eChapters

Principles to create effects

Balance

It is a visual equilibrium of different garden elements.

Formal Garden : Balance is achieved by positioning plants, other landscape objects at equal distance from a real (or) imaginary plane (or) axis.

Informal Garden : Balancing is mainly a neutralizing effect. (eg.) Opposite colours in the colour wheel, contrasting texture, different numbers, shapes, forms, line and pattern are cleverly employed to neutralize one another.

Proportion

It refers to the share of the different parts (or) components to the whole. It refers to all ingredients being mixed in right measure, not essentially in equal measure.

1. House Plant

The screwpines or kewda plants are characteristics of many tropical regions with long ringed trunks, bracing roots and crowns of Dracaena-like foliage. The young plants are amongst the most popular foliage plants for home decoration as the plants do not flower at early stages (Wickham, 1950). They are also grown as pot and tub specimens for green house, residence, veranda and lawn decoration where their stiff clustered foliage gives them a formal decorative character. They may be kept as indoor ornamental foliage plants in the warm and semi light places of a house. (Wickham, 1982a).

2. Fence

The plant is useful for binding the soil, so checks soil erosion and not browsed by the cattle due to its spiny leaves; hence sometimes used as fence around the crop field in the coastal districts of Odisha, Andhra Pradesh, Tamil Nadu, Kerala and Gujrat. The plants are often used for hedges as in the Casuarina plantations at Puri of Odisha (Haines, 1961a) (Fig. 17).

Kewda plants are mostly propagated through vegetative means. The common propagating materials used are ground suckers. The planting materials are planted in paired-row method maintaining a spacing of 4m from plant to plant and row to row keeping a spacing of 6 m between paired rows. In a field of one hectare, a minimum plant population of 500 plants in the field and 150 plants on the field bunds with a total of 650 plants are maintained. A fertilizer dose of 30:15:15 kg NPK/ha and 4 cartloads (100 cft) of FYM/ha are applied. The planting of collected ground suckers is normally done in the field just before monsoon after thorough land preparation under rainfed condition.The earthing-up of the plants are done up to five years of planting for quick initiation of flowering at the age of 5 years after planting. During the first year, the operational cost per hectare comes to Rs.28,900/- and from 2^nd to 5^th years, it comes to Rs.6,600 per year and then the maintenance cost from 6^th year onwards comes to Rs.6,000/- per year. The details of the operational cost per hectare of kewda cultivation under rainfed condition of coastal Ganjam district is given at Table 23. Kewda plant comes to flower on the 5^th year of planting, but the annual net profit begins on the 6^th year of planting and the cumulative net profit starts on the 10^th year (Table 24). The economic viability of kewda plantations is observed from 10^th to 30^th year of planting and after 30^th year, the net profit declines. A farmer can earn an annual profit of Rs.61,000/- per hectare of kewda cultivation from 11^th to 15^th year, which goes on increasing and from 26^th to 30^th year, the annual net return reached to Rs.1,23,400/- with a cumulative return of Rs.4,04,970/- on the 30^th year of planting. Then at the age of 35^th year, it declines to Rs.1,07,800/ - and at 40^th year to Rs.87,000/- per annum (Table 24). Although the profit was calculated only on the basis of sale of flowers yield, some additional profit can be obtained from other plant parts like leaves and stilt roots. After distillation of one lakh flowers, the spent over flowers and plant parts can be utilized as fertilizer/manure by selling at a rate of Rs.1000/- per batch. In the two blocks (viz., Chhatrapur and Rangeilunda) of Ganjam district, about 7,000 women are engaged for collection of flowers, leaves and stilt roots and they prepare ropes and other household items from the roots and leaves. It has been observed that one female can prepare 12 bundles of ropes each of 12 m length and the sale rate of rope is about Rs.10/- per metre. The ropes are sent to the markets of Visakhapatnam (Andhra Pradesh) and Chennai (Tamil Nadu) for sale. The profit can also be increased by incorporating some inter-crops like Casuarina, coconut, Agasti and medicinal crops like Patchouli etc. Further, kewda can be taken on the sand dunes and waste saline land of the coastal lines, where no other crops can be grown profitably. Hence, kewda needs better attention for its extensive cultivation with a foresight on the perfume industry.

The world trade in flavour and fragrances in 1987 was US $ 7,000 million and at present, it is estimated at more than $ 10,000 million annually. In 1975, perfume was used by one woman in ten, but today it is used by eight out of ten women; even reticent Japanese women are adopting the habit (Anonymous, 1995 c). The average annual industry growth rate in perfumes of India is valued at about US $ 20 million with an annual growth rate of 12% (Murty, 1993),while the UK market is Rs. 2000 crores and the US market supersedes it by Rs. 4000 crores (Walia, 1997). However, the domestic luxury perfume market is estimated to grow at a rate of 20-25 % (Biswas, 2012). Besides domestic market, India earns a lot of foreign exchange from the export of total essential oils and perfumes and is fast growing as it is showed from the trends in export earnings of Rs. 11.1 corers in 1982-83 rose to 4-fold in 1986-87 of Rs. 41.1 crores (CHEMEXCIL, 1988). According to a market survey report, Ahmed (1999) reported that the daily turn over of the attar market in India is more than 50 crores.

Middle East countries continue to be the big buyers of our traditional perfumes. Kewda flavour which is used in pan masala and tobacco is a familiar one in this part of the world. Kewda essence, being one of the few flavouring oils, has a good scope for export to other developed countries where the food flavouring industry is well developed. India is the leading producer of kewda perfumes in the world and the market for kewda perfumes is fast expanding specifically in the Arab countries. India exported the kewda water of Rs. 266.2 lakhs in 1986-87 which rose to Rs. 276.4 lakhs in 1987-88 (CHEMEXCIL, 1990). Anonymous (2007) reported that about 140 distilleries (bhattis), both local and outsider, earn about Rs.1.3 crore by way of extraction charges and annually they extract 332 kgs of kewda oil (Rs.8.3 crore), 7823 kgs of kewda attar (Rs.15.65 crores) and 150 MTs of kewda water (Rs.4.47 crore), the total coming to around Rs.28 crore. For extracting attar , the extractors use about Rs. 8 crore worth of sandal wood oil procured mainly from other states, while Rs.18 crore goes to the plantation owners as flower cost and to the flower collectors.

French author Jean Giono once remarked, “The God creates the Odours, but the men manufacture the perfumes”. In today’s world, fragrances play bigger role than just being associated with a tiny bottle of liquid. It now serves the larger purpose of linking itself with anything you can imagine, from soaps to your favourite sweater knitted by your grandmother (Biswas, 2012). In the modern day, these products find their applications in items for personal sophistication to culinary delights and beverages, to a host of industrial products (Dev, 1993). India, a country known for its vast range of fragrant flowers and herbs, has used extracts from such raw material to produce incense sticks, medicines, body massage oils and sweet savouries.

The word ‘perfume’ is derived from the Latin term ‘perfumen’, meaning ‘through smoke’. Perfume is a fragrant liquid mainly distilled from natural oils, aromatic chemicals and resinoids; cologne is a lightly scented liquid used to cool the skin and deodorant contains chemicals to counter offensive body odour. Perfume is basically used by women, cologne by men and deodorant by both (Saha and Sareen, 1997). Throughout antiquity there was a continuous demand for incense, to mark the rites of scenting passage from birth to the grave, for the daily rituals of incensing rooms, linen and clothing. The South Asian synonym for perfume, ‘attar’, on the other hand, is derived from the Arabic word ‘aettr’ meaning ‘fat’ or ‘extract’. Almost all attars are basically aromatic oils extracted from flowers, plants and herbs through steam distillation. Some fragile flowers and oils that can not stand the heat of distillation are, however, crushed and the oil expelled by mechanical force (Mahmud, 1992).

Kewda plants are hardly attacked by the insect pests and diseases. However, a few fungal and bacterial diseases are found to reduce the yield of flowers significantly. Some important insect pests and diseases of this plant with their nature of damage and suggested control measures are discussed here as reported by Jagadev et al. (2001).

Pests

1. Bag worm

During the dry season, leaves are found to be attacked by bag worm (Manatha albipes; Fam. Psychidae; order- Lepidoptera) (Plate 36). The larva, a foliage feeder, feeds on the chlorophyll and veins of leaves leaving the mid-rib resulting in perforation of leaves. In case of heavy infestation, the leaves become dry. Extensive damage arrests the vegetative growth resulting in significant reduction of flowering. Thus, the insect is considered to be of economic importance, but till date neither the extent of economic loss caused to the crop nor its control measures have been worked out.

The volatile oil in the flower determines the odour and flavour of kewda and it has been of particular fascination to the chemists. There are only a few reports on the chemical composition of kewda essential oil (rooh or otto) Dhingra et al. (1954) distilled the kewda flowers collected from five places of Ganjam (Odisha) and Ghazipur (Uttar Pradesh) districts. He found the oil yield to vary from 0.015 to 0.031% and the compounds identified were methyl ether of β- phenyl ethyl alcohol (65.97%), d-linalool (18.70%), dipentene (8.31%), phenyl ethyl acetate (3.48%) and citral (1.82%). The oil was of light to golden yellow in colour having the following physico-chemical properties viz., specific gravity (d20o) 0.932-0.958; refractive index (n20o) 1.485-1.491; optical rotation ([α]D) + 1.350 to + 2.080; acid value 1.4 – 6.7; ester value 15.9 – 40.9 and soluble in equal volume of 80 % alcohol (Deshaprabhu, 1966). Sadgopal (1959) also reported the major constituent of oil as methyl ether of β-phenyl ethyl alcohol (65 – 80%) and minor constituents as dipentene, α-linalool, phenyl ethyl alcohol, citral and some terpene esters.

According to Chandra (1985), the oil contained dipentene (6.0%), d -linalool (19.0%), phenyl ethyl acetate (4.6%), citral (1.8%), caproic acid (0.5%) and stearoptene (0.2%) besides the major constituent methyl ether of β-phenyl ethyl alcohol (67.0%).

Kewda plant occurs wild in the entire coastal belt of Odisha , but abundant in Chhatrapur and Keluapalli areas of Ganjam district. There were about 3-4 lakhs trees of kewda in Ganjam district (Deshaprabhu, 1966). Main season of flowering starts from July-August and lasts for 2-3 months and a few flowers also come during November-December and March-May (Haines, 1961). Averagely, a plant produces 15-20 flowers per season depending on branching of the tree (Plate 32). A fully matured tree bears 30-40 spadices in a year (Deshaprabhu, 1966). Flowering is also dependant on rainfall, being better in years of high rainfall. Size of flower is bigger during rainy season. The spadices take a fortnight to mature, depending upon the weather condition. Ripe spadices, creamy in colour, give higher yield of perfume and of better quality than immature ones (Plate 33). The kewda flower of Ganjam district is also registered under the geographical indications (GI) of goods (Registration and Protection) act (Panigrahy, 2019).

In practice, flowers are collected from wild plantations. Recently kewda has emerged as one of the important commercial commodities. A systematic cultivation practice is essential to develop a successful plantation and to increase the productivity.

Planting

Kewda suckers or crowns are generally planted during June-July. i.e. in the beginning of the monsoon, when the soil is not too wet. Planting in wet soil delayd the root formation and reduces the success level. Just after the first shower of rain or during the summer shower close to monsoon, kewda is planted.

In a full grown plant, stilt roots originate at a few feet above the ground to render a support for the huge canopy of the plant. Each part of the stem is capable enough for development of root initials, but it is retarded once the stem became old and leafless. The root initials develop at the terminal portion, where more leaves cluster, but they do not grow. Hence, the stem cuttings collected from the flowering or non-flowering shoots bear the rudimentary roots and when planted, they establish quickly.

In practice, the cuttings are collected and scattered on the ground for two to three days. Before planting, a few leaves closed to the base of the cuttings are removed to expose the root development sites. The cuttings are planted in trenches of 45 cm depth horizontally or at an angle of 30^o. The new leaves appear on the growing points one month after planting.

Kewda plants are usually planted on the field bunds for fencing and subsequently used for collection of flowers. A 30 years old plant can produce a crown of 6-7 m, for which it is difficult to develop a commercial plantation in a close spacing. It has been observed in the natural plantations that the plants may be spaced at 8-10 m distance to achieve a full length of plantation life. It is, therefore, suggested by the authors to follow a paired row method of planting maintaining a spacing of 4 m between plants and rows of a paired row and 6 m between two paired rows; which provides all facilities for plant growth upto 10-12 years and then pruning of a few branches are required. Hence, a plant population of 500 plants in the field and 150-200 plants on field bunds are maintained in a land of one hectare.

Kewda is exclusively propagated through ground suckers and leaf bearing terminal cuttings. In kewda growing areas, predominantly the terminal shoot cuttings are used in commercial plantations. However, the seeds are also capable to germinate and give rise to plants, but it is not in practice due to hard mesocarp and seed coat (Bailey, 1950, Deshaprabhu, 1966, Mott, 1975, Maharana and Jagadev, 1993).

Seed propagation

In kewda, the flowers develop into berries, which fuse to form a multiple fruit. The receptacle and bracts are included in the fruit. The seeds are deep seated and very difficult to extract, hence seeds are sown along with the fibrous drupes. Each drupe contains 2-9 seeds. Seeds collected from ripe fruits are sown during spring. The seeds normally, take about 3 months for germination due to the hard seed coat and impervious fibrous covering. Experimentally, it was observed that one hour sulphuric acid scarification treatment of the drupes reduced the germination period by about one month increasing the germination percentage as compared to direct sowing, however, scarification for more than one hour was deterimental (Table 14) (Maharana and Jagadev, 1993). Bailey (1950) reported that seed soaking in tepid water for 24 hours would aid the germination. The seed propagated plants (Plate-27) take about 2-3 years more for flowering as compared to vegetatively propagated plants.

Soil

Soil has a pronounceed effect on the plant growth and productivity in kewda. Well drained sandy-loam soil with adequate supply of moisture is best suited for its vigorous growth and flower production. Thickly distributed profitableKewda plantations with normal flowering are found in the lateritic belts with deposits of silty loam soil and adequate moisture supply. In heavy clay soil with inadequate moisture supply, the plants grow vegetatively with poor flowering. At places close to the Bay of Bengal like Rangiagarh, Kujang, Paradeep of Jagatsinghpur district, where a silt-loam soil deposit is found over the clay zone, the dense plantations of kewda with free flowering ability are noticed. But surprisingly, the female plants are more at few places close to the Paradeep port, which may be due to seed propagation by drifting of ripe fruits from the uplands; while in Ganjam district, the farmers are used to plant the selected male plants in their field resulting in high flower production.

The tentative age of the natural plantations is estimated from the rates of leaf production, stem and branch growth (5-50 cm / year) and development of branching pattern (primary and secondary) in conjuction with the interactions made with the local farmers of kewda (Fig. 9). The plants of different age groups (1 to 5 years) are observed for growth characters and flower production at Tulu of Ganjam and Konark of Puri districts under farmers’ field condition and it is observed that the initiation of flowers started at 5 years of age and the rate of flower production was 1.7 to 2.2 per plant (Table 9).

No breeding work has so far been done on kewda except selection of some promising morphotypes. Varietal improvement in kewda by breeding poses problems mainly due to dioecious nature and long life cycle of the plants, besides heterozygosity. Lack of promising strains is a major drawback. The wild growing population of kewda has a measure of variation and this has never been documented and utilized, which naturally offer a good scope for improvement of kewda by resorting to selection and subsequently propagating them vegetatively. Since a wide range of variation is available and the plants are mostly propagated by vegetative means, it is worthwhile to collect genetic stocks, access variability in morphological characters and attempt a breeding programme after selecting the desirable types for high flower production as the ultimate economate economic value of the plantations depends on the quantity of flower production to be used industrially in the distillation units.

The screwpines are tropical shrubby plants grown for the highly scented flowers or the ornamental foliage. The ornamental foliage types are generally cultivated in the green house and protected from direct sun. The variegated types loose the colour in a rich soil and hence should be grown in a rather poor soil containing just sufficient nutrients and moisture. Some species are good for potting and indoor decoration. The common screwpine is used as a hedge also (Randhawa and Mukhopadhyay, 1986)

The screwpine (Pandanus), is highly polymorphic with numerous forms and varieties and selected in various countries for specific uses as maintained by vegetative propagation, e.g. P. leram (Plate 14), the Nicober-bread fruit, is grown in the Andaman Islands for its edible fruit providing a starchy food that is enjoyed locally; another species, P. utilis (Plate 15), on the remote Island of Mauritius, provides fibre from the leaves, used in making bags and a species from Polynesia, P.veitchii (Plate 16) is most commonly grown in green houses and outdoors as an ornamental, where the winter weather is mild and in the species the prop roots and branching stems are particularly well developed attracting attention from many people who might not otherwise notice the stranger from the tropics (Lorus and Milne, 1967). However, these three species give a striking foliage effect and especially useful in seaside gardens as P. utilis with green leaves; P. veitchii with banded white and P. leram with even longer leaves (Thomas, 1965). An unarmed form, forma laevis warb., is cultivated for the fragrant bracts of the inflorescence, while forma samak, a group of prickly Pandanus, is preferred for the tough leaves suitable for matting; another form with longitudinal yellow bands on leaves (forma variegatus) is grown for ornamental purposes (Deshaprabhu, 1966; Ambasta, 1986). In the Pacific Islands, some of the forms (e.g pulposus) are cultivated for their edible fruits (Purseglove, 1975; Ambasta, 1986). Burkill (1966) states that the common wild armed form of the sea-coasts was var. littoralis and that flower growers had selected various races for cultivation, which included the prickly var. samak and thronless var. laevis, grown in India, Malay and Indonesia, are used for making mats.

Botany

Several vernacular names of kewda are reported in different languages all over the world ; viz.

Keora, Ketgi, Keura, Gagandhul in Hindi; Keya, Ketaki, Kea, Ketkikea in Bengali; Kiya, Kia in Odia; Kewoda in Gujrati; Ato, Keto, Covasso in Konkani; Keoda, Keora in Marathi; Talemara in Kannada; Gedaji, Gedangimogali, Gojjangi, Ketaki, Mugali, Mogali in Telugu; Kaidai, Talhai, Thasai, Thazh, Kechiya, Kedagi, Kedagai, Muchali in Tamil; Kaita, Ketaki, Palliyambu in Malayalam; Gandhapuspa, Dalapushpa, Shivadvishta, Ketaki, Suchika pushpa in Sanskrit; Leram in Nicoberese; Mudukeyiya, wetakey in Sinhalese; Keora in Urdu; Gulkiri, Kader, Kadi in Persian; Satthapu, Tsatthapu in Burmese; Nalu in Nepalese; Togenashiadan in Japanese; Kadar, Kadhi, Kazi in Arabic Kaide, Kedige, Ketaki, Gedege, Mundige in Canarese; Kedgi in Deccan; Vaquois odorant in French and Schrauben palme in German. (Kirtikar and Basu, 1935; Randhawa and Mukhopadhyay, 1986; Kapoor, 1990).

Kewda (Pandanus fascicularis Lam.) is a native of the old world extending from Africa to Australia (Chittenden, 1956; Lorus and Milne, 1967; Mott, 1975). About 600 species of Pandanus are widely distributed in the moist tropics of the old world and kewda is the most widespread species being recorded from Mauritius Islands in the west to Polynesian and Micronesian Islands in the east (Deshaprabhu, 1966).

It occupies an important position in the mythology of Melanesian, Polynesian and Micronesian Islands (Massal and Barrau, 1956). Kewda has been mentioned in the Indian mythology with several available legends. In Skandha Puran, it is mentioned that Ketaki (P. odorattisimus L.f.) flower is unfit to worship Shiva (Bhattacharjee, 1987). As regards to popularity of Kewda, one of the Gujarati tribal songs says that the sun rises behind the Kewda tree, the moon applies antimony to its eyes, the night is lit with soft moon light. Another mythological legend mentioned that during Satya Yuga, there was a fight between Brahma and Vishnu to know, to prove their greatness. Lord Shiva decided a simple method that the one, who can see his head or his feet, shall be greater than the other. Shiva disappeared and became so great that Brahma and Vishnu couldn’t see his head or feet and searched in different directions. Vishnu went up to patal, but couldn’t find his feet and Brahma had gone up to the highest peak and could not see the head of Shiva. On the returned way, Bramha found a Kewda flower and claimed that he had brought the flower from the head of Lord Shiva. On questioning by Vishnu, Kewda flower also replied that she was adorned by Shiva (Gandhi, 1989).

Among the vast resources of plants, aromatic and medicinal plants are highly beneficial to mankind for supplying medicines and essence. Olfactory gland bearing aromatic plants are few and many of them are located mainly in tropics and sub-tropics. Ecological conditions in the tropics are so conducive for such plants that out of 75,000 edible plants, majority are found in this region. (Chai et al., 1979, Jong, 1979)

Among the aromatic plants, kewda (Pandanus fascicularis Lam.), a common species of screwpine, is commercially important for its highly aromatic male spadices used in the production of highly prized kewda perfumes. Kewda attar, water and oil (rooh kewda) are the important perfumery products. Kewda attar blends well with most of the fancy perfumes, in preparation of lotions, cosmetics, soaps, hair oils, agarbatis (incense sticks), scenting clothes and flavouring betel masala, chewing tobacco and bouquets. Kewda water is used for flavouring various foods, confectionaries, sweets, syrups and soft drinks. The oil and attar are considered as stimulant, antispasmodic and administered for headache and rheumatism (Chopra et al., 1956). The kewda is mentioned frequently in Tamil classics as having flowers which neutralize the foul fish odour pervading the sea coast with their strong perfume. Jehangir in his memoirs, Tuzuk-i-Jahangiri, described kewda flower for its strong and penetrating scent, which even obscures that of musk (Gandhi, 1989).

Odisha state lying between 17^o 52′ N to 22^o 45′ N latitude and 81^o 50′ E to 87^o 50′ E longitude has a prosperous agriculture. Nearly 75 % of its working population are either cultivators or agricultural labourers and remaining 25 % are engaged in the categories of household industry and other works (Anonymous, 1988). The wastelands occupy 13.79 % of the total area of Odisha and are mostly scattered throughout the state. The areas of wastelands in the state mainly accounted for the hilly slopes, degraded forests, over grazed revenue wastelands, oil eroded valleys, drought stricken pastures, saline and marshy lands, etc. The changes in land use leading to creation of wastelands include overgrazing forest degradation and development of marginal cropland due to flood, drought and soil erosion etc. (Fig. 1).

NTSYSpc 2.0 software is used for various types of analysis including calculation of similarity index values and construction of dendrogram. Construction of dendrogram using gel data in the form of bands. This software accepts zero-one data.

After the DNA is run on the gel, the polymorphic bands or the bands cosegregating with a target trait are tagged. The bands identification is either done by calculating their relative mobilities (Rm / Rf values in case of isoenzymes) or by calculating their molecular weights (in case of proteins and DNA).

There are several methods to calculate molecular weights of DNA bands on the gel. Graphical approach is one of them. The approaches include (1) use of computer software to generate molecular weights and (2) running unknown DNA fragments with the fragments of known molecular weights (standard markers available from private companies, see examples in the figure). An example is given here (see figure) to illustrate the method to calculate molecular weights of unknown DNA fragments. This method is usually called as Graphical Approach.

In genetics, microRNAs (miRNA) are single-stranded RNA molecules of 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (i.e. they are non-coding RNAs); instead each primary transcript (a pri-miRNA) is processed into a short stem-loop structure called a pre-miRNA and finally into a functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression. They were first described in 1993 by Lee and colleagues in the Victor Ambros lab .

MicroRNAs can be encoded by independent genes, but also be processed (via the enzyme Dicer) from a variety of different RNA species, including introns, 3' UTRs of mRNAs, long noncoding RNAs, snoRNAs and transposons.

The genes encoding miRNAs are much longer than the processed mature miRNA molecule; miRNAs are first transcribed as primary transcripts or pri- miRNA with a cap and poly-A tail and processed to short, 70-nucleotide stem-loop structures known as pre-miRNA in the cell nucleus. These pre- miRNAs are then processed to mature miRNAs in the cytoplasm by interaction with the endonuclease Dicer, which also initiates the formation of the RNA-induced silencing complex (RISC). This complex is responsible for the gene silencing observed due to miRNA expression and RNA interference. The pathway in plants varies slightly due to their lack of Drosha homologs; instead, Dicer homologs alone effect several processing steps. The pathway is also different for miRNAs derived from intronic stem-loops; these are processed by Dicer but not by Drosha. Either the sense strand or antisense strand of DNA can function as templates to give rise to miRNA.

In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells These organelles range from 0.5–10 micrometers (µm) in diameter. Mitochondria are sometimes described as “cellular power plants” because they generate most of the cell’s supply energy in form of adenosine triphosphate (ATP), used as a source of chemical energy. In addition to supplying cellular energy, mitochondria are involved in a range of other processes, such as signaling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth. Mitochondria have been implicated in several human diseases, including mitochondrial disorders and cardiac dysfunction, and may play a role in the aging process.

Several characteristics make mitochondria unique. The number of mitochondria in a cell varies widely by organism and tissue type. Many cells have only a single mitochondrion, whereas others can contain several thousand mitochondria. The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the intermembrane space, the inner membrane, and the cristae and matrix. Mitochondrial proteins vary depending on the tissue and the species. In humans, 615 distinct types of proteins have been identified from cardiac mitochondria; whereas in Murinae (rats), 940 proteins encoded by distinct genes have been reported. The number of proteins encoded in plant mitochondrial DNA is probably not much higher than the number encoded in mammalian mitochondria.Experiments have shown that most of the protein synthesis in isolated maize mitochondria can be accounted for by some 18-20 polypeptidesThe mitochondrial proteome is thought to be dynamically regulated. Although most of a cell’s DNA is contained in the cell nucleus, the mitochondrion has its own independent genome. Further, its DNA shows substantial similarity to bacterial genomes.

The biological diversity of each country is a valuable and vulnerable natural resource. Sampling, identifying, and studying biological specimens are among the first steps toward protecting and benefiting from biodiversity. Knowledge about biodiversity and the ability to identify organisms that comes with it are global public goods. That is, this knowledge can create benefits for all countries - benefits that no one country can create by itself.

DNA Barcoding: Documenting Biodiversity with a Gene Sequence

“DNA barcoding” is an exciting new tool for taxonomic research. The DNA barcode is a very short, standardized DNA sequence in a well-known gene. It provides a way to identify the species to which a plant, animal or fungus belongs. The Consortium for the Barcode of Life (CBOL) is promoting international partnerships that will enable people in all countries to better understand and protect their biodiversity.

DNA barcoding is a taxonomic method that uses a short genetic marker in an organism’s mitochondrial DNA to identify it as belonging to a particular species. It is based on a relatively simple concept: most eukaryote cells contain mitochondria and mitochondrial DNA (mtDNA) has a relatively fast mutation rate, which results in significant variance in mtDNA sequences between species and, in principle, a comparatively small variance within species.

What is FISH ?

Fluorescent in situ hybridization is a technique in which single-stranded nucleic acids (usually DNA, but RNA may also be used) are permitted to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences. Through nucleic acid hybridization, the degree of sequence identity can be determined, and specific sequences can be detected and located on a given chromosome. Fluorescent in situ hybridization (FISH) is a powerful technique for detecting RNA or DNA sequences in cells, tissues, and tumors. FISH provides a unique link among the studies of cell biology, cytogenetics, and molecular genetics.

Principle of FISH

FISH involves the preparation of short sequences of single-stranded DNA, called probes, which are complementary to the DNA sequences the researchers wish to paint and examine. These probes hybridize, or bind, to the complementary DNA and, because they are labeled with fluorescent tags, allow researchers to see the location of those sequences of DNA. Unlike most other techniques used to study chromosomes, which require that the cells be actively dividing, FISH can also be performed on non dividing cells, making it a highly versatile procedure.

The transfer foreign gene to the plant cell is a very crucial method to production of transgenic plant. So improvement of plant quality requires to transfer our interest gene or we can say useful for production of our interest product. To achieve genetic transformation in plants, we need the construction of a vector (genetic vehicle) which transports the genes of interest, flanked by the necessary controlling sequences i.e. promoter and terminator, and deliver the genes into the host plant. The two kinds of gene transfer methods in plants are.

1. Vector-mediated or Indirect Gene Transfer

Among the various vectors used in plant transformation, the Ti plasmid of Agrobacterium tumefaciens has been widely used. This bacteria is known as “natural genetic engineer” of plants because these bacteria have natural ability to transfer T-DNA of their plasmids into plant genome upon infection of cells at the wound site and cause an unorganized growth of a cell mass known as crown gall. Ti plasmids are used as gene vectors for delivering useful foreign genes into target plant cells and tissues. The foreign gene is cloned in the T-DNA region of Ti-plasmid in place of unwanted sequences.

To transform plants, leaf discs (in case of dicots) or embryogenic callus (in case of monocots) are collected and infected with Agrobacterium carrying recombinant disarmed Ti-plasmid vector. The infected tissue is then cultured (co-cultivation) on shoot regeneration medium for 2-3 days during which time the transfer of T-DNA along with foreign genes takes place. After this, the transformed tissues (leaf discs/calli) are transferred onto selection cum plant regeneration medium supplemented with usually lethal concentration of an antibiotic to selectively eliminate non-transformed tissues. After 3-5 weeks, the regenerated shoots (from leaf discs) are transferred to root-inducing medium, and after another 3-4 weeks, complete plants are transferred to soil following the hardening (acclimatization) of regenerated plants. The molecular techniques like PCR and southern hybridization are used to detect the presence of foreign genes in the transgenic plants.

DNA Sequencing

DNA sequencing is the determination of the precise sequence of nucleotides in a sample of DNA. Sequencing can be done on a short fragment of DNA to cover the entire genome. The maps thus constructed using the nucleotide sequences in the correct order is called as sequence map.

In 1977, twenty-four years after the discovery of the structure of DNA, two separate methods for sequencing DNA were developed: the chain termination method (Sanger et al., 1977) and the chemical degradation method (Maxam and Gilbert, 1977). Both methods were equally popular to begin with, but, for many reasons, the chain termination method is the method more commonly used today. In chemical degradation method, chemicals specific to each base remove the last base, which has been labelled. The method uses toxic chemicals which required high care while handling.

In chain termination method, DNA polymerase extends a DNA strand in which dideoxynucleotide becomes incorporated terminating the chain extension (phosphodiester formation) at the 3’OH site making an array of fragments differing in length. This method is based on the principle that single-stranded DNA molecules that differ in length by just a single nucleotide can be separated from one another using polyacrylamide gel electrophoresis.

Eastern blotting is a technique to detect protein post translational modifications (PTM) and is an extension of the biochemical technique of western blotting. There are multiple versions of the method, but in general proteins or lipids are blotted from one or two-dimensional SDS-PAGE gel on to a PVDF or nitrocellulose membrane are analyzed for post-translational protein modifications using probes that may detect lipids, carbohydrate, phosphorylation or any other protein modification. Eastern blotting should be used to refer to methods that detect their targets through specific interaction of the PTM and the probe, distinguishing them from a standard Far-western blot. The most common application is lectin blotting, however, a variety of other probes can be used for detecting different PTMs.

History and Multiple Definitions

Definition of the term Eastern blotting is somewhat confused due to multiple sets of authors dubbing a new method as Eastern blotting, or a derivative therof. All of the definitions are a derivative of the technique of Western blotting developed by Towbin in 1979. The current definitions are summarized below in order of the first use of the name, however all are based on some earlier works. In some cases, the technique had been in practice for some time before the introduction of the term.

Northern Blot

The northern blot is a technique used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample.

Introduction

The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.

There are now many reagent companies that specialize in providing antibodies (both monoclonal and polyclonal antibodies) against tens of thousands of different proteins. Commercial antibodies can be expensive, although the unbound antibody can be reused between experiments. This method is used in the fields of molecular biology, biochemistry, immunogenetics and other molecular biology disciplines.

Other related techniques include using antibodies to detect proteins in tissues and cells by immunostaining and enzyme-linked immunosorbent assay (ELISA).

The method originated from the laboratory of George Stark at Stanford. The name western blot was given to the technique by W. Neal Burnette and is a play on the name Southern blot, a technique for DNA detection developed earlier by Edwin Southern. Detection of RNA is termed northern blotting and the detection of post-translational modification of protein is termed Eastern blotting.

Introduction

Southern blotting was named after Edward M. Southern who developed this procedure at Edinburgh University in the 1970s. To oversimplify, DNA molecules are transferred from an agarose gel onto a membrane. Southern blotting is designed to locate a particular sequence of DNA within a complex mixture. For example, Southern Blotting could be used to locate a particular gene within an entire genome. The amount of DNA needed for this technique is dependent on the size and specific activity of the probe. Short probes tend to be more specific. Under optimal conditions, you can expect to detect 0.1 pg of the DNA for which you are probing.

QTL Traits

Polygenic inheritance, also known as quantitative or multifactorial inheritance refers to inheritance of a phenotypic characteristic (trait) that is attributable to two or more genes and their interaction with the environment. Unlike monogenic traits, polygenic traits do not follow patterns of Mendelian inheritance (qualitative traits). Instead, their phenotypes typically vary along a continuous gradient depicted by a bell curve. Though not necessarily genes themselves, quantitative trait loci (QTLs) are stretches of DNA that are closely linked to the genes that underlie the trait in question. QTLs can be molecularly identified (for example, with PCR or AFLP) to help map regions of the genome that contain genes involved in specifying a quantitative trait. This can be an early step in identifying and sequencing these genes.

Genetic Mapping

Perhaps one of the most powerful applications of markers is genetic mapping. This technology allows researchers identify markers located within or very close to genes of interest. With this it is possible to trace these genes through generations of crosses.

If the trait in question is complex and multigenic, mapping will also be of tremendous help to dissect the various genes or loci that contribute to the overall characteristic. Determining the amount of impact each locus delivers is a process called Quantitative Trait Loci or QTL mapping.

Deoxyribonucleic acid (DNA) is a molecule made up of pairs of building blocks called nucleotides. The four kinds of nucleotides that make up DNA are adenine (abbreviated as the single letter A), guanine (G), cytosine (C), and thymine (T). The DNA molecule has the shape of two intertwined spirals, referred to as a double helix. DNA is packaged into chromosomes that are located within the nucleus of all cells. These chromosomes are the same in every cell of an organism and together make up the organism’s genetic information, its genome. Chromosomes contain stretches of DNA called genes that code for amino acids that make proteins. It is the proteins that are the foundation of life for all organisms. The interaction and structure of proteins determine the visible characteristics or phenotype of an organism, while the genetic makeup of an organism is called its genotype.

The sequence of nucleotides that make up a gene can differ among individuals. The different forms of a gene are called alleles. The alleles are the result of nucleotide differences in a gene that affect an amino acid sequence of a protein. This can result in a change, addition, or deletion of a protein that can affect the phenotype.

Silver Staining for Protein

Silver staining is one of the procedures, in addition to Coomassie Blue, R and G types, and fluorescent dyes that are available for detecting proteins separated by gel electrophoresis. Switzer introduced silver staining in 1979, a technique that today provides a very sensitive tool for protein visualization with a detection level down to the 0.3-10 ng level.

The basic mechanisms underlying silver staining of proteins in gels are relatively well understood. Basically, protein detection depends on the binding of silver ions to the amino acid side chains, primary the sulfhydril and carboxiyl groups of proteins, followed by reduction to free metallic silver. The protein bands are visualized as spots where the reduction occurs and, as a result, the image of protein distribution within the gel is based on the difference in oxidation-reduction potential between the gel’s area occupied by proteins and the free adjacent sites. A number of alteration in the silver staining procedure can shift the oxidation-reduction equilibrium in a way that gel- separated proteins will be visualized either as positively or negatively stained bands. Silver staining protocols can be divided into two general categories: 1) silver amine or alkaline methods, and 2) silver nitrate or acidic methods. In general, the detection levels’ using the various procedures is determined by how quickly the protein bands develop in relationship to the background (e.g. signal-to-noise ratio). The silver amine or alkaline methods usually have lower background and as a result are most sensitive but require longer procedures. Acidic protocols, on the other hand, are faster but slightly less sensitive. Clearly, each protocol has different advantages regarding timing, sensitivity, cost, and compatibility with other analytical methods, especially mass-spectrometry (MS) a tool that is being used in combination with gel electrophoresis or chromatographic methods for rapid protein identification. Until recently most of the silver staining protocols used either glutaraldehyde- of formaldehyde-based sensitizes in the fixing and sensitization step, thus, introducing the chemical modifications into proteins. The utilization of those chemicals causes the cross-linking of two lysine residues within protein chain, thus, strongly affecting two most crucial steps for the subsequent MS analysis: hampering the trypsin digestion and highly reduces the protein extraction from the gel .

What are Retrotransposons?

The presence of mobile elements, capable of moving from one region of the genome to another, has been known and thoroughly studied since the 1950’s. These elements are capable of exciding and inserting themselves from one region of the chromatin to another, through their peculiar terminal repeat regions. This process is mediated by enzymes encoded by the transposon itself.

Retrotransposons are a class of mobile elements, widespread in plant genomes, where they account for a significant part of noncoding DNA. Barley, for example, contains thousands of copies of the Bare-1 element, dispersed throughout the euchromatic regions of chromosomes and exhibiting sequence identity higher than 95% to each other.

Unlike other classes of mobile elements, retrotransposons insert into the genome via an RNA intermediate, synthesized by their own reverse transcriptase, without the loss of the parental copy. Unique sequence properties show that retrotransposons of the Ty1-copia group are close to retroviruses, and their mode of integration in the host genome is also very similar.

The number and exact point of insertion of retrotransposons may differ from one individual to another and this can be exploited to characterize individuals, varieties or species, depending on how recent the transpositional event is. Furthermore, insertion of a retrotransposon is an irreversible event, a characteristic that can be helpful when tracing an ancestry.

Single strand conformation polymorphism (SSCP), or single strand chain polymorphism, is defined as conformational difference of single stranded nucleotide sequences of identical length as induced by differences in the sequences under certain experimental conditions. This property allows to distinguish the sequences by means of gel electrophoresis, which separates the different conformations.

Background

A single nucleotide change in a particular sequence, as seen in a double stranded DNA, cannot be distinguished by electrophoresis, because the physical properties of the double strands are almost identical for both alleles. Contrarily, after denaturation, single stranded DNA undergoes a 3- dimensional folding and may assume a unique conformational state based on its DNA sequence. The difference in shape between two single-stranded DNA strands with different sequences can cause them to migrate differently on an electrophoresis gel, even though the number of nucleotides is the same. Predictability, however, is a shortfall of SSCP - since conformational states are subject to many experimental conditions and sequence differences that cause minimal changes in strand conformation may not be detected.

Synonym : PCR-RFLP (PCR- Restriction Fragment Length Polymorphism)

The Cleaved Amplified Polymorphic Sequence or CAPS method is a technique in molecular biology for the analysis of genetic markers. It is an extension to the Restriction Fragment Length Polymorphism (RFLP) method, using polymerase chain reaction (PCR) to more quickly analyse the results.

Like RFLP, CAPS works on the principle that genetic differences between individuals can create or abolish restriction endonuclease restriction sites, and that these differences can be detected in the resulting DNA fragment length after digestion.

In the CAPS method, PCR amplification is directed across the altered restriction site, and the products digested with the restriction enzyme. When fractionated by agarose or acrylamide gel electrophoresis, the digested PCR products will give readily distinguishable patterns of bands. Alternatively, the amplified segment can by analyzed by Allele specific oligonucleotide (ASO) probes, a process that can often be done by a simple Dot blot.

SCARs are DNA fragments amplified by the Polymerase Chain Reaction (PCR) using specific 15-30 bp primers, designed from nucleotide sequences established in cloned RAPD (Random Amplified Polymorphic DNA) fragments linked to a trait of interest. By using longer PCR primers, SCARs do not face the problem of low reproducibility generally encountered with RAPDs. Obtaining a codominant marker may be an additional advantage of converting RAPDs into SCARs. However, SCARs may exhibit dominance when one or both primers partially overlap the site of sequence variation. SCARs are locus specific and have been widely applied in gene mapping studies and marker assisted selection (Paran & Michelmore, 1993).

Since the mid 1980s, genome identification and selection has progressed rapidly with the help of PCR technology. A large number of marker protocols that are rapid and require only small quantities of DNA have been developed. Three widely-used PCR-based markers are RAPDs (Williams et al., 1990), SSRs or microsatellites (Tautz, 1989), and AFLPs (Vos et al., 1995). Each marker technique has its own advantages and disadvantages. RAPD markers are very quick and easy to develop (because of the arbitrary sequence of the primers) but lack reproducibility (Karp et al., 1997; Hansen et al., 1998; Jones et al., 1999; Virk et al., 2000). AFLP has medium reproducibility but is labour intensive and has high operational and development costs (Karp et al., 1997). Microsatellites are specific and highly polymorphous (Karp et al., 1997, Jones et al., 1999), but they require knowledge of the genomic sequence to design specific primers and, thus, are limited primarily to economically important species.

The choice of a molecular marker technique depends on its reproducibility and simplicity. The best markers for genome mapping, marker assisted selection, phylogenic studies, and crop conservation have low cost and labour requirements and high reliability. Since 1994, a new molecular marker technique called inter simple sequence repeat (ISSR) has been available (Zietkiewicz et al., 1994). ISSRs are semiarbitrary markers amplified by PCR in the presence of one primer complementary to a target microsatellite. Amplification in the presence of nonanchored primers also has been called microsatellite-primed PCR, or MP-PCR, (Meyer et al., 1993).

Minisatellite is a section of DNA that consists of a short series of bases 10– 60bp. These occur at more than 1000 locations in the human genome. Some minisatellites contain a central (or “core”) sequence of letters “GGGCAGGANG” (where N can be any base) or more generally a strand bias with purines (Adenosine (A) and Guanine (G)) on one strand and pyrimidines (Cytosine (C) and Thymine (T)) on the other. It has been proposed that this sequence per se encourages chromosomes to swap DNA. In alternative models, it is the presence of a neighbouring cis-acting meiotic double-strand break hotspot which is the primary cause of minisatellite repeat copy number variations. Somatic changes are suggested to result from replication difficulties (which might include replication slippage, among other phenomena). When such events occur, mistakes are made, this causes minisatellites at over 1000 locations in a persons genome to have slightly different numbers of repeats, thereby making them unique. The most highly mutable minisatellite locus described so far is CEB1 (D2S90) described by Vergnaud.

Also Referred to as Microsatellites

SSR markers are based short sequences of nucleotides (2-6 units in length) that are repeated in tandem:

Di-nucleotide repeat: CACACACA

Tri-nucleotide repeat: ATGATGATGATG

It is believed that when DNA is being replicated, errors occur in the process and extra sets of these repeated sequences are added to the strand. Over time, these repeated sequences vary in length between one cultivar and another.

Introduction

The AFLP amplified fragment polymorphism also known as selective restriction fragment amplification (SRFA) technique is used to visualize hundreds of amplified DNA restriction fragments simultaneously. The AFLP band patterns, or fingerprints, can be used for many purposes, such as monitoring the identity of an isolate or the degree of similarity among isolates. Polymorphisms in band patterns map to specific loci, allowing the individuals to be genotyped or differentiated based on the alleles they carry. produces highly complex DNA profiles by arbitrary amplification of restriction fragments ligated to double-stranded adaptors with hemi-specific primers harboring adaptor-complementary 5' termini.The technique has been widely used in the construction of genetic maps containing high densities of DNA marker loci.

The AFLP protocol amplifies restriction fragments obtained by endonuclease digestion of target DNA using “universal” AFLP primers complementary to the restriction site and adapter sequence. However, not all restriction fragments are amplified because AFLP primers also contain selective nucleotides at the 3' termini that extend into the amplified restriction fragments. These arbitrary terminal sequences result in the amplification of only a small subset of possible restriction fragments. The number of amplified fragments can therefore be “tailored” by extending the number of arbitrary nucleotides added to the primer termini. Alternatively, the use of endonuclease combinations that vary in their restriction frequency can also be used to tune the number of amplicons. Generally, the abundant restriction fragments produced from complex genomes require of AFLP primers with longer selective regions. Conversely, analysis of small genomes require of only few arbitrary nucleotides added at the primer 3' termini. The resulting AFLP fingerprints are usually a rich source of DNA polymorphisms that can be used in mapping and general fingerprinting endeavors.

In 1985, Sir Alec Jeffreys developed restriction fragment length polymorphism (RFLP), which quickly became the standard technique for DNA testing throughout the 1980s. RFLP provided the world with the first form of genetic testing based on DNA, the body’s genetic material.

Definition : RFLP analysis is a difference in homologus DNA sequences that can be detected by the presence of fragments of different lengths after digestion of the samples in question with specific restriction endonucleases (RE).

A restriction fragment length polymorphism , or RFLP, (commonly pronounced “rif lip”), is a variation in the DNA sequence of a genome that can be detected by breaking the DNA into pieces with restriction enzymes and analyzing the size of the resulting fragments by gel electrophoresis. It is the sequence that makes DNA from different sources different, and RFLP analysis is a technique that can identify some differences in sequence (when they occur in a restriction site). Though DNA sequencing techniques can characterize DNA very thoroughly, RFLP analysis was developed first and was cheap enough to see wide application. Analysis of RFLP variation was an important tool in genome mapping, localization of genetic disease genes, determination of risk for a disease, genetic fingerprinting, and paternity testing.

RAPD stands for Random Amplification of Polymorphic DNA. It is a type of PCR reaction, but the segments of DNA that are amplified are random. The scientist performing RAPD creates several arbitrary, short primers (8-12 nucleotides), then proceeds with the PCR using a large template of genomic DNA, hoping that fragments will amplify. By resolving the resulting patterns, a semi-unique profile can be gleaned from a RAPD reaction.

No knowledge of the DNA sequence for the targeted gene is required, as the primers will bind somewhere in the sequence, but it is not certain exactly where. This makes the method popular for comparing the DNA of biological systems that have not had the attention of the scientific community, or in a system in which relatively few DNA sequences are compared (it is not suitable for forming a DNA databank). Because it relies on a large, intact DNA template sequence, it has some limitations in the use of degraded DNA samples. Its resolving power is much lower than targeted, species specific DNA comparison methods, such as short tandem repeats. In recent years, RAPD is used to characterize, and trace, the phylogeny of diverse plant and animal species.

Allele-Specific PCR

This diagnostic or cloning technique is used to identify or utilize single- nucleotide polymorphisms (SNPs) (single base differences in DNA). It requires prior knowledge of a DNA sequence, including differences between alleles, and uses primers whose 3' ends encompass the SNP. PCR amplification under stringent conditions is much less efficient in the presence of a mismatch between template and primer, so successful amplification with an SNP-specific primer signals presence of the specific SNP in a sequence.

Amplification Refractive Mutation System (ARMS) - PCR

In ARMS, the primer pair is designed so that one of the 3' ends coincides with a variant nucleotide in the target sequence. When the primer mismatches the template the frequency of extension is very low and consequently the effective number of sequence copies available for amplification is greatly reduced. ARMS PCR exploits a thermostable polymerase that lacks 3' exonuclease activity (usually Taq polymerase). Such enzymes extend primers bound to their target sequences very inefficiently when the 3' base is mismatched. Because the 3' exonuclease activity required for mismatch repair is not present, the extension of such primers in PCR is a rare event and amplification is retarded. However, once mismatch extension has occurred amplification proceeds normally from the newly synthesised target strand. Thus an important principle of ARMS is that non-matching (i.e. non-matching at only the 3' end of one primer) template may be amplified. The factors that contribute to this apparent ‘failure’ of ARMS are that when very high numbers of template molecules are added to the reaction, amplification is likely to proceed because the small proportion of mismatched primer extensions reach the sensitivity threshold of the reaction. Second, certain mismatches are extended more efficiently than others so that proportion extended in each PCR cycle varies.

Polymerase Chain Reaction

The Polymerase Chain Reaction (PCR) technique, invented in 1985 by Kary B. Mullis, allowed scientists to make millions of copies of a scarce sample of DNA. The technique has revolutionized many aspects of current research, including the diagnosis of genetic defects and the detection of the AIDS virus in human cells. The technique is also used by criminologists to link specific persons to samples of blood or hair via DNA comparison. PCR also affected evolutionary studies because large quantities of DNA can be manufactured from fossils containing but trace amounts.

Kary Mullis invented the PCR technique in 1985 while working as a chemist at the Cetus Corporation, a biotechnology firm in Emeryville, California. The procedure requires placing a small amount of the DNA containing the desired gene into a test tube. A large batch of loose nucleotides, which link into exact copies of the original gene, is also added to the tube. A pair of synthesized short DNA segments, that match segments on each side of the desired gene, is added. These “primers” find the right portion of the DNA, and serve as starting points for DNA copying. When the enzyme Thermus aquaticus (Taq) is added, the loose nucleotides lock into a DNA sequence dictated by the sequence of that target gene located between the two primers.

The test tube is heated, and the DNA’s double helix separates into two strands. The DNA sequence of each strand of the helix is thus exposed and as the temperature is lowered the primers automatically bind to their complementary portions of the DNA sample. At the same time, the enzyme links the loose nucleotides to the primer and to each of the separated DNA strands in the appropriate sequence. The complete reaction, which takes approximately five minutes, results in two double helices containing the desired portion of the original. The heating and cooling is repeated, doubling the number of DNA copies. After thirty to forty cycles are completed a single copy of a piece of DNA can be multiplied to hundreds of millions.

Restriction Enzymes

Restriction enzymes are enzymes isolated from bacteria that recognize specific sequences in DNA and then cut the DNA to produce fragments, called restriction fragments. Restriction enzymes play a very important role in the construction of recombinant DNA molecules, as is done in gene cloning experiments. Another application of restriction enzymes is to map the locations of restriction sites in DNA.

Restriction endonucleases, often called restriction enzymes, cut DNA within the molecule by hydrolyzing the phosphodiester bonds between the nucleotides. Restriction enzymes were discovered in bacteria and there are now more than 1200 known restriction enzyme types. These enzymes are named using a simple system. EcoRI, for example, was isolated from E. coli and was the first enzyme isolated from a particular strain, hence the designation of I. HaeIII was isolated from Haemophilus aegyptius. HindIII was isolated from Haemophilus influenzae, and was the third enzyme discovered in a particular strain.

Usually, restriction enzymes only cut the DNA at or near a very specific nucleotide sequence known as a recognition site. This “restrictive” nature of these enzymes allows molecular biologists to pin-point exactly where the DNA is to be cut. In many cases, the recognition site of a restriction enzyme consists of a palindromic sequence where the order of the bases is read the same on each side of the helix. The two sides of the helix are antiparallel and the recognition sequence reads from 5’ to 3’ on either side of the helix. For example the recognition site for EcoRI is as follows;

Agriculture Scenario

It has been seen since last few decades there is huge decrease in the production of the agricultural production. Three factors which can be held responsible for the increase of agricultural production per hectare:

1. Overall increase in efficiency due to the merger of farms and a more efficient redistribution of farm land.
2. More efficient cultural practises and better quality and availability of inputs (fertilizer, pesticides).
3. Genetic improvement of crops.

At this moment over 6 billion people need to be fed and it is expected that in the year 2050 more than 10 billion people will inhabit the earth (FAO, 1996). Moreover, demands per capita will rise when standards of living in developing counties improve. As a consequence there will be a huge increase in the demand for food, and production will need to triple in the coming 40 years. A continued effort to secure agricultural production in the future will therefore be vital. Reduction of losses caused by a-biotic and biotic stress will be a key issue. Scenario studies on world food security generally assume that a large increase in production will be achieved by genetic improvement of crop species and biotechnology. History has indeed shown a continuous increase in crop yields, resulting from plant breeding efforts. However, in the light of the speed at which the human population develops, and taking into account the expected reduction of available arable land due to climate change and human intervention, it may be necessary to accelerate the rate at which genetic improvement is achieved. Modern biotechnology provides new tools that can facilitate development of improved plant breeding methods and augment our knowledge of plant genetics. The knowledge that is obtained with these new tools can be used to contribute to an enhanced food security throughout the world.

There are many different methods of extracting DNA bands from an agarose gel. Which one you choose will probably depend on the consumables you have available in your lab. Another important consideration is the yield/ purity of the DNA after extraction. Agarose contains various impurities which may inhibit downstream reactions if not efficiently removed from the DNA. We used to give the generic term ‘hoonose’ to the unspecified carbohydrates that co-purified along with the DNA and inhibited enzyme reactions. Modern spin-column kits are very good at removing impurities, old-fashioned ‘kitchen sink’ methods are less good.

Cutting Out the DNA Band

Most of the methods require you to cut out the band. You must visualise the band, in an ethidium bromide stained gel, in a dark-room on a UV light- box (a trans-illuminator). UV is dangerous, wear gloves, long-sleeves and face protection. Never look at UV with unprotected eyes. If possible, set the trans-illuminator to long-wavelegth UV (or low-power) and minimise the amount of time the DNA is exposed. This is because the UV mutagenises the DNA at a measurable rate. Use a scalpel blade to cut around the band of interest. Switch off the transilluminator, switch on the white light and carefully remove the band from the gel and place it on the glass. It is good to trim off as much empty agarose as possible so go back to UV illumination briefly to do this. Place the excised band in a 1.5mL microfuge tube.

Hunter and Mohler discovered the isozymes. In 1959 Markert and Moler introduced the concept of isozymes, which they defined as the different molecular forms in which proteins may exist with the same enzymatic specificity (Buth 1984). This means that different variants on the same enzymes have identical or similar functions and are present in the same individual. As such, their importance for understanding gene action in development and differentiation was exploited during the1960s in both animals and plants. Nevertheless, isozymes played a minor role in research on plant biochemistry until 1966 when genetic polymorphism for isozymes within the same population was discovered (Stebbins 1989, Wendel 1989). That revealed the possibility for population genetics to make precise quantitative estimates of genetic variability based upon one parameter of the molecular structure of the primary products of the genes themselves.

Plant population genetics were not long in following their zoological colleagues and the investigation of both animals and plants increased explosively. This application, however, necessitated a partitioning of the isozyme concept, since the relevant isozyme subset, defined by Prakash (Buth 1984) as the variant proteins produced by allelic forms of the same locus, to avoid the now common confusion with isozymes which are the various polymer produced from monomers specified by different loci. The development of genetic distance or similarity coefficients (Lukasová 1985) allowed the summarization of isozyme data for intersample comparisons and so quantified isozyme data were soon applied to comparative studies of taxa.

Proteins

Proteins are of central importance in the structure and function of all living organisms. Some proteins serve as structural components while others function in communication, defense, and cell regulation. Some proteins serve as enzymes that act as biological catalysts which control the pace and nature of essentially all biochemical events. Although DNA serves as the genetic blueprint of a cell, none of the life processes would be possible without the proteins.

Electrophoresis of Proteins

Proteins can be separated and purified. Methods for separating proteins take advantage of properties such as charge, size, and solubility, which vary from one protein to the next. Because many proteins bind to other biomolecules, proteins can also be separated on the basis of their binding properties. The source of a protein is generally tissue or microbial cells. The cell must be broken open and the protein must be released into a solution called a crude extract. If necessary, differential centrifugation can be used to prepare subcellular fractions or to isolate organelles. Once the extract or organelle preparation is ready, a variety of methods are available for separation of proteins. Ion-exchange chromatography can be used to separate proteins with different charges (similar to the way amino acids are separated). Other chromatographic methods take advantage of differences in size, binding affinity, and solubility. Nonchromatographic methods include the selective precipitation of proteins with salt, acid, or high temperatures. In addition to chromatography, another important set of methods is available for the separation of proteins, based on the migration of charged proteins in an electric field, a process called (gel) electrophoresis. Gel electrophoresis is especially useful as an analytical method. Its advantage is that proteins can be visualized as well as separated, permitting a researcher to estimate quickly the number of proteins in a mixture or the degree of purity of a particular protein preparation. Also, gel electrophoresis allows determination of crucial properties of a protein such as its isoelectric point and approximate molecular weight.

Polyacrylamide

Polyacrylamide is a cross-linked polymer of acrylamide. The length of the polymer chains is dictated by the concentration of acrylamide used, which is typically between 3.5 and 20%. Polyacrylamide gels are significantly more annoying to prepare than agarose gels. Because oxygen inhibits the polymer- ization process, they must be poured between glass plates (or cylinders).