and quantitative estimation of antigens and antibodies in a sample. Some of commonly used techniques in immunology are:

One of the characteristics of the immune system is to recognize and discriminate self from the non-self antigens.  But, sometimes, there is a failure to discriminate between self and non-self antigens in the body and an autoimmune response occurs. Body starts producing antibodies against its own cells/antigens. These antibodies are called autoantibodies and this state is called autoimmunity.

The well-being of a person depends on his immune system. Any deficiency in any component of immune system may lead to defects in the normal functioning of his body and makes him more susceptible to diseases. The immunodeficiency may be either in specific components (B cells or T cells) or nonspecific component (phagocytes and complement) of the immune system.

A tumor is said to be an abnormal growth of cells to form a lump or mass of transformed cells. This growth occurs due to loss of regulatory control of cell division. The majority of cells and organs have a balance between cell renewal and cell death. A cell has a particular life span;when it dies a new cell is generated. In normal condition, this system is regulated through cell cycle and cell division but at the time of any abnormality this growth mechanism is totally disturbed and failed. These cells give rise to clone of the cells and eventually produce tumor.

Transplantation refers to the implantation of a tissue or organ from one site  to another site in an individual or from one individual to another.It involves implanting of organs or grafting of tissues to repair defects and to stimulate regeneration. Auto-transplantation or autoplasty of the skin, cartilage, bone, muscle, tendon, nerve and fatty tissue is used in plastic and cosmetic surgery. The replacement of a diseased organ by a transplant of a healthy tissue is called transplantation.

Immunity is defined as the resistance to infection. This is carried out by the process of identification and removal of non-self material. In contrast to this, our body has to maintain immune tolerance to our own cells and tissues and develop the ability to distinguish these self-antigensfrom non-self (foreign) antigens. Tolerance means unresponsiveness of the immune system to an antigen. Immune tolerance is the process by which the immune system does not destroy an antigen. Tolerance can be either natural or induced.

One of the greatest achievements in science is the development of vaccines. Vaccines have been revolutionary for the prevention of infectious diseases. They have prevented a large number of deaths caused, every year, by dreadful diseases like smallpox, polio, hepatitis etc. Diseases like smallpox and polio have been successfully eradicated by vaccination. Normally, when the body encounters a microbe, both humoral and cytotoxic immune responses are induced to neutralize its effect. In addition to eliminate the invader, body forms memory cells which help the body to protect itself from the same pathogen, in future. Vaccines not only function to kill the pathogens but they also stimulate the body to form memory cells which provide immunity against a specific pathogen

Infection refers to the invasion of harmful microorganisms into the body and causing disease. The most important function of the immune system is to protect the body of the host against various viruses, bacteria, fungi and parasites. The grounds of immune surveillance stand on the basis of innate and specific immunity that build up against the evasive mechanisms of the disease causing organisms. Infectious disease is result of a complex interaction between  the host and the microbes. Evasions of protective immunity by the parasites critically determine the survival and pathogenicity of the microbes. The invasion of the body by harmful microorganisms is called infection. Infections are dangerous in any part of the body. Microorganisms spread vary easily into the blood stream and cause blood poisoning which is called septicemia.

The immune system has been designed to provide protection to the body from various diseases. But the same system which is aimed to provide protection may sometimes become harmful to the body and may even life-threatening. There are situations when immune response against harmless and inert antigens is exaggerated and actually causes diseases. Such a condition is called hypersensitivity or commonly as allergy. Though the term ‘hypersensitivity’ indicates an increased response but the immune response is not always heightened, instead it may be an inappropriate response to an antigen.

Cytokines are the chemical messengers that are involved in interactions between the cells of innate and adaptive immune responses. They are secreted by leukocytes and many other cells in the body. They are low molecular weight proteins or glycoproteins which are produced in response to various kinds of stimuli. Cytokines have important role in immune and inflammatory responses.  Their functions are not limited to immune system only.They also stimulate the development of hematopoietic cells and also act as therapeutic agents.

Major Histocompatibility Complex (MHC) is a closely linked cluster of genes which have codes for cell surface proteins known as  MHC molecules. These molecules have very important role in presentation of processed antigens to the T cells in initiation of an immune response as T cells recognize an antigen only when it is presented along with MHC molecule. These are highly polymorphic and are the major barrier to organ/tissue transplantation. All vertebrates have MHC. MHC differs among members of a species and are thus called alloantigens. MHC participates in the development of both humoral and cell-mediated immune responses.

The complement system is a group of about 20 heat labile plasma proteins which constitute nearly 10% of total serum proteins. These are important in activation of phagocytes, control of inflammation and cytolysis. They form one of the major immune defense systems of the body. The complement system plays important role both in innate and adaptive immune system. The main functions of complement are chemotaxis; opsonization and cell activation; immune clearance of immune complexes from circulation; lysis of target cells; triggering and amplification of inflammatory reactions and development of antibody responses. Evolutionary, the system is very ancient and is present even in invertebrate organisms like starfish and worms.

Cell mediated immune response performs different functions in protecting the immune system. When antigens are destroyed by cells, without producing antibodies, the immunity is called cell-mediated immunity (CMI) or cellular immunity. In this immunity T cells play a major role. The principal role of cell mediated immunity is to detect and eliminate the cells that have intracellular pathogens. When the antigen remains inside the cell the antibody cannot handle them. The intracellular pathogens are controlled by cell- mediated immunity. CMI is invited by the recognition of antigens by T cells. T cell lymphocytes recognize protein antigens of intracellular microbes that are displayed on the cell surface of infected cells. It is also important for elimination of cells which express foreign MHC molecules. Antigen specific and nonspecific cells can contribute to the cell-mediated immune response. The activities of both specific and non-specific components usually depend on effective local concentration of cytokines.

The immune system protects the body from harmful substances by recognizing and responding to antigens. Antigens are the protein molecules which are present on bacteria, virus, fungi or some other microorganisms.Some toxins can also be antigens. These antigens are recognized by immune system. The destruction of antigens by producing antibody is called antibody-mediated immune response. As antibodies are present in the body fluids i.e. humors,this type of response is called humoral immune response.

All blood cells arise from a basic cell called the hematopoietic stem cell. Stem cells are undifferentiated embryonic cells.They are self renewing and their population by cell division. Stem cells have the ability to develop into any type of blood cell. The formation of blood cells begins in the embryonic yolk sac during the first week of development. Every mature cell is derived from the same type of stem cell. In contrast to an unipotent cell which differentiates into a single cell type, a hematopoietic stem cell is multipotent or pluripotent. In the mammalian embryo, the blood corpuscles are normally formed in yolk sac, liver, spleen and thymus gland.

Antigen-antibody interaction is very specific one in which an antibody recognizes an antigen through complementarities of shapes on paratope and epitope.  It is like lock and key, as occurs in case of enzyme-substrate reaction. It does not involve covalent linkage rather a spatial complementarity occurs between antigen and antibody. For example, when antibodies, raised against m-amino benzene sulphonate, are tested for their ability to bind with ortho-, meta- and para-isomers of the hapten, the antibodies show highest strength with meta than ortho- isomer.  Antibodies show poor reactivity with para isomer. This is because though chemically all these molecules are same but structurally they are different.

Antibodies are a group of glycoproteins having a globular compact structure. They are known as immunoglobulins. On the basis of their experiments, Tiselius and Kabat, in 1939, demonstrated that most antibodies are found in the g globulin fraction of serum proteins. When serum from rabbit, immunized with ova albumin, was subjected to electrophoresis, it showed a peak for g globulin (Fig. 4.1). Studies have revealed that the major part of IgG is found in the g globulin fraction of the serum proteins. Other fractions, a and b, too, have other immunoglobulins along with small part of IgG.

The main purpose of the immune system is to protect the body from foreign substances, diseases or infections. When the body is exposed to a microbe or a foreign substance (antigen), the body makes some response which is called immune response. The purpose of immune response is to recognize, neutralize and eliminate the antigens from the body. Generally, the term immunogen is also used for antigen. Both, antigen and immunogen are used as synonyms but specifically, they are different from each other.

Like any other organ system in the body, immune system comprises of various organs and cells. The major component of the immune system is the lymphocytes which constitute lymphoid system. The lymphoid organs are classified into two categories: primary and secondary lymphoid organs.

Primary lymphoid organs: These are the organs where B and T lymphocytes undergo maturation. Bone marrow and thymus are the primary lymphoid organs. These are the organs where lymphocytes differentiate, proliferate, get selected and mature into functional cells.

Everyone on this earth wishes to have a healthy life free from all ailments, stress and strain. But it is a common observation that some of us are more susceptible to diseases and fall victim of many infections while others have the capacity to resist many such infections. They are not so much susceptible to diseases. Is there anything which distinguishes them from others? An organism is made up of organs and organs systems. Like many other organ systems, in the body there is a system which is concerned with the protection of the body from infections.

Reducing insecticide application to the lowest level is the motto of IPM in vegetables. Monitoring for the initial build up and timely mechanical removal of the first population is a must in vegetables. Always remove the first affected plants, by diseases like mosaic, and destroy them by burying or burning. Remove insect eggs, insect affected plant parts and adults and immature stages of insects, and destroy them every day. Do not throw them in the field. They will either come back, or pupate and attack later. During nursery stage, use wood ash, cow dung solution, and plant extracts to deter all pests. Use only low residual insecticides like Dichlorvos 1ml/l, Malathion 2ml/l, Endosulfan 2ml/l or Quinalphos 2ml/l, in spots, at the beginning of attack itself.

Fruit borer: Helicoverpa armigera: Noctuidae

This is a medium sized moth yellowish brown in colour with a wing

span of about 3 cm and a body length up to 1.4 cm. There is a dark speck and a dark area on the outer margin of each forewing. The forewings also have greyish wavy lines and black spots of different sizes on the upper side.

Sciarid(mushroom flies): Bradysia paupera, Lycoriella auripila: Sciaridae

The larvae feed on the mycelial attachments and restrict the growth of the spawn. The maggots also feed on the developing mushrooms or pinheads and thus cause loss in yield. They also bore the developing mushrooms and render them hollow.

Fruit flies: Bactrocera cucurbitae:Tephritidae

This pest is more serious in bitter gourd, snake gourd and to a certain extent on ridge gourd. Other cucurbits are attacked to a lesser level. Damage by this pest causes losing the fruit quality, rotting and fruit drop. The adults lay many eggs inside the fruit sing their big ovipositor that hatch out into worm like apodous maggots. Feeding by the maggots on the pulp of fruits result in rotting, yellowing and fruit drop. The dropped fruits allow pupation by the maggots in the soil from where they emerge out as adults and start egg laying on fresh frits.

The cowpea aphid: Aphis craccivora: Aphididae

Hosts
 
Groundnut, red gram, peas, beans, safflower, lab-lab niger

Symptoms of damage
 
Both nymphs and adults cause the damage by sucking the plant sap from shoot tips, pods and leaves.  Infested pods become malformed and withered.  Severe infestation may result in complete drying of affected pods.  They also act as vector of virus diseases in pea. 

Chilli thrips: Scirtothrips dorsalis, Thrips palmi: Thripidae

The adults of this insect are small brownish black with fringed wings. The nymphs are slender and yellowish straw coloured, later acquiring more brownish hue. They lacerate the tissues and feed on the exuding sap. Leaves become crinkled, curled upward and shed. The attack can be confused with chilli mosaic symptom.  In capsicum and chilli, they also feed beneath calyx of flowers and fruits causing flower/fruit drop and reduction in yield and market value of capsicum. Buds become brittle and drop down. Plants get stunted and bronzed. The fruits if at all formed are crinkled and small.

Diamond back moth: Plutella xylostella: Plutellidae
 
The adults of this moth are small, greyish brown having pale whitish narrow wings and with inner margins yellow. There are three pale whitish triangular markings on hind margins of each forewing. At rest, when both forewings come together, they form a dorsal median patch of three diamond shaped yellowish white spots that give them their name diamond back moth. Hind wings have a fringe of long hairs.

Shoot and fruit borer: Leucinodes orbonalis: Pyraustidae

The pest is active throughout year, but more during monsoon period. Heavy losses up to 60% can occur.

The adult is a greyish brown medium sized moth with white and hyaline wings, having triangular brown and red markings on forewing. A crescent shaped mark facing outside at the apical margin is typical for the species. About 150-250 creamy white eggs are laid singly on leaves, tender shoots, flowers and developing fruits. Egg period is 3-5 days and the hatched larva completes its life in 15 days with 5 instars.

Shoot and fruit borer: Earias vitella (=E.fabia), E. insulana: Noctuidae

This is a pest on cotton, bhendi, hibiscus, holly hock and other malvaceous vegetables. The damage is due to the larva that bores into tender terminal shoots in the vegetative stage and flower buds;  flowers and young fruits in the fruit formation stage.  The damaged shoot drops, wither and dry up.  The infested fruits have bore holes, are deformed and become unfit for consumption.  Bore holes are plugged with excreta.

Amaranthus stem weevil: Hypolixus truncatulus :Curculionidae
 
It is an important pest of amaranthus and is widely distributed in India. It attacks both wild and cultivated amaranthus, especially the leafy varieties with large leaves. Hence, management involves destruction of unwanted, weedy wild amaranthus plants, to reduce the breeding place for the weevil. Adults are ash-grey in colour, with elbowed antennae and brown elytra. Females lay eggs singly in holes made on the stem, branches, petioles or midribs. Eggs are smooth, oval and pale yellow in colour. Incubation period is 3 to 8 days.

Sweet potato weevil: Cylas formicarius: Apionidae

It is a specific pest of sweet potato and the most important one. Adult weevils are ant-like, slender bodied having elongated snout-like bluish-brown head with geniculate antenna, bright red thorax and leg tips and bluish-brown elytra. Females make small cavities on the tubers or stems and lay eggs singly. Each female lays 180-200 eggs. Grubs are elongate, legless, pale-yellowish white in colour with smaller brown head. Pupation takes place in larval tunnels in the tuber. Incubation, grub and pupal stages last for 5 to 8, 14 to 17 and 4 to 5 days respectively. Life cycle is completed in 4-5 weeks and adults live for 95-110 days. The grubs bore into stems, tunnel inside and feed on soft tissues. Grubs and adults bore into tubers both in field and storage godowns. Affected tubers develop dark patches, which later start rotting. Feeding holes and adult emergence holes can be seen on vines and tubers.  In severe infestation the collar region of the plants shows unusual thickening due to proliferation and hypertrophy of tissues causing a characteristic terpenoid odour.  Even the slightly damaged tubers are unsuitable for cooking and consumption.  Hence yield loss in practice may come to 100% in many cases.

Aphids: Myzus persicae, Lipaphis erysimi and Brevicoryne brassicae Aphididae
 
Aphids suck the sap from potato foliage, causing wrinkling, cupping and downward curling of young leaves. The older leaves will become yellow, wilt and fall off.  They also excrete honeydew on which sooty mould develops covering affected parts with a thin superficial black coating that hinders photosynthetic activity of leaves resulting in stunted growth of plants. In addition, they also act as vectors, for transmitting potato leaf roll virus. Major damage by M.persicae and A. gossypii is through transmission of potato leaf roll virus.

Leaf-and shoot folders: Hymenia recurvalis : Pyraustidae

Pycnarmon cribrata;Phostria piasusalis

Cassava scale : Aonidomytilus albus: Diaspididae

White elongated scales appear in colonies on stems. Plants die in the field and under storage.  Stem becomes weak and dry, causing side branching to give bushy appearance.  Viability of planting material is reduced, resulting in poor establishment.

Aphids: Aphis gossypii :Aphididae

The aphids congregate on growing points and suck the sap. Honey dew secreted by the aphids can cause sooty mould in severe infestation. Attack leads to yellowish speckling and curling of leaves.
 
Thrips: Caliothrips indicus: Thripidae

Characteristic silvery white specks with black dots which are mostly faecal pellets, develop on leaves. Consequently, the leaves dry up.

Pollu beetle: Longitarsus nigripennis:Chrysomelidae

This pest is monophagous to pepper and no alternate host has been reported so far.

Nature of Damage

Adult is a shining blue flea beetle with yellow head and thorax and has thick enlarged femur and tibia. The adult beetle is only the size of a pin head.  The infested berries dry up and turn dark in colour. Berries become hollow and crumble when pressed and such hollow berries are called “Pollu” meaning empty. The eggs are laid on the berries @ 1-2 eggs in each hole. Eggs hatch in 5-8 days. The grub period extends for 30-32 days. The emerging grubs feed on the berries of pepper and consume the internal contents.

Thrips: Thrips tabaci: Thripidae

The nymphs and adults of the thrips desap from the narrow spaces between the inner leaf axils. Leaves are faded, with curled tips and shining silver streaks or brown spots.  Many minute yellow or white insects are seen moving, generally near the base or middle of leaves and they suck the sap from the plants.  Plants are faded and the yield is reduced.

Scale insects:Pseudaulacaspis cockerelli, Parasaisettia nigra:Coccidae

Attack Adults and nymphs feed on plant sap and cause wilting and drying of seedlings and young plants.
 
Brown soft scale: Lecanium sp. (=Coccus) hesperidum : Coccidae

Grasshoppers: Mecopoda elongata :Tettigonidae; Oxya velox: Acrididae

These pests occur both in nurseries and plantations. Both adults and nymphs feed on leaves by scrapping and eating outer tissues and margins. The emerging leaves are nibbled and the spot holes appear when the leaf unfurls. In severe conditions the entire leaf is eaten leaving behind only the midrib.

Shoot borer: Conogethes punctiferalis: Pyraustidae

The main damage done by the caterpillar of this pest is to bore holes in the pseudostem and to plug it with excreta, causing dead hearts. Larva is pale greenish with pinkish tinge and dark head and has fine hairs on the body with a pro thoracic shield. Adult is a medium sized moth, pale yellowish with small black spots on the fore and hind wings.

Management involves spraying dimethoate or malathion 1.5 ml/lit or phosphamidon 0.75 ml/lit of water. This is mainly intended to manage the adults flying in the crop canopy and the first instar caterpillars that are seen on the outside of the plants and before thsy enter the pseudostem. The spray has to be given at the very first spotting of dead haearts.

Coriander aphid: Hyadaphis coriandri: Aphididae

Coriander aphids are yellow-green in color, dusted with grayish wax. They have short, dusky, slightly swollen, siphunculi (or cornicles). The Aphids form dense, damaging colonies on leaves, heads, and stems of their host plants.

In its native land, Florida, USA, the life cycle of the coriander aphid is similar to that of other host-alternating aphids. Overwintering eggs occur on other hosts.  A fundatrix (or stem mother) hatches from the egg in the spring. Her offspring are parthenogenetic, and the winged-females are spring migrants. They colonize summer host plants in the family Umbelliferae.

Stem-borer: Sahyadrassus malabaricus: Hepialidae

Presence of the pest is understood when chewed tissue is seen at at the col­lar region. The mouth of the tunnel in which the borer feeds show pieces of bark, wood and frass particles held together by silk. The saplings break off at the point of injury. When the main stem is attacked, there is mat-like frass at basal region of stem. Larvae girdle main stem and bores downward killing the tree.

Adult moth is peculiar and hangs vertically down by the support of two pairs of legs. Egg period is for 7-10 days, and larvae live for about 10 months inside the larval tunnels. They pupate for 3-5 weeks.

Cinnamon butterfly: Chilasa clytia clytia : Papilionidae

Larvae defoliate plants. The larvae are pests on many crop plants and weeds and are common in the plains. The larvae are jet black at hatching. They develop a series of broad white patches. The adult is a common butterfly rich velvety brown, and spotted with white dots. The hind wings have arrow shaped streaks and crescent shaped spots.

Cardamom thrips: Sciothrips cardamomi: Thripidae

Thysanoptera

This thrips attacks other crops like amomum,  tea, colocasia, grapevine, castor, cotton, ginger and turmeric also. The thrips are minute greyish brown insects with fringed wings. They breed on unopened leaves, spindles, leaf sheath, flower bracts and floral tubes .

Scale insect: Lepidosaphes sp.: Diaspididae

The mature scale is elongated and oval in shape and dark grey in colour. They infest the stems, leaves and petioles, causing shriveled leaves due to sucking of the sap. The affected parts wither and dry up. In severe infestation leaves dry up and give sticky look and gradually the vine wilts.

Tea tortrix/flushworm: Homona coffearia:Tortricidae

The tortrix is  an important pest of tea leaves. The larvae make leaf nests by webbing the leaves using silken threads and feed from inside. A single caterpillar makes several cases. Young larvae prefer tender leaves, while the older larvae are seen in mature leaves. The economic produce being the leaves, and since chemical control is not advised, especially during the picking phase, the pest becomes a management problem.