Chapter 16

CHAPTER 16 – ENVIRONMENTAL ISSUES

Human population is increasing tremendously; therefore there is a lot of demand for food, electricity, clothing, roads, housing, vehicles etc. These are exerting a lot of pressure on land, water, air and other resources. This leads to pollution and degradation of the environment and biodiversity that is a part of it.

Pollution
Pollution is any undesirable change in physical, chemical or biological composition of air, water and land, and the agents that cause these are called pollutants.

Air pollution
    It’s the increase in amount of particles in the air, especially particles smaller than 2.5um such as CO, NO, lead, arsenic, cyanide CFCs ammonia etc., that cause respiratory diseases, lung cancer, Tuberculosis, lack of O2 to the brain and premature deaths.

CAUSES:
    Use of vehicles is the main cause of air pollution due to release of harmful gases. Use of petrol & coal in industries and cigarette smoking also contribute to air pollution. Improper disposal of domestic & industrial wastes led to the release of methane.

Smog: Mixture of air pollutants (like arsenic, lead, NO, CO etc), dust & fog is called smog and is deadly to the body as it results in deposition of dry mucus in the alveoli of lungs, tuberculosis, lung cancer, aging, premature death etc

Health fact: Studies show that living in cities like Delhi, Mumbai, Banglore, Kolkata and many others is equal to smoking an average of 20 cigarettes a day and this problem is fast increasing.

Ways we can help reduce air pollution and global warming:

•          Reducing the use of vehicles for travelling short distances & carpooling.
•          Use of hydrogen power in cars & machines or Hybrid cars.
•          By planting trees across town or growing plants in our homes.
•          Use of Electrostatic precipitators, Bag houses, Particulate scrubbers.
•          Use of magnetic trains.
•          Upgrading industries, factories & aircraft with better engines & turbines
•          Use of renewable sources of energy such as wind, water, solar & infrared, geothermal, tidal etc
•          Carbon credits are the most effective way of reducing carbon footprint. These credits can be sold to companies or individuals for cash and at the same time reduce CO2 production.
•          An electrostatic precipitator is a particulate removing device that removes particles such as dust, smoke etc from air using force of an electrostatic charge. They are highly effective & consume very less energy for their use.
•          In particulate scrubbers, the polluted gas is passed through a layer of scrubbing liquid, or forced through a pool of liquid. These are highly effective in the removal of pollutants from the gas. But these scrubbers have a high chance of corrosion as the toxic gases removed are highly acidic & these scrubbers require large amount of power. Also it is hard to dispose of the waste – water.

Laws passed by some countries to control Air Pollution:
•          Environmental Protection Act (1990)_Environment Act (1995)_British Clean Air Act (1956)~UK
•          Air Pollution Control Act (1955)_Clean Air Act (1963,1970,1990)~US
•          Air Act (1981)_Environment Act (1986)~India
•          Environmental Promotion Act (1994)_Environmental Compatibility Act (1994)~Austria

Water pollution:
•              It’s the pollution of water bodies with substances like domestic wastes, industrial, thermal, mineral, toxic, nitrogen & phosphorous rich wastes. The nutrient rich wastes multiply the algae concentration in the water bodies & this leads of depletion of oxygen in these bodies & hence leads to the death of fish and other biodiversity in the area.
It’s harmful effects include:
•          Biomagnification: It is increase in the toxicity among the food chain at successive trophic levels. This phenomenon is well known with mercury and DDT.
•          Accelerated Eutrophication: Eutrophication is the aging of a lake to convert into land, which generally takes 1000s of years or more. But human activities have accelerated this natural process & as a result many lakes are already extinct. It is caused due to dumping of nutrient rich and thermal waste into lakes.
•          Death of biodiversity living near the polluted water bodies, accelerated global warming & extinction of many species.

 DDT reduces fat levels, it is an endocrine disruptor, causes cancer, causes developmental and reproductive toxicity, causes parkinsons & asthma & thinning of eggshells.

India has the most polluted rivers in the world. The excuse of religion & spirituality has been the main reason for their degradation.

BOD : Biochemical Oxygen Demand for various organisms.

BOD is the amount of oxygen required by the biodegradable material & the organic matter living in a certain water body like lake or pond.

Invasive plant water hyacinth: It is used to control and remove BOD, suspended solids, nutrients (phosphorous, nitrogen), heavy metals & organochlorides from water bodies that have been polluted with mineral, industrial & chemical wastes. Water Hyacinth Scrubbers manage and optimize water hyacinth’s natural capability to extract nutrient pollutants to ensure sustainability and increased treatment performance. But if their growth is unchecked then it spreads across water bodies quickly. In India it is also called ‘Terror of Bengal’.

It is necessary to control water pollution as it leads to diseases like jaundice, cholera, typhoid, dysentery, dengue, malaria etc many of which are very hard to cure.

•          The waste water should be treated before dumping in rivers and lakes.
•          Domestic waste water can be mildly treated and used for irrigation.
•          Planting of trees to reduce acid rain & pollution of ground water.
•          Rainwater harvesting to conserve water and reduce wastage of fresh water.
•          Prevention/control of use of rivers for purposes related to religious ceremonies.
•          Use of dry composting toilets that do not require water, also the human waste collected can be used as a good natural fertilizer.

Some important actions taken by governments to reduce pollution of water bodies:

•          The International Convention for the Prevention of Pollution from Ships, 1973, as modified by the Protocol of 1978.
•          International Convention on Oil Pollution Preparedness, Response and Cooperation, 1990.
•          International Convention on Liability and Compensation for Damage in Connection with the Carriage of Hazardous and Noxious Substances   
            (HNS) by Sea.
•          Water Act 1974-India
•          Agricultural Nitrates Directive-UK
•          Anything that is thrown out along with garbage such as wastes from our homes, schools, offices, shops, hospitals etc are classified as solid
           wastes. These include glass, plastic, wood, metals, organic matter, food, electrical equipment etc.

It is classified into three main types:

•          Bio Degradable waste.
•          Non-Bio Degradable waste.
•          Recyclable waste.
•          Everyday humans produce millions of tonnes of waste all over the world. But what happens to this waste produced?
•          In many countries the waste produced is burnt to reduce it’s volume, but burning is not an effective way to reduce waste as it causes pollution &
           release of toxic wastes.
•          Wastes are also dumped in landfills- a landfill is a deep trench covering a very large area in which waste is dumped. In countries like Germany, the methane produced from the wastes is collected & used as fuel, & the decomposed waste is used as fertilizer as it is highly rich in nutrients. Modern landfills are designed such that the waste is fully made use of & such that they do not pollute the ground water levels. The toxic seepage from under the landfills is collected & treated before being used as fertilizer.

Landfills aren’t much of a solution to solving the problem of the large amounts of wastes generated as they get filled up overtime, faster than the waste can be removed or recycled.

Only we can reduce the amount produced by us. We could:
•          Use jute bags for shopping instead of plastic or even paper.
•          Glass or metal waste must be recycled & reused.
•          Waste produced from hospitals must be incinerated before dumping into landfills as these wastes contain pathogens & harmful germs, & toxic
           chemicals.
•          Using E-Book readers for reading and writing instead of using books. Use of E-Books can save hundreds of millions of trees around the world
            every year.
•          Recycling of electronic items instead of dumping or burning them.
•          Use of bio degradable plastic for packaging.

Agro-chemicals and their effects

Over the years the use of agro chemicals has increased considerably. Most of the crops are treated with Pesticides, in-organic fertilizers, insecticides etc to increase crop yield.
•          But use of these chemicals results in bio-magnification & eutrophication.
•          Many useful insects, rodents & micro-organisms are also killed by the use of these chemicals.
•          These chemicals seep into the ground & pollute the soil & ground water.
•          These cause cancer and inhibit development of brain and the body.

The use of agro-chemicals can be overcome by smart farming strategies:
•          Bee-keeping. Placing a bee hive in the centre of a crop field drastically increases crop yield & provides honey & beeswax that can be sold for
           profit. Also bees help keep elephants away as elephants are afraid of bees.
•          Use of ladybugs and worms. Lady bugs help protect the crops against smaller insects & worms help aerate the soil.
•          Using cow manure or plant waste to fertilize the soil.
•          Planting tree belts around the crop fields helps protect the crops from winds & rains.
•          Growing more than one crop in a given farmland per year not only provides variety but also helps replenish nutrients in the soil.
•          Placing guard dogs such as German Shepards helps protect the farmlands against animals like rabbits & wild cattle.

                Steps such as these can help reduce the use of chemicals in growing crops and help to increase crop yield. Growing of crops in such a manner is called organic farming.

Radioactive wastes

The waste produced from the nuclear fission of heavy atoms such as uranium, thorium etc for the production of power is radioactive waste.

This waste is highly toxic and causes mutations and cancer. It has to be dealt with utmost caution.

The nuclear waste should be stored after heavy treatment and packed in special containers. It should be buried deep under the ground for minimum of 60 – 80 years for the waste to stabilize. Even then there is a high chance of nuclear contamination of the surrounding areas & the ground water. Failure of nuclear power plants can have disastrous consequences. The use of nuclear fuels should be avoided if possible.

Greenhouse effect and global warming

Global warming refers to the heating up of the Earth due to greenhouse effect. Greenhouse effect is caused when gases such as CO2, CH4 etc increase in the atmosphere & this leads to the heating up of the earth as these are good absorbers of heat. These gases prevent the excess heat from leaving the Earth’s atmosphere thus resulting in greenhouse effect.

Presently the earth is 0.9oC hotter than normal, if earth’s temperature continues to rise then it could give rise to runaway global warming or the El Nino Effect. Over time this could disrupt the delicate pattern of ocean currents & give rise to another Ice Age which could be followed by mass extinction of several species and even endanger the Human Race.

Global warming can have grave consequences on the health of the planet & the biodiversity within it. Already thousands of species of flora & fauna have become extinct. The melting of ice caps will result in flooding of low lying areas; massive tsunamis; more powerful, fierce & unpredictable tornados; terrible storms & droughts etc.

                Scientists predict that about 3 – 4 billion humans would lose their lives mostly from developing countries by the year 2050. Finally the resulting Ice Age would have a devastating effect on the planet.

                We must control global warming to ensure that the biodiversity on Earth is conserved. The following steps can help reduce global warming

• Use of Hydrogen fuels & reducing the dependence on fossil fuels.
• Improving the efficiency of engines & turbines can drastically reduce pollution & also help save millions of Dollars\Euros every year.
• Controlling & reducing the human population.
• Planting hundreds of trees across cities & in homes.
• Using Magnetic trains. Mag - Lev trains are faster than planes & cause very little or no pollution compared to electric trains.
•  Preventing Deforestation & use of Carbon Credits.

Depletion of ozone layer

The depletion of ozone layer is one of the major cause for cancer.

Ozone is formed in the stratosphere by the effect of UV rays on O2. The thickness of ozone is measured in Dobson units.

The UV rays act on the CFCs to release freons that react with ozone to release pure oxygen. The freons merely act as catalysts & are not used up in the reaction. Hence the released freons have a continuous harmful effect on the ozone layer.

The CFCs released in the lower part of the atmosphere move upwards towards the south pole, hence depleting the ozone layer over Antarctica.

There are around 10 types of UV rays. Out of these the most common ones are UVa, UVb, UVc.

UV-a or black light (long wave) : It is used in tanning beds & to find counterfeit money.

UV-b (medium wave): Absorbed by ozone layer under normal conditions. It causes snow blindness, cataract, inflammation of cornea, aging of skin, skin cancer etc if exposed to the body.

UV-c (short wave) : Used as a germicidal , in laboratories & in the treatment of water.

Realizing the harmful effects of CFCs an international treaty called the Montreal Protocol was signed at Montreal, Canada in 1987 (effective 1989) to control CFCs emission throughout the world.

Degradation by improper utilization & maintenance of resources

Soil erosion & Desertification: It is a result of poor maintenance of top soil. Fertile top soil takes years to form but it can easily be removed especially due to human activities such as over – cultivation, over – grazing, deforestation, poor irrigation practices, use of chemicals etc. It results in degradation of the top soil & the land becomes barren. Urbanization is also a major problem of desertification.

                Water logging & soil salinity: Over irrigation especially without proper drainage leads to water logging of the soil. It also increases the salt content of the soil which heavily affects the health of plants. It is a post – green revolution problem.

 
Deforestation

Deforestation refers to the cutting down of trees for wood for furniture, fire wood, paper, to make cigarettes, to clear land for cultivation, due to the expansion of cities etc. Jhum cultivation is also a major contributor to deforestation in India.

                Deforestation has a very harmful effect on the environment. It leads to desertification, global warming, acid rain, depletion & pollution of ground water levels, loss of biodiversity in the affected areas etc.

There are various efforts to conserve the forests.

•          Hug a tree movement.
•          Organizations fighting to save trees.
•          In India Amrita Devi Bishnoi Wildlife Protection Award is given to individuals or organizations that show courage & dedication towards biodiversity.

There are various ways in which we can help to conserve trees:

•          Avoiding the use paper to read books & news.
•          Reforestation
•          Controlling growth of Human population & the expansion of cities.
•          Forming groups and communities to fight against deforestation.
•          Seeking help from governmental and non – governmental organizations for the conservation of forests.
•          Creating awareness about illegal selling of forestlands to companies & rich social groups.
•          Pressurizing the governments to pass laws to conserve trees & to check the deforestation caused by private companies, to limit the deforestation
           they cause.

Chapter 15

CHAPTER 15 – BIODIVERSITY & CONSERVATION

•       Definition- Biodiversity can be defined as the totality of genes, species and ecosystems of a given region.
•       This term was coined by EDWARD WILSON
•       Diversity ranges from macromolecules to biomes.
•       Biodiversity can be studied at-
                                1. Genetic diversity
                                 2. Species diversity
                                3. Ecological/Ecosystem diversity

1. GENETIC DIVERSITY
•       Greater the genetic diversity among organisms of a species, more sustenance it has against environmental perturbations.
•       Genetically uniform populations are highly prone to disease harsh environment.
•       Rauwolfia vomitoria shows genetic variation in terms of concentration and potency of chemical reserpine
•       There are more than 50,000 varieties of rice and nearly 1000 varieties of mangoes.

2. SPECIES DIVERSITY

Important measures-
   1. Species richness: It refers to the number of species per unit area.
   2. Species Evenness: It refers to the relative abundance with which each species is represented in an area.

•       The variety and number of individuals determine the level of diversity of an ecosystem.
•       The Western Ghats have a greater diversity of amphibian species than the Eastern Ghats.

3. ECOLOGICAL DIVERSITY
•       Ecological Diversity is related to species diversity.
•       India has greater ecosystem diversity than any other Scandinavian country.
•       India has several biomes like alpine meadows, rain forests, deserts, wetlands, mangroves…etc..
GLOBAL BIODIVERSITY

• According to the IUCN(2004) the total number of plant and animal species is about 1.5 million.
• More than 70% of the species recorded are animals and plants account for about 22%; 70% of the animals are insects.
• A more conservative and scientifically sound estimate has been made by Robert May ; it puts the global species diversity at about seven million.

These estimates do not give any figure for prokaryotes for the following reasons:

1.The conventional taxonomic methods are not sufficient for identifying these microbial species
2. Many of these species cannot be cultured under laboratory conditions.
3. Biochemical and molecular biology techniques would put their diversity into millions.

BIODIVERSITY IN INDIA
•       India is one of the twelve mega biodiversity countries of the world.
•       India has only 2.4% of the land area of the world, it has 8.1% of the global species biodiversity.
•       There are about 45,000 species of plants and about 90,000-1,00,000 species of animals.
•       New species are yet to be discovered and named.
•       Applying Robert May’s global estimate, only 22% of the total species have been recorded, India has probably more than 1,00,000 species of plants and 3,00,000 species of animals to be discovered and described.

PATTERNS OF BIODIVERSITY
•       Biodiversity is not uniform throughout the world but varies with latitude and altitude.
•       Favourable environmental conditions favour speciation and make it possible for a larger number of species to exist there , i.e., biodiversity is more in such areas than the others.

1.Latitudinal Gradients

• Species diversity decreased from equator towards poles.
• The tropics harbor more species than temperate and polar regions.
• Example- Colombia (near equator) has 1400 species of birds whereas New York(41° N) has 105 species, Greenland(71 ° N) has 56 species and India(equator region) has 1200 species.

VARIATION OF SPECIES WITH LATITUDE
•       The number of species of vascular plants in tropics is about ten times more than that of temperate forests.
•       Amazonian Rainforest has the greatest biodiversity on earth. It has more than 40000 species of plants, 1,25,000 species of insects, 300 species of fish, 427 of amphibian and 378 of reptiles, 1300 species of birds and 427 of mammals.

2.Species-Area Relationship
•       Alexander Von Humboldt has observed that within a region, species richness gets increased when explored area is increased, but only up to a limit.
•       The relationship between species richness and area for a number of taxa like angiospermic plants, fresh water fishes and birds is found to be a rectangular hyperbola.

Graph showing Species-Area Relationship

The equation is described by –

        log S = log C + Z log A

S – Species Richness
Z – Slope of the line (regression coefficient)
A – Area
C – y-intercept

•       Ecologists have found that Z value ranges between 0.1 & 0.2 irrespective of the taxonomic group or the region.
•       In very large area like continents, Z value ranges between 0.6 & 1.2.

IMPORTANCE OF SPECIES DIVERSITY TO ECOSYSTEM
•       Ecologists believe that communities with more species tend to be more stable than those with less species.

Attributes of a stable community-

1. It shall not show too much of variations in the year-to-year productivity.
2. It must be either resistant or resilient to seasonal disturbances.
3. It must be resistant also to alien species.

Feature of David Tilman’s ecology experiments-
1. The plots with more species showed less year-to-year variation in the total biomass.
2. Plots with increased diversity showed higher productivity.

      Hence, we realize that species richness and diversity are essential for ecosystem health as well as survival of human race on earth.

LOSS OF BIO-DIVERSITY :
•       Caused  by Population, Urbanisation and Industrialisation.
•       The colonisation of tropical Pacific Islands by human has led to the extinction of more than 2000 species of native birds.
•       15,500 species are facing the threat all around.
•       At now 31% gymnosperms,32%amphibians,12% bird species and 23% of mammals face the threat.
•       Loss of bio-diversity in a region leads to :
        (1) decrease in plant production.
        (2) less resistance to environmental disturbances such as droughts.
        (3) increases variability in ecosystem processes like plant productivity, water use, pest
             and disease cycles etc.

CAUSES OF BIODIVERSITY LOSSES.

1. Habitat  loss  and fragmentation
2. Over-exploitation
3. Alien  species  invasion
4. Co-extinction

I. HABITAT LOSS AND FRAGMENTATION
•       Destruction of habitat is the primary cause of extinction of species.
•       The tropical rainforests initially covered 14% of land but now only 6%.
•       The Amazon rain forest is also called ‘‘The lungs of the planet’’.
•       When large sized habitats are broken or fragmented due to human settlements, buildings of roads, digging of canals etc.., animals requiring large territories and some animals with migratory habitats are badly affected.

ll. OVER-EXPLOITATION
•       When biological system is over exploited by man for the natural resources ,it results in degradation and extinction of the resources , e.g Steller’s sea cow, passenger pigeon etc.

III. ALIEN SPECIES INVASIONS.
•       Some alien invasion has become invasive and causes maximum harmful impact and the extinction of the indigenous species.
•       Introduction of African catfish for aquaculture purposes is posing a threat to the existing species of catfishes of Indian rivers.

IV. CO-EXTINCTIONS
•       When a species become extinct, the plant and animal species associated with it in an obligatory manner, also become extinct.
•       For example, if the host fish species becomes extinct, all those parasites exclusively found on it will also become extinct.

Recent extinctions
·         Quagga, Africa
·         The Dodo Bird, Mauritius
·         Thylanine ,Australia
·         Steller’s sea cow.
·         Dugong resembling the steller’s sea cow

BIO-DIVERSITY CONSERVATION

1. Narrowly utilitarian
•       Humans derive a number of economic benefits from nature like food, firewood, fibres, medicines and more…
•       More than 25% of the drugs are derived from plants and more than 25,000 species of plants are used by natives for medicine.

2.  Broadly utilitarian
•       Biodiversity plays an important role in maintaining and sustaining supply of goods and services.
•       Amazon forest contributes 20% of the total oxygen in the atmosphere on earth.
•       Pollination of plants by providing pollinators, layer bee, birds and bats etc..

Ethical
•       There are thousands of plants, animals and microbes on this earth which are not useless.
•       Each one has some intrinsic value even if it is not of any economic value to us.
•       It is therefore our moral duty to ensure well-being of all the living creatures for the utilization.

CONSERVATION OF BIODIVERSITY
There are two basic approaches towards conservation of bio diversity:

• In situ conservation
• Ex situ conservation

I. In situ conservation:

a)  Biosphere reserves: Out of 425 biosphere reserves in the world, 14 are in India.  Hot spots are the areas / regions of high endemism and very high levels of species richness.  There are 34 hot spots in the world, of which three are in India; namely Western Ghats and Sri Lanka, Indo-Burma and Himalaya.

b) National parks and wildlife sanctuaries: India has 90 nationals parks and 448 wildlife sanctuaries.

c) Sacred groves: These are forest patches which were venerated and given total protection.  It includes a number of rare, endangered and endemic species. Ex. Western Ghats, Khasi and Jaintia Hills in Meghalaya.

II.  Ex situ conservation: India has 35 botanical gardens and 275 zoological parks. By using Cryopreservation (-196o C) technique, sperms, eggs, animal cells, tissues and embryos can be stored for long period.  Plants are propagated by using tissue culture methods called micropropagation.

CONVENTIONS ON BIODIVERSITY

•       The Earth Summit-Rio de Janeiro, 1992.
•       The World Summit, South Africa 2002.

     In the Summit, 190 countries pledged to reduce the current rate of biodiversity loss at global, regional and local levels by 2010.

Chapter 14

CHAPTER – 14 : ECOSYSTEM

British ecologist Arthur Tansley first defined the term Ecosystem.

ECOSYSTEM :- the functional unit of nature, where living organisms interact among themselves and with the surrounding physical environment.

Types of Ecosystems:

New Species Discovered in Different Ecosystems:
·         Pinocchio: long nosed frog found in Indonesia
·         Bald headed parrot in Amazon
·         Yeti Crab (Kiwa hirsuta) near Easter islands.

Structure of Ecosystems
An Ecosystem has two components:
·         Biotic components and
·         Abiotic components

Stratification:

This is the Vertical Distribution of Different Species occupying Different Levels.

The levels are called STRATA.

Aspects Affecting the Functioning of an Ecosystem are:

1. PRODUCTIVITY
The rate of synthesis of organic matter (biomass) during a given period of time. It is measured as weight (g-2) or as energy (kcal m-2). It is used to compare productivity of different ecosystems.

• Primary productivity:

It is the amount of biomass produced per unit area in a given time period by Plants during Photosynthesis.
GPP – R = NPP
*GPP-Gross Primary Productivity             *NPP-Net Primary Productivity

• Secondary productivity

It is the amount of biomass produced at any of the Consumer levels in a given period of time.

2. DECOMPOSITION

It is the process of breaking down of dead organic matter into smaller organic molecules and inorganic molecules by Decomposers (bacteria, fungi)

DETRITUS: Dead remains of plants and animals is called detritus.

DETRITIVORES: Animals that feed on decaying organic matter (detritus).

Examples: earthworms, termites, snails etc

Mechanism of Decomposition:

1. Fragmentation of Detritus: Detritivores feed on detritus ---breakdown --- increases the surface area of detritus particles for microbial action.
2. Leaching: Soluble inorganic nutrients dissolve in water -– percolate through the soil ---removed due to leaching action.
3. Catabolism: Decomposers (bacteria, fungi) release enzymes --- decompose detritus --- simpler inorganic compounds.
4. Humification: Simplified detritus--- converted to HUMUS

- Humus is a Dark, Amorphous substance.
- Highly resistant to Microbial Action
- Undergoes Decomposition very Slowly.
- Reservoir of nutrients (due to colloidal nature)

5. Mineralisation: Humus is degraded – releases inorganic substances
     ( CO2, H2O etc) and nutrients (Ca2+, Mg2+,K+ etc)

Factors affecting rate of Decomposition:

• Chemical composition - decomposition rate will be slow when detritus is rich in lignin and chitin and rate increases when detritus is rich in nitrogen and water soluble substances like sugsrs.
• Climatic conditions – warm and moist environment favour decomposition and low temperature and anaerobiosis inhibit decomposition.

3. ENERGY FLOW
►     SUN- Main Source of energy
►     50% of incident light is PHOTOSYNTHETICALLY ACTIVE  RADIATION (PAR)
►     2- 10 % of PAR is captured by plants.
►     Only a small fraction of this (stored as organic compounds) is transferred to consumers; the rest is used up in respiration and other life-supporting activities of the plants.
►     As energy is transferred as food, most part is lost as heat at each stage (10% LAW)

Unidirectional flow of Energy:
Sun        ->    Producers   ->   Consumers

Transfer of energy / food from the producer through a series of organisms is known as FOOD CHAINS.

FOOD CHAINS

• Food chains represent energy flow through ecosystems.
• Different steps in a food chain are TROPHIC LEVELS
• Basic terms: 

        Producers, Herbivores, Carnivores, Omnivores.

1.GRAZING FOOD CHAIN (GFC)

• Primary source of energy - Solar radiations.
• First trophic level includes - All Herbivores.
•  -GFCs are Long-sized chains

2) DETRITUS FOOD CHAIN (DFC)
·         Primary source of energy is Detritus.
·         First trophic level includes Detritivores.
·         Detritus Food Chains are small-sized chains.

SAPROPHYTES:These include decomposers (fungi, bacteria) which feed on detritus.

FOOD WEBS
•       The Natural Interconnection of Several Food Chains forms a FOOD WEB.
•       Provides alternate pathways for food availability.
•       Unlike food chains, food webs are never straight.
•       Help in ecosystem development and stability.

TEN PERCENT LAW:

Ø  By Lindemann in 1942

Ø  States that : during transfer of energy from one trophic level to another, only about 10% is stored at higher levels; remaining 90% is lost in respiration (heat)

4. ECOLOGICAL PYRAMIDS

• Developed by Charles Elton in 1927.
• Pyramids are an expression of the relationship between organisms at different trophic levels in terms of their number, biomass or energy.
• Three types of pyramids:

1.       Pyramid of Number
2.       Pyramid of Biomass
3.       Pyramid of energy

1. Pyramid of Number:  The relationship between producers and consumers in an ecosystem can be represented in the form of a pyramid in terms of number called pyramid of number.
2. Pyramid of Biomass:  The relationship between producers and consumers in an ecosystem can be represented in the form of a pyramid in terms of biomass called pyramid of biomass.  It can be of two types:

a)      Upright (in case of grassland ecosystem)
b)      Inverted (in case of pond ecosystem)


3.      Pyramid of energy:  The relationship between producers and consumers in an ecosystem can be represented in the form of a pyramid in terms of flow of energy called pyramid of energy.  It is always upright.
Learn more from your teachers in class along with diagram

Limitations of Ecological Pyramids:

• ž  It does NOT consider the same species belonging to two or more trophic levels.
• ž  It is based on simple food chains, which hardly exist. It does NOT accommodate food webs.
• ž  Saprophytes (decomposers) are NOT given any place in the ecosystem. 

Climax Community:

• Changes that lead finally to a community that is in near equilibrium with the environment.
• It remains stable as long as the environment remains unchanged.

The Rainforest is an example of climax community ecosystem.

Ecological Succession:

• Refers to predictable and orderly change in the composition or structure of a community.
• May be initiated either by formation of new, unoccupied habitat or by some form of disturbance of an existing community.
• Sere – entire sequence of community that successively change in a given area.
• Seral stages – individual transitional communities.

Seral Communities:

Hydrosere - Community in freshwater
Lithosere - Community on rock
Pssamosere - Community on sand
Halosere - Community in saline body
Xerosere - Community in dry area
Primary Succession

• If the development begins on an area that has not been previously occupied by a community.
• Pioneer species – lichens, phytoplankton, etc.
• Examples:

        - newly exposed rock or sand surface
        -  a lava flow
        -  glacial tills
        -  newly formed lake,

Secondary Succession

• If the community development is proceeding in an area from which a community was removed.
• Pioneer species – grasses, wildflowers, algae.
• Examples:

        -  an abandoned crop field
        -  cut-over forest
        -  natural forces such as wind storms and floods

Succession in Plants:

Hydrarch succession

• It takes place in wetter areas and the successional series progress from hydric to the mesic conditions.

Phytoplankton in pond -> Submerged plant stage-> Submerged free floating plant stage -> Reed – swamp stage -> Marsh – meadow stage – scrub stage -> Forest

Xerarch succession

• It takes place in dry areas and the series progress from xeric to mesic condition.

Bare rock -> Lichens and mosses -> Annual grasses -> Perennial grasses -> Shrubs -> Tall Trees

The Nutrient Cycle

• Also known as biogeochemical cycle.
• Environmental factors like soil, moisture, temperature, etc. regulate the rate of release of nutrients into the atmosphere.
• Standing state – amount of nutrients, such as C, N, P, Ca, etc. present in the soil at any given time.
• Nutrients are never lost from the ecosystem; they are recycled time an again indefinitely.
• There are two types:

                -  Gaseous cycle
                -  Sedimentary cycle

Ecosystem Services

• Humankind benefits from a multitude of resources and processes that are supplied by natural ecosystems. Collectively, these benefits are known as ecosystem services.

1. Purify air and water
2. Decomposition of waste materials
3. Cycle nutrients
4. Pollinate crops
5. Maintain biodiversity

• Researchers have put an average price tag of US $33 trillion a year on these fundamental ecosystems services, which is largely taken for granted because they are free.

Chapter 13

CHAPTER 13 – ORGANISMS AND POPULATIONS

ECOLOGY:Branch of Science which deals with relationship between organisms & their physical & biological environment.

LEVELS OF ORGANISATION:
•          Organisms- every individual of a species
•          Population- individuals of the same species at a given place
•          Communities- assembly of population of all different species living in an area and interacting.
•          Biomes- large unit of flora and fauna in a specific climatic zone

ENVIRONMENT
Sum of all biotic and abiotic factors that surround and influence an organism in it’s survival and reproduction.

Factors affecting environment:
•          Rotation of earth
•          Seasonal and annual  variation in temperature and precipitation
•          Habitats

MAJOR BIOMES
1.       Artic & Alpine Tundra
2.       Coniferous Forest
3.       Temperate Forests
4.       Grassland
5.       Tropical Forest
6.       Desert

MAJOR  ABIOTIC FACTORS
•          Temperature
•           Water
•           Light
•           Soil
Temperature
•          Ecologically most imp. Factor
•          Decreases progressively from equator towards pole and from plane to mountain tops
•           Polar Region and high altitudes- sub zero level Tropical deserts > 50°C
•          Organisms survive only in suitable range of temperature
•          Based on tolerance to temperature

            -   Eurythermal
                Organisms that tolerate wide range of temperature
            -   Stenothermal
                Organisms that tolerate only narrow range of temperature

Water
•          Life on earth originated in water
•           Productivity and distribution of plants depends on water

Based on tolerance to salinity
             - Euryhaline
                Organisms that can tolerate wide range of salinity
             - Stenohaline
                Organisms that can only tolerate narrow range of salinity

•          Freshwater animals cannot live in sea water and vice versa because of osmotic problems.

Light
•          sunlight source of energy- photosynthesis
•           Small plants (canopied by tall plants) adapted to photosynthesize at low light conditions.
•           Flowering dependent on sunlight
•           Foraging, Reproductive and migratory activities of animals depend on seasonal variation in light intensity
•           UV component – harmful to organisms

Soil
Nature of soil depends on
I.            climate
II.           weathering process
III.          sedimentary or transported
IV.          soil development

Characteristics of soil
a.       soil composition
b.      grain size
c.       aggregation- determine percolation and water holding capacity of soil

RESPONSES TO ABIOTIC FACTORS
Homeostasis: The ability of an organism to maintain the constancy of its internal environment despite varying external environmental conditions.

Q: How does Homeostasis occur?

1. Regulate: maintain homeostasis by ensuring constant body temp (thermoregulation), and constant osmotic concentration (osmoregulation). Examples – mammals regulate temperature by  shivering in cold and sweating in heat

2. Conform: internal environment of conformers changes with external environment

Q:Why small animals are rarely found in polar regions?

A: Small animals have large surface area compared to volume so they lose heat easily in cold and have to expend energy to generate body heat.

But, if stressful external conditions are localized or remain for short duration, then alternatives are migrate / suspend.

3. Migrate: Move from stressful habitat temporarily to hospitable area and return when stressful period over.

E.g.- Migration of birds to Keolado National Park, Rajasthan from Siberia

4. Suspend: Organisms develop mechanisms to deal with stressful situation

Examples- Spores (bacteria and fungi)

                - Seeds (angiosperms)- dormancy
                - Hibernation (Bears)
                - Aestivation ( snails)
                - Diapause (stage of suspended development) in zoo plankton

Adaptation

Any ability of an organism that enables an organism to survive and reproduce in its habitat

ADAPTATIONS IN ORGANISMS

1. Kangaroo rat: internal fat oxidation to produce water as by product- concentrated urine
2.Desert plants: thick cuticle, stomata in deep pits to minimize transpiration and special photosynthetic pathway (CAM).  Ex. OPUNTIA - leaves reduced to spines, photosynthetic stems
3. Cold climate mammals: short ears and limbs to minimize heat loss. This is Allen’s Rule.
4. People living at high altitude: increased RBC production and increased breathing rate
5. Desert lizards: bask in sun when cold and move to shade when hot.

POPULATION

Group of individuals living in a well defined area which share or compete for similar resources and potentially interbreed

Example: Lotus plants in a pond

                Bacteria in a culture plate

Population ecology is therefore, an imp. area of ecology because it links ecology to population genetics and evolution

POPULATION ATTRIBUTES

1.Birth rate- Average no. of young ones born in  a period of time with reference to the  members of the population.
2. Death rates- Average no. of deaths in a period of time with reference to the members of the population.
3.Sex Ratio- No. of females and males per 1000 individuals
4. Age pyramid: Plot of age distribution (% individuals of a given age or age group)

It reflects whether growth is
   (i)            Expanding
   (ii)           Stable
   (iii)          Declining

POPULATION DENSITY:
Number of individuals present per unit area at a given time.

POPULATION GROWTH
Factors affecting change in population density

1. Food availability
2. Predation pressure
3. Weather

Density changes by change in four basic processes
(a)    Natality              -     Increase population     
(b) Immigration      -    Increase population
(c)  Mortality           -    Decrease population
(d) Emigration        -    Decrease population

1.Natality (B) : Number of births during given period in the population that are added to the initial density
2.Mortality (D) : Number of deaths in the population during a given period.
3.Emigration (E) : Number of individuals of the population who left the habitat and went elsewhere during the given period
4. Immigration (I) : Number of individuals of the same species that have come into the habitat from elsewhere during the time under consideration.

• If N is the population density at time ‘t’, then its density at time ‘t+1’

                             Nt+1 = Nt + [(B + I) – (D + E)]

• Population density will increase if (B+I) > (D+E)

GROWTH MODELS

• EXPONENTIAL
• LOGISTIC

EXPONENTIAL GROWTH

•           When resources are unlimited, each species realizes its innate potential to grow in no. – population grows exponentially
•           N – Population size
                  b – Birth rates( per capita births)
                 d – Death rates (per capita deaths
                dN/dt – increase/decrease in N during time t

Then,   dN/dt = (b – d)*N
Let (b – d) = r, then
          dN/dt = r*N
Where, r – intrinsic rate of natural increase
For human population in 1981, r = 0.0205

Integral form of exponential growth eq.

                  Nt = N0ert

Where Nt = Population density after t
            N0 =Initial population density
            r   = Intrinsic rate of natural increase
            e  = base of natural logarithms

•           Species growing exponentially under unlimited resources reaches enormous population density in short time.

LOGISTIC GROWTH
•           No population has unlimited resources-leads to competition for resources
•          Fittest individual survive and reproduce
•          Carrying capacity (K)- Maximum population density a habitat’s resources can support
•          When a population has limited resources it shows

1. lag phase
2. phase of acceleration
3. asympote- population density = K    

Verhulst Pearl Logistic Growth

                          dN/dt = rN [(K – N)/K]

Where   N = Population density at time t
             r = Intrinsic rate of natural increase
             K = Carrying capacity

•           As resources for most organisms are finite logistic growth more realistic

LIFE HISTORY VARIATIONS

•          Darwinian fitness – Reproductive fitness
•          Organisms adopt most efficient reproductive strategy suited to their habitat

Examples:

1. Breed once in lifetime – pacific salmon fish ,Bamboo
2. Breed many times in life time – birds,  mammals
3. Produce large no. of small sized offspring  - Oysters, pelagic fishes
4. Produce small no. of large sized offspring - birds, mammals

Ecologists say life history traits depend on constraints of biotic and abiotic parts

 
Population Interactions

Minimum requirement of species- one more species to feed on.

Interspecific interactions - Interactions of populations of two different species.

Types of Interactions:

Name of Interaction        Species A       Species B

Mutualism                         +                   +
Competition                       -                    -
Predation                          +                   -
Parasitism                         +                   -
Commensalism                   +                   0
Ammensalism                     -                    0

+   Positive effect                    -  Detrimental effect                      0  Neutral effect 


PREDATION

It is an Interspecific Interaction where one animal kills and consumes the other weaker animal.

Roles of Predators

• Transfer energy from plants to higher trophic levels (position of organism in food chain)
• Control Prey population – Prickly pear cactus- moth
• Biological control of Agricultural pest
• Maintain species diversity by reducing intensity of competition among competing prey species

Q: Why predators are prudent?

A: Over exploitation of prey by the predators results in extinction of prey and predator.

Defense to lessen impact of predation

• Insects and frog – camouflage
• Monarch butterfly – poisonous

PLANTS MORPHOLOGICAL AND CHEMICAL DEFENCES

• Thorns- cactus and Acacia
• Produce and store chemical – Calotropis 
• Nicotine, Caffeine, Quinin, Strychnine, opium – against grazers & browsers

COMPETITION
Interaction either among individuals of same species or between individuals of different species.

Occurs among closely related species but not always true

1. Unrelated species also compete- flamingo & fish compete for zooplankton  
2. Feeding efficiency of a species reduce due to other species even if resources are plenty – Abingdon tortoise.


Evidence for competition
Competitive release – species distribution restricted to small areas due to competitively superior species.

GAUSE’S COMPETITION EXCLUSION PRINCIPLE
“Two closely related species competing for same resources cannot coexist as the competitively inferior one will be eliminated.”

Resource partition- Two competing species avoid competition by diff. feeding and foraging patterns-Mc Arthur (warblers foraging activities)

PARASITISM
It is the interaction where one species (parasite) depends on the other species (host) for food and shelter, host is harmed.

• Parasites and host self-evolve.
• Adaptations of parasites

               - Loss of unnecessary sense organs
               - Hooks and sucker
               - Loss of digestive system
               - High Reproductive capacity

• Parasites-

     (i) Reduce the survival of host
     (ii) Growth and reproductive rate are reduced
     (iii) Render the host vulnerable to its predators by making them weak

Types of parasite

ECTOPARASITES-depend on external surface of host
Example - head lice on humans, ticks on dogs

ENDOPARASITES-take shelter within the body of the host organism
Example - Liverfluke, Plasmodium

MUTUALISM
It is interaction in which both the interacting species are benefited

Examples
1. Lichen – fungi and algae
2. Mycorrhizae - fungi and roots of higher plants
3. Pollination of plants by insects
4. Mediterranean orchid- sexual deceit for pollination- appears as female bee

AMENSALISM
Interaction between two different species, in which one species is harmed and the other species is neither harmed nor benefited. Example.  Bacterial culture, after few days fungus growth will be there on it like Pencillium, and its secretions of chemical will kill bacteria, but no benefits to fungi.

Chapter 12

CHAPTER – 12 : BIOTECHNOLOGY AND ITS APPLICATIONS

The applications of biotechnology include therapeutics, diagnostics and genetically modified crops for agriculture, processed food, bioremediation, waste treatment, and energy production.

Three critical research areas of biotechnology are;

• Providing the best catalyst in the form of improved organism usually a microbe or pure enzyme.
• Creating optimal conditions through engineering for a catalyst to act, and
• Downstream processing technologies to purify the protein / organic compound.

Biotechnological Applications in Agriculture:
The three options that can be thought for increasing food production are,

• Agro-chemical based agriculture
• Organic agriculture; and
• Genetically engineered crop-based agriculture.

The Green Revolution has succeeded in tripling the food supply but yet it was not enough to feed the growing human population. Scientists have decided that use of genetically modified crops is a possible solution.

Plants, bacteria, fungi and animals whose genes have been altered by manipulation are called Genetically Modified Organisms (GMO).  Genetic modification has;

• Made crops more tolerant to abiotic stresses
• Reduced reliance on chemical pesticides
• Helped to reduce post harvest losses
• Increased efficiency of mineral usage by plants
• Enhanced nutritional value of food, eg., Vitamin ‘A’ enriched rice.

Bt Cotton:
Some strains of Bacillus thuringiensis produce a toxic insecticidal protein.  The Bt toxin protein exist as inactive protoxins but once an insect ingest the inactive toxin, it is converted into an active form of toxin due to the alkaline pH of the gut which solubilise the crystals.  The activated toxin binds to the surface of midgut epithelial cells and creates pores that cause cell swelling and lysis and eventually cause death of the insect.

Bt toxin genes were isolated from B. thuringiensis and incorporated into the several crop plants such as cotton.  The toxin is coded by a gene named ‘cry’.  There are a number of them, for example, the proteins encoded by the genes cryIAc and cryIIAb control bollworms and cryIAb controls corn borer.

Pest Resistant Plants: A nematode Meloidegyne incognitia infects the roots of tobacco plants and causes a great reduction in yield.  A novel strategy was adopted to prevent this infestation which was based on the process of RNA interference (RNAi).  This method involves silencing of a specific mRNA due to a complementary dsRNA molecule that binds to and prevents translation of the mRNA (silencing).

Using Agrobacterium vectors, nematode-specific genes were introduced into the host plant.  The introduction of DNA was such that it produced both sense and anti-sense RNA in the host cells.  These two RNA’s being complementary to each other formed a double stranded (ds DNA) that initiated RNAi and thus, silenced the specific mRNA of the nematode.  The consequence was that the parasite could not survive in a transgenic host expressing specific interfering RNA.  The transgenic plant therefore got itself protected from the parasite.

Biotechnological Application in Medicine: The rDNA technological processes have made immense impact in the area of healthcare by enabling mass production of safe and more effective therapeutic drugs.  At present, about 30 recombinant therapeutics have been approved for human use the world over. In India, 12 of these are presently being marketed. 

Genetically Engineered Insulin: Insulin consists of two short polypeptide chains; chain A and chain B, that are linked together by disulphide bridges.  In mammals, including humans, insulin is synthesized as a prohormone, which contains an extra stretch called the C peptide. This C peptide is not present in the mature insulin and is removed during maturation into insulin.

In 1983, Eli Lilly an American company prepared two DNA sequences corresponding to A and B, chains of human insulin and introduced hem in plasmids of E.coli to produce insulin chains.  Chains A and B were produced separately, extracted and combined by creating disulfide bonds to form human insulin.
Gene Therapy: Gene therapy is a collection of methods that allows correction of a gene defect that has been diagnosed in a child / embryo.  Correction of a genetic defect involves delivery of a normal gene into the individual or embryo to take over the function of and compensate for the non-functional gene.

The first clinical gene therapy was given in 1990 to a 4-year old girl with adenosine deaminase (ADA) deficiency.  This enzyme is crucial for the immune system to function. 

As a first step towards gene therapy, lymphocytes from the blood of the patient are grown in a culture outside the body.  A functional ADA cDNA is then introduced into these lymphocytes, which are subsequently returned to the patient.  However, if the gene isolate from marrow cells producing ADA is introduced into cells at early embryonic stages, it could be a permanent cure.

Molecular Diagnosis:
Recombinant DNA technology, Polymerase Chain Reaction (PCR) and Enzyme Linked Immuno-sorbent Assay (ELISA) are some of the techniques that serve the purpose of early diagnosis.

PCR:
A very low concentration of a bacteria or virus can be detected by amplification of their nucleic acid by PCR.  PCR is now routinely used to detect HIV in suspected AIDS patients. It is being used to detect mutations in genes in suspected cancer patients too.

ELISA:
It is based on the principle of antigen-antibody interaction.  Infection by pathogen can be detected by presence of antigens or by detecting the antibodies synthesized against the pathogen.

Transgenic Animals:
Animals that have their DNA manipulated to possess and express an extra (foreign) gene are known as Transgenic Animals.

Reasons for the production of transgenic animals:
a)         Normal physiology and development:  Transgenic animals can be specifically designed to allow the study of how genes are regulated and how they affect the normal functions of the body and its development.
b)         Study of disease:  Many transgenic animals are designed to increase our understanding of how genes contribute to the development of disease, so that investigation of new treatments for diseases is made possible.
c)          Biological products:  Transgenic animals that produce useful biological products can be created by the introduction of the portion of DNA (gene) which codes for a particular product such as human protein (alpha – 1-antitrypsin) used to treat emphysema.  The first transgenic cow, Rosie, produced human protein-enriched milk (alpha-lactalbumin - 2.4 gm / litre).
d)         Vaccine safety:  Transgenic mice are being developed for use in testing the safety of vaccines before they are used on humans (polio vaccine).
e)         Chemical safety testing:  Transgenic animals are made that carry genes which make them more sensitive to toxic substances than non-transgenic animals. They are then exposed to the toxic substances and the effects studied.

Ethical Issues:
The Indian Government has set up organizations such as GEAC (Genetic Engineering Approval Committee), which will make decisions regarding the validity of GM research and the safety of introducing GM-organisms for public services.

Biopatent:
A patent is the right granted by a government to an inventor to prevent others from making commercial use of his invention. Now, patents are granted for biological entities and for products derived from biological resources. 

Biopiracy:
It is the term used to refer to the use of bio-resources by multinational companies and other organizations without proper authorization from the countries and people concerned without compensatory payment.

In 1997, an American company got patent rights on Basmati rice through the US Patent and Trademark Office.  This allowed the company to sell a ‘new variety of Basmati, in the US and abroad.  This ‘new’ variety of Basmati had actually been derived from Indian farmer’s varieties. Indian Basmati was crossed with semi-dwarf varieties and claimed as an invention or a novelty.

Several attempts have also been made to patent uses, products and processes based on Indian traditional herbal medicines, e.g., turmeric and neem.

Chapter 11

CHAPTER – 11 : BIOTECHNOLOGY : PRINCIPLES AND PROCESSES

• Biotechnology deals with techniques of using live organisms or enzymes from organisms to produce products and processes useful to humans.

• The definition given by EFB (European Federation of Biotechnology) is as follows; ‘The integration of natural science and organisms, cells, parts thereof, and molecular analogues for products and services’.

Principles of Biotechnology:

• Genetic engineering: Techniques to alter the chemistry of genetic material (DNA and RNA), to introduce these into host organisms and thus change the phenotype of the host organism.
• Maintenance of sterile ambience in chemical engineering processes to enable growth of only the desired microbe / eukaryotic cell in large quantities for the manufacture of biotechnological products like antibiotics, vaccines, enzymes, etc.

The techniques of genetic engineering which include creation of recombinant DNA, use of gene cloning and gene transfer,helps to overcome the limitation of undesired genes getting multiplied along with the desired genes in traditional hybridisation techniques and allow us to isolate and introduce only one or a set of desirable genes without introducing undesirable genes into the target organism.

In a chromosome there is a specific DNA sequence called the origin of replication, which is responsible for initiating replication.  Therefore, for the multiplication of any alien piece of DNA in an organism it needs to be a part of a chromosome which has a specific sequence known as ‘origin of replication’.  Thus, an alien DNA is linked with the origin of replication, so that, this alien piece of DNA can replicate and multiply itself in the host organism.  This is known as Cloning.

The construction of the first recombinant DNA emerged from the possibility of linking a gene encoding antibiotic resistance with a native Plasmid of Salmonella typhimurium.

The cutting of DNA at specific locations became possible with the discovery of the so-called ‘Molecular scissors” – restriction enzymes.  The cut piece of DNA was then linked with the plasmid DNA with the help of another enzyme called DNA ligase.  These plasmid DNA act as vectors to transfer the piece of DNA attached to it. A plasmid can be used as vector to deliver an alien piece of DNA into the host organism.

“Recombinant DNA technology” or also called “Genetic Engineering” deals about, the production of new combinations of genetic material (artificially) in the laboratory.  These “recombinant DNA” (rDNA) molecules are then introduced into host cells, where they can be propagated and multiplied. 

Basic steps in rDNA:

• Identification of DNA with desirable genes
• Introduction of the identified DNA into the host
• Maintenance of introduced DNA in the host and transfer of the DNA to its progeny.

Tools of Recombinant DNA Technology:

Restriction Enzymes (Molecular Scissors):
Restriction enzymes belong to a larger class of enzymes called Nucleases.  There are of two kinds; Exonucleases and Endonucleases.  Exonucleases remove nucleotides from the ends of the DNA whereas, endonucleases make cuts at specific position within the DNA.

Example, the first restriction endonuclease – Hind II, always cut DNA molecules at a particular point by recognizing a specific sequence of six base pairs. This specific base sequence is known as the Recognition Sequence for Hind II.

Each restriction endonuclease recognizes a specific Palindromic Nucleotide Sequences in the DNA.

What are Palindromes?
These are groups of letters that form the same words when read both forward and backward, eg. “MALAYALAM”.  The palindrome in DNA is a sequence of base pairs that reads same on the two strands when orientation of reading is kept the same.

Restriction enzymes cut the strand of DNA a little away from the centre of the palindrome sites, but between the same two bases on the opposite strands.  This leaves single stranded portions at the ends called Sticky ends. The same enzyme cuts both DNA (vector and foreign DNAs) strands at the same site with sticky ends and these can be joined together using DNA-ligase.

Separation and Isolation of DNA fragments (DNA of interest):

• The cutting of DNA by restriction endonucleases results in the fragments of DNA.
• These fragments can be separated by a technique known as Gel Electrophoresis.
• The DNA fragments are separated according to their size.
• The separated DNA fragments can be visualized only after staining the DNA with Ethidium bromide followed by exposure to UV radiation.  Now DNA fragments appear bright orange coloured bands.
• The separated bands of DNA are cut out from the agarose gel and extracted from the gel piece. This step is known as Elution.
• These DNA fragments are purified and used in constructing recombinant DNA with cloning vector.

Cloning Vectors (Vehicles for Cloning):
Vector serves as a vehicle to carry a foreign DNA sequence into a given host cell.

Salient features of  a Vector:

• It should contain an origin of replication (ori) so that it is able to multiply within the host cell.
• It should incorporate a selectable marker (antibiotic resistance gene), which will allow to select those host cells that contain the vector from amongst those which do not.
• The vector must also have atleast one unique restriction endonuclease recognition site to enable foreign DNA to be inserted into the vector during the generation of a recombinant DNA molecule.
• The vector should be relatively small in size.

The most commonly used vectors are – Plasmids and Bacteriophages.

Identification of recombinants:

Insertional inactivation:
The most efficient method of screening for the presence of recombinant plasmids is based on the principle that the cloned DNA fragment disrupts the coding sequence of a gene.  This is termed as Insertional Inactiviation.

For example, the powerful method of screening for the presence of recombinant plasmids is referred to as Blue-White selection.  This method is based upon the insertional inactivation of the lac Z gene present on the vector.  The lac Z gene encodes the enzyme beta-galactosidase, which can cleave a chromogenic substrate into a blue coloured product.  If this lac Z gene is inactivated by insertion of a target DNA fragment into it, the development of the blue colour will be prevented and it gives white coloured colonies.  By this way, we can differentiate recombinant (white colour) and non-recombinant (blue colour) colonies.
Competent Host (Introduction of recombinant DNA into host cells):
In rDNA technology, the most common method to introduce rDNA into living cells is transformation, during which cells take up DNA from the surrounding environment.
1)      Simple chemical treatment with divalent calcium ions increases the efficiency of host cells (through cell wall pores) to take up the rDNA plasmids.
2)      rDNA can also be transformed into host cell by incubating both on ice, followed by placing them briefly at 42oC (Heat Shock), and then putting them back on ice. This enables the bacteria to take up the recombinant DNA.
3)      In Microinjection method, rDNA is directly injected into the nucleus of  cells by using a glass micropipette.
4)      Biolistics / Gene gun method, it has been developed to introduce rDNA into mainly plant cells by using a Gene / Particle gun.  In this method, microscopic particles of gold / tungsten are coated with the DNA of interest and bombarded onto cells.
5)      The last method uses “Disarmed Pathogen” Vectors (Agrobacterium tumefaciens), which when allowed to infect the cell, transfer the recombinant DNA into the host.

                                                                                                                   
Processes of Reombinant DNA Technology:
rDNA technology involves several steps in specific sequence such as,

• Isolation of DNA
• Fragmentation of DNA by restriction endonucleases
• Isolation of desired DNA fragment
• Ligation of the DNA fragment into a vector
• Transferring the recombinant DNA into the host
• Culturing the host cells in a medium at large scale and extraction of the desired product

Isolation of DNA:
DNA should be isolated in pure form, without macromolecules.  Hence cell wall can be broken down by treating the bacterial cells / plant or animal tissue with enzymes such as Lysozyme (bacteria), cellulose (plant cells), chitinase (fungus).

DNA should be removed from its histones proteins and RNAs.  This can be achieved by using enzymes ribonuclease for RNA and Proteases for histone proteins.

Finally purified DNA precipitates out after the addition of chilled Ethanol.
Fragmentation of DNA:

• Restriction enzyme digestions are performed by incubating purified DNA molecules with the restriction enzyme.
• DNA is a negatively charged molecule, hence it moves towards the positive electrode (anode).
• After having cut the source DNA as well as the vector DNA with a specific restriction enzyme, the cut out gene of interest from the source DNA and the cut vector with space are mixed and ligase is added.  This results in the preparation of recombinant DNA.

Amplification of Gene of Interest using PCR: PCR stands for Polymerase Chain Reaction.  In this reaction, multiple copies of the gene of interest is synthesized in vitro using two sets of primers and the enzyme DNA polymerase.

The process of replication of DNA is repeated many times, the segment of DNA can be amplified to approximately billion times. Such repeated amplification is achieved by the use of a themostable DNA polymerase (Taq DNA Polymerase – isolated from a bacterium, Thermus aquaticus).  The amplified fragment if desired can now be used to ligate with a vector for further cloning.

Insertion of Recombinant DNA into the Host Cell / Organism: There are several methods of introducing the ligated DNA into recipient cells. If a recombinant DNA bearing gene for resistance to an antibiotic (ampicillin) is transferred into E.coli cells, the host cells become transformed into ampicillin-resistant cells. If we spread the transformed cells on agar plates containing ampicillin, only transformants will grow, untransformed recipient cells will die. The ampicillin resistance gene in this case is called a selectable marker.

Obtaining the Foreign Gene Product: The cells harbouring cloned genes of interest may be grown on a small scale in the laboratory.  The cultures may be used for extracting the desired protein and then purifying it by using different separation techniques.

Bioreactors : To produce in large quantities, the development of bioreactors, where large volume of culture can be processed, was required.  Thus, bioreactors can be thought of as vessels in which raw materials are biologically converted into specific products, individual enzymes, etc., using microbial plant, animal or human cells. A bioreactor provides the optimal conditions for achieving the desired product by providing optimum growth conditions (temperature, pH, substrate, salts, vitamins, oxygen).

Stirred-tank reactor: It is usually cylindrical or with a curved base to facilitate the mixing of the reactor contents.  The stirrer facilitates even mixing and oxygen availability throughout the bioreactor.  Alternatively air can be bubbled through the reactor.  The bioreactor has an agitator system, an oxygen delivery system and a foam control system, a temperature control system, pH control system and sampling ports so that small volumes of the culture can be withdrawn periodically.

Downstream Processing: The processes include separation and purification, which are collectively referred to as downstream processing.  Strict quality control testing for each product is also required.