Biotechnology

Insulin crystals.

Biotechnology is a field of applied biology that involves the use of living organisms and bioprocesses in engineering, technology, medicine and other fields requiring bioproducts. Modern use similar term includes genetic engineering as well as cell- andtissue culture technologies. The concept encompasses a wide range of procedures (andhistory) for modifying living organisms according to human purposes - going back to domestication of animals, cultivation of plants, and "improvements" to these through breeding programs that employ artificial selection and hybridization. By comparison to biotechnology, bioengineering is generally thought of as a related field with its emphasis more on higher systems approaches (not necessarily altering or using biological materials directly) for interfacing with and utilizing living things. The United NationsConvention on Biological Diversity defines biotechnology as:[1]

"Any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use."

Biotechnology draws on the pure biological sciences (genetics, microbiology, animal cell culture, molecular biology, biochemistry,embryology, cell biology) and in many instances is also dependent on knowledge and methods from outside the sphere of biology (chemical engineering, bioprocess engineering, information technology, biorobotics). Conversely, modern biological sciences (including even concepts such as molecular ecology) are intimately entwined and dependent on the methods developed through biotechnology and what is commonly thought of as the life sciences industry.

[edit]History

Brewing was an early application of biotechnology

Main article: History of Biotechnology

Biotechnology is not limited to medical/health applications (unlike Biomedical Engineering, which includes much biotechnology). Although not normally thought of as biotechnology, agriculture clearly fits the broad definition of "using a biotechnological system to make products" such that the cultivation of plants may be viewed as the earliest biotechnological enterprise. Agriculture has been theorized to have become the dominant way of producing food since the Neolithic Revolution. The processes and methods of agriculture have been refined by other mechanical and biological sciences since its inception. Through early biotechnology, farmers were able to select the best suited crops, having the highest yields, to produce enough food to support a growing population. Other uses of biotechnology were required as the crops and fields became increasingly large and difficult to maintain. Specific organisms and organism by-products were used to fertilize, restore nitrogen, and control pests. Throughout the use of agriculture, farmers have inadvertently altered the genetics of their crops through introducing them to new environments and breeding them with other plants—one of the first forms of biotechnology. Cultures such as those in Mesopotamia, Egypt, and Indiadeveloped the process of brewing beer. It is still done by the same basic method of using malted grains (containing enzymes) to convert starch from grains into sugar and then adding specific yeasts to produce beer. In this process the carbohydrates in the grains were broken down into alcohols such as ethanol. Ancient Indians also used the juices of the plant Ephedra vulgaris and used to call it Soma.[citation needed] Later other cultures produced the process of Lactic acid fermentation which allowed the fermentation and preservation of other forms of food. Fermentation was also used in this time period to produce leavened bread. Although the process of fermentation was not fully understood until Pasteur’s work in 1857, it is still the first use of biotechnology to convert a food source into another form.

For thousands of years, humans have used selective breeding to improve production of crops and livestock to use them for food. In selective breeding, organisms with desirable characteristics are mated to produce offspring with the same characteristics. For example, this technique was used with corn to produce the largest and sweetest crops.[2]

In the early twentieth century scientists gained a greater understanding of microbiology and explored ways of manufacturing specific products. In 1917, Chaim Weizmann first used a pure microbiological culture in an industrial process, that of manufacturing corn starchusing Clostridium acetobutylicum, to produce acetone, which the United

Kingdom desperately needed to manufacture explosives duringWorld War I.[3]

Biotechnology has led to the development of antibiotics. In 1928, Alexander Fleming discovered the mold Penicillium. His work led to the purification of the antibiotic by Howard Florey, Ernst Boris Chain and Norman Heatley penicillin. In 1940, penicillin became available for medicinal use to treat bacterial infections in humans.[2]

The field of modern biotechnology is thought to have largely begun on June 16, 1980, when the United States Supreme Court ruled that a genetically modified microorganism could be patented in the case of Diamond v. Chakrabarty.[4] Indian-born Ananda Chakrabarty, working for General Electric, had developed a bacterium (derived from the Pseudomonas genus) capable of breaking down crude oil, which he proposed to use in treating oil spills.

Revenue in the industry is expected to grow by 12.9% in 2008. Another factor influencing the biotechnology sector's success is improved intellectual property rights legislation—and enforcement—worldwide, as well as strengthened demand for medical and pharmaceutical products to cope with an ageing, and ailing, U.S. population.[5]

Rising demand for biofuels is expected to be good news for the biotechnology sector, with the Department of Energy estimating ethanolusage could reduce U.S. petroleum-derived fuel consumption by up to 30% by 2030. The biotechnology sector has allowed the U.S. farming industry to rapidly increase its supply of corn and soybeans—the main inputs into biofuels—by developing genetically modified seeds which are resistant to pests and drought. By boosting farm productivity, biotechnology plays a crucial role in ensuring that biofuel production targets are met.[6]

[edit]Applications

A rose plant that began as cells grown in a tissue culture

Biotechnology has applications in four major industrial areas, including health care (medical), crop production and agriculture, non food (industrial) uses of crops and other products (e.g. biodegradable plastics, vegetable oil, biofuels), and environmental uses.

For example, one application of biotechnology is the directed use of organisms for the manufacture of organic products (examples include beer and milk products). Another example is using naturally present bacteria by the mining industry in bioleaching. Biotechnology is also used to recycle, treat waste, clean up sites contaminated by industrial activities (bioremediation), and also to produce biological weapons.

A series of derived terms have been coined to identify several branches of biotechnology, for example:

. Bioinformatics is an interdisciplinary field which addresses biological problems using computational techniques,

and makes the rapid organization and analysis of biological data possible. The field may also be referred to as computational biology, and can be defined as, "conceptualizing biology in terms of molecules and then

applying informatics techniques to understand and organize the information associated with these molecules, on a large scale."[7] Bioinformatics plays a key role in various areas, such as functional genomics, structural genomics, andproteomics, and forms a key component in the biotechnology and pharmaceutical sector.

. Blue biotechnology is a term that has been used to describe the marine and aquatic applications of biotechnology, but its use is relatively rare.

. Green biotechnology is biotechnology applied to agricultural processes. An example would be the selection

and domestication of plants via micropropagation. Another example is the designing of transgenic plants to grow

under specific environments in the presence (or absence) of chemicals. One hope is that green biotechnology might produce more environmentally friendly solutions than traditional industrial agriculture. An example of this is

the engineering of a plant to express a pesticide, thereby ending the need of external application of pesticides. An example of this would be Bt corn. Whether or not green biotechnology products such as this are ultimately more environmentally friendly is a topic of considerable debate.

. Red biotechnology is applied to medical processes. Some examples are the designing of organisms to produce antibiotics, and the engineering of genetic cures through genetic manipulation.

. White biotechnology, also known as industrial biotechnology, is biotechnology applied to industrial processes.

An example is the designing of an organism to produce a useful chemical. Another example is the using of enzymes as industrial catalysts to either produce valuable chemicals or destroy hazardous/polluting chemicals. White biotechnology tends to consume less in resources than traditional processes used to produce industrial goods.[citation needed] The investment and economic output of all of these types of applied biotechnologies is termed as bioeconomy.

[edit]Medicine

In medicine, modern biotechnology finds promising applications in such areas as

. drug production

. pharmacogenomics

. gene therapy

. genetic testing: techniques in molecular biology detect genetic diseases. To test the developing fetus for Down syndrome,Amniocentesis and chorionic villus sampling can be used.[2]

[edit]Pharmacogenomics

DNA Microarray chip – Some can do as many as a million blood tests at once

Main article: Pharmacogenomics

Pharmacogenomics is the study of how the genetic inheritance of an individual affects his/her body’s response to drugs. It is a coined word derived from the words ―pharmacology‖ and ―genomics‖. It is hence the study of the relationship between pharmaceuticals and genetics. The vision of pharmacogenomics is to be able to design and produce drugs that are adapted to each person’s genetic makeup.[8]

Pharmacogenomics results in the following benefits:[8]

1. Development of tailor-made medicines. Using pharmacogenomics, pharmaceutical companies can create

drugs based on the proteins, enzymes and RNA molecules that are associated with specific genes and diseases. These tailor-made drugs promise not only to maximize therapeutic effects but also to decrease damage to nearby healthy cells.

2. More accurate methods of determining appropriate drug dosages. Knowing a patient’s genetics will enable doctors to determine how well his/ her body can process and metabolize a medicine. This will maximize the value of the medicine and decrease the likelihood of overdose.

3. Improvements in the drug discovery and approval process. The discovery of potential therapies will be made easier using genome targets. Genes have been associated with numerous diseases and disorders. With

modern biotechnology, these genes can be used as targets for the development of effective new therapies, which could significantly shorten the drug discovery process.

4. Better vaccines. Safer vaccines can be designed and produced by organisms transformed by means of genetic engineering. These vaccines will elicit the immune response without the attendant risks of infection. They will be inexpensive, stable, easy to store, and capable of being engineered to carry several strains of pathogen at once.

[edit]Pharmaceutical products

Computer-generated image of insulin hexamers highlighting the threefold symmetry, the zinc ions holding it together, and the histidine residues involved in zinc binding.

Most traditional pharmaceutical drugs are relatively simple molecules that have been found primarily through trial and error to treat the symptoms of a disease or illness.[citation needed] Biopharmaceuticals are large biological molecules known asproteins and these usually target the underlying mechanisms and pathways of a malady (but not always, as is the case with using insulin to treat type 1 diabetes mellitus, as that treatment merely addresses the symptoms of the disease, not the underlying cause which is autoimmunity); it is a relatively young industry. They can deal with targets in humans that may not be accessible with traditional medicines. A patient typically is dosed with a small molecule via a tablet while a large molecule is typically injected.

Small molecules are manufactured by chemistry but larger molecules are created by living cells such as those found in the human body: for example, bacteria cells, yeast cells, animal or plant cells.

Modern biotechnology is often associated with the use of genetically alteredmicroorganisms such as E. coli or yeast for the production of substances like synthetic insulin or antibiotics. It can also refer totransgenic animals or transgenic plants, such as Bt corn. Genetically altered mammalian cells, such as Chinese Hamster Ovary (CHO) cells, are also used to manufacture certain pharmaceuticals. Another promising new biotechnology application is the development ofplant-made pharmaceuticals.

Biotechnology is also commonly associated with landmark breakthroughs in new medical therapies to treat hepatitis B, hepatitis C,cancers, arthritis, haemophilia, bone fractures, multiple sclerosis, and cardiovascular disorders. The biotechnology industry has also been instrumental in developing molecular diagnostic devices that can be used to define the target patient population for a given biopharmaceutical. Herceptin, for example, was the first drug approved for use with a matching diagnostic test and is used to treat breast cancer in women whose cancer cells express the protein HER2.

Modern biotechnology can be used to manufacture existing medicines relatively easily and cheaply. The first genetically engineered products were medicines designed to treat human diseases. To cite one example, in 1978 Genentech developed synthetic humanizedinsulin by joining its gene with a plasmid vector inserted into the bacterium Escherichia coli. Insulin, widely used for the treatment of diabetes, was previously extracted from the pancreas of abattoir animals (cattle and/or pigs). The resulting genetically engineered bacterium enabled the production of vast quantities of synthetic human insulin at relatively low cost.[9] According to a 2003 study undertaken by the International Diabetes Federation (IDF) on the access to and availability of insulin in its member countries, synthetic 'human' insulin is considerably more expensive in most countries where both synthetic 'human' and animal insulin are commercially available: e.g. within European countries the average price of synthetic 'human' insulin was twice as high as the price of pork insulin.[10]Yet in its position statement, the IDF writes that "there is no overwhelming evidence to prefer one species of insulin over another" and "[modern, highly purified] animal insulins remain a perfectly acceptable alternative.[11]

Modern biotechnology has evolved, making it possible to produce more easily and relatively cheaply human growth hormone, clotting factors for hemophiliacs, fertility drugs, erythropoietin and other drugs.[12] Most drugs today are based on about 500 molecular targets. Genomic knowledge of the genes involved in diseases, disease pathways, and drug-response sites are expected to lead to the discovery of thousands more new targets.[12]

[edit]Genetic testing

Gel electrophoresis

Genetic testing involves the direct examination of the DNA molecule itself. A scientist scans a patient’s DNA sample for mutated sequences.

There are two major types of gene tests. In the first type, a researcher may design short pieces of DNA (―probes‖) whose sequences are complementary to the mutated sequences. These probes will seek their complement among the base pairs of an individual’s genome. If the mutated sequence is present in the patient’s genome, the probe will bind to it and flag the mutation. In the second type, a researcher may conduct the gene test by comparing the sequence of DNA bases in a patient’s gene to disease in healthy individuals or their progeny.

Genetic testing is now used for:

. Carrier screening, or the identification of unaffected individuals who carry one copy of a gene for a disease that requires two copies for the disease to manifest;

. Confirmational diagnosis of symptomatic individuals;

. Determining sex;

. Forensic/identity testing;

. Newborn screening;

. Prenatal diagnostic screening;

. Presymptomatic testing for estimating the risk of developing adult-onset cancers;

. Presymptomatic testing for predicting adult-onset disorders.

Some genetic tests are already available, although most of them are used in developed countries. The tests currently available can detect mutations associated with rare genetic disorders like cystic fibrosis, sickle cell anemia, and Huntington’s disease. Recently, tests have been developed to detect mutation for a handful of more complex conditions such as breast, ovarian, and colon cancers. However, gene tests may not detect every mutation associated with a particular condition because many are as yet undiscovered, and the ones they do detect may present different risks to different people and populations.[12]

[edit]Controversial questions

The bacterium Escherichia coli is routinely genetically engineered.

The absence of privacy and anti-discrimination legal protections in most countries can lead to discrimination in employment or insurance or other use of personal genetic information. This raises questions such as whether genetic privacy is different from medical privacy.[13]

1. Reproductive issues. These include the use of genetic information in reproductive decision-making and the possibility of genetically altering reproductive cells that may be passed on to future generations. For example, germline therapy changes the genetic make-up of an individual’s descendants. Thus, any error in technology or judgment may have far-reaching consequences (though the same can also happen through natural reproduction). Ethical issues like designed babies and human cloning have also given rise to controversies between and among scientists and bioethicists, especially in the light of past abuses witheugenics (see reductio ad hitlerum).

2. Clinical issues. These center on the capabilities and limitations of doctors and other health-service providers, people identified with genetic conditions, and the general public in dealing with genetic information.

3. Effects on social institutions. Genetic tests reveal information about individuals and their families. Thus, test results can affect the dynamics within social institutions, particularly the family.

4. Conceptual and philosophical implications regarding human responsibility, free will vis-à-vis genetic determinism, and the concepts of health and disease.

[edit]Gene therapy

Main article: Gene therapy

Gene therapy using an Adenovirus vector. A new gene is inserted into an adenovirus vector, which is used to introduce the modified DNA into a human cell. If the treatment is successful, the new gene will make a functional protein.

Gene therapy may be used for treating, or even curing, genetic and acquired diseases like cancer and AIDS by using normal genes to supplement or replace defective genes or to bolster a normal function such as immunity. It can be used to target somatic (i.e., body) or gametes (i.e., egg and sperm) cells. In somatic gene therapy, the genome of the recipient is changed, but this change is not passed along to the next generation. In contrast, in germline gene therapy, the egg and sperm cells of the parents are changed for the purpose of passing on the changes to their offspring.

There are basically two ways of implementing a gene therapy treatment:

1. Ex vivo, which means ―outside the body‖ – Cells from the patient’s blood or bone marrow are removed and

grown in the laboratory. They are then exposed to a virus carrying the desired gene. The virus enters the cells, and the desired gene becomes part of the DNA of the cells. The cells are allowed to grow in the laboratory before being returned to the patient by injection into a vein.

2. In vivo, which means ―inside the body‖ – No cells are removed from the patient’s body. Instead, vectors are used to deliver the desired gene to cells in the patient’s body.

As of June 2001, more than 500 clinical gene-therapy trials involving about 3,500 patients have been identified worldwide. Around 78% of these are in the United States, with Europe having 18%. These trials focus on various types of cancer, although other multigenic diseases are being studied as well. Recently, two children born with severe combined immunodeficiency disorder (―SCID‖) were reported to have been cured after being given genetically engineered cells.

Gene therapy faces many obstacles before it can become a practical approach for treating disease.[13] At least four of these obstacles are as follows:

1. Gene delivery tools. Genes are inserted into the body using gene carriers called vectors. The most common

vectors now are viruses, which have evolved a way of encapsulating and delivering their genes to human cells in a pathogenic manner. Scientists manipulate the genome of the virus by removing the disease- causing genes and inserting the therapeutic genes. However, while viruses are effective, they can introduce

problems like toxicity, immune and inflammatory responses, and gene control and targeting issues. In addition, in order for gene therapy to provide permanent therapeutic effects, the introduced gene needs to

be integrated within the host cell's genome. Some viral vectors effect this in a random fashion, which can introduce other problems such as disruption of an endogenous host gene.

2. High costs. Since gene therapy is relatively new and at an experimental stage, it is an expensive treatment

to undertake. This explains why current studies are focused on illnesses commonly found in developed countries, where more people can afford to pay for treatment. It may take decades before developing countries can take advantage of this technology.

3. Limited knowledge of the functions of genes. Scientists currently know the functions of only a few genes.

Hence, gene therapy can address only some genes that cause a particular disease. Worse, it is not known exactly whether genes have more than one function, which creates uncertainty as to whether replacing such genes is indeed desirable.

4. Multigene disorders and effect of environment. Most genetic disorders involve more than one gene.

Moreover, most diseases involve the interaction of several genes and the environment. For example, many people with cancer not only inherit the disease gene for the disorder, but may have also failed to inherit specific tumor suppressor genes. Diet, exercise, smoking and other environmental factors may have also contributed to their disease.

[edit]Human Genome Project

DNA Replication image from the Human Genome Project (HGP)

The Human Genome Project is an initiative of the U.S. Department of Energy (―DOE‖) that aims to generate a high- quality reference sequence for the entire human genome and identify all the human genes.

The DOE and its predecessor agencies were assigned by the U.S. Congress to develop new energy resources and technologies and to pursue a deeper understanding of potential health and environmental risks posed by their production and use. In 1986, the DOE announced its Human Genome Initiative. Shortly thereafter, the DOE and National Institutes of Health developed a plan for a joint Human Genome Project (―HGP‖), which officially began in 1990.

The HGP was originally planned to last 15 years. However, rapid technological advances and worldwide participation accelerated the completion date to 2003 (making it a 13 year project). Already it has enabled gene hunters to pinpoint genes associated with more than 30 disorders.[14]

[edit]Cloning

Main article: Cloning

Cloning involves the removal of the nucleus from one cell and its placement in an unfertilized egg cell whose nucleus has either been deactivated or removed.

There are two types of cloning:

1. Reproductive cloning. After a few divisions, the egg cell is placed into a uterus where it is allowed to develop into a fetus that is genetically identical to the donor of the original nucleus.

2. Therapeutic cloning.[15] The egg is placed into a Petri dish where it develops into embryonic stem cells, which have shown potentials for treating several ailments.[16]

In February 1997, cloning became the focus of media attention when Ian Wilmut and his colleagues at the Roslin Institute announced the successful cloning of a sheep, named Dolly, from the mammary glands of an adult female. The cloning of Dolly made it apparent to many that the techniques used to produce her could someday be used to clone human beings.[17] This stirred a lot of controversy because of its ethical implications.

[edit]Agriculture

Main article: Genetically modified food

[edit]Crop yield

Using the techniques of modern biotechnology, one or two genes (Smartstax from Monsanto in collaboration with

Dow AgroSciences will use 8, starting in 2010) may be transferred to a highly developed crop variety to impart a new character that would increase its yield.[18] However, while increases in crop yield are the most obvious applications of modern biotechnology in agriculture, it is also the most difficult one. Current genetic engineering techniques work best for effects that are controlled by a single gene. Many of the genetic characteristics associated with yield (e.g., enhanced growth) are controlled by a large number of genes, each of which has a minimal effect on the overall yield.[19] There is, therefore, much scientific work to be done in this area.

[edit]Reduced vulnerability of crops to environmental stresses

Crops containing genes that will enable them to withstand biotic and abiotic stresses may be developed. For example, drought and excessively salty soil are two important limiting factors in crop productivity. Biotechnologists are studying plants that can cope with these extreme conditions in the hope of finding the genes that enable them to do so and eventually transferring these genes to the more desirable crops. One of the latest developments is the identification of a plant gene, At-DBF2, from Arabidopsis thaliana, a tiny weed that is often used for plant research because it is very easy to grow and its genetic code is well mapped out. When this gene was inserted into tomato and tobacco cells (see RNA interference), the cells were able to withstand environmental stresses like salt, drought, cold and heat, far more than ordinary cells. If these preliminary results prove successful in larger trials, then At-DBF2 genes can help in engineering crops that can better withstand harsh environments.[20] Researchers have also created transgenic rice plants that are resistant to rice yellow mottle virus (RYMV). In Africa, this virus destroys majority of the rice crops and makes the surviving plants more susceptible to fungal infections.[21]

[edit]Increased nutritional qualities

Proteins in foods may be modified to increase their nutritional qualities. Proteins in legumes and cereals may be transformed to provide the amino acids needed by human beings for a balanced diet.[19] A good example is the work of Professors Ingo Potrykus and Peter Beyer in creating Golden rice (discussed below).

[edit]Improved taste, texture or appearance of food

Modern biotechnology can be used to slow down the process of spoilage so that fruit can ripen longer on the plant and then be transported to the consumer with a still reasonable shelf life. This alters the taste, texture and appearance of the fruit. More importantly, it could expand the market for farmers in developing countries due to the reduction in spoilage. However, there is sometimes a lack of understanding by researchers in developed countries about the actual needs of prospective beneficiaries in developing countries. For example, engineering soybeans to resist spoilage makes them less suitable for producing tempeh which is a significant source of protein that depends on fermentation. The use of modified soybeans results in a lumpy texture that is less palatable and less convenient when cooking.

The first genetically modified food product was a tomato which was transformed to delay its ripening.[22] Researchers in Indonesia,Malaysia, Thailand, Philippines and Vietnam are currently working on delayed-ripening papaya in collaboration with the University of Nottingham and Zeneca.[23]

Biotechnology in cheese production:[24] enzymes produced by micro-organisms provide an alternative to animal rennet – a cheese coagulant – and an alternative supply for cheese makers. This also eliminates possible public concerns with animal-derived material, although there are currently no plans to develop synthetic milk, thus making this argument less compelling. Enzymes offer an animal-friendly alternative to animal rennet. While providing comparable quality, they are theoretically also less expensive.

About 85 million tons of wheat flour is used every year to bake bread.[25] By adding an enzyme called maltogenic amylase to the flour, bread stays fresher longer. Assuming that 10–15% of bread is thrown away as stale, if it could

be made to stay fresh another 5–7 days then perhaps 2 million tons of flour per year would be saved. Other enzymes can cause bread to expand to make a lighter loaf, or alter the loaf in a range of ways.

[edit]Reduced dependence on fertilizers, pesticides and other agrochemicals

Most of the current commercial applications of modern biotechnology in agriculture are on reducing the dependence of farmers on agrochemicals. For example, Bacillus thuringiensis (Bt) is a soil bacterium that produces a protein with insecticidal qualities. Traditionally, a fermentation process has been used to produce an insecticidal spray from these bacteria. In this form, the Bt toxinoccurs as an inactive protoxin, which requires digestion by an insect to be effective. There are several Bt toxins and each one is specific to certain target insects. Crop plants have now been engineered to contain and express the genes for Bt toxin, which they produce in its active form. When a susceptible insect ingests the transgenic crop cultivar expressing the Bt protein, it stops feeding and soon thereafter dies as a result of the Bt toxin binding to its gut wall. Bt corn is now commercially available in a number of countries to controlcorn borer (a lepidopteran insect), which is otherwise controlled by spraying (a more difficult process).

Crops have also been genetically engineered to acquire tolerance to broad-spectrum herbicide. The lack of herbicides with broad-spectrum activity and no crop injury was a consistent limitation in crop weed management. Multiple applications of numerous herbicides were routinely used to control a wide range of weed species detrimental to agronomic crops. Weed management tended to rely on preemergence—that is, herbicide applications were sprayed in response to expected weed infestations rather than in response to actual weeds present. Mechanical cultivation and hand weeding were often necessary to control weeds not controlled by herbicide applications. The introduction of herbicide-tolerant crops has the potential of reducing the number of herbicide active ingredients used for weed management, reducing the number of herbicide applications made during a season, and increasing yield due to improved weed management and less crop injury. Transgenic crops that express tolerance to glyphosate, glufosinate and bromoxynil have been developed. These herbicides can now be sprayed on transgenic crops without inflicting damage on the crops while killing nearby weeds.[26]

From 1996 to 2001, herbicide tolerance was the most dominant trait introduced to commercially available transgenic crops, followed by insect resistance. In 2001, herbicide tolerance deployed in soybean, corn and cotton accounted for 77% of the 626,000 square kilometres planted to transgenic crops; Bt crops accounted for 15%; and "stacked genes" for herbicide tolerance and insect resistance used in both cotton and corn accounted for 8%.[27]

[edit]Production of novel substances in crop plants

Biotechnology is being applied for novel uses other than food. For example, oilseed can be modified to produce fatty acids fordetergents, substitute fuels and petrochemicals. Potatoes, tomatoes, rice tobacco, lettuce, safflowers, and other plants have been genetically engineered to produce insulin and certain vaccines. If future clinical trials prove successful, the advantages of edible vaccineswould be enormous, especially for developing countries. The transgenic plants may be grown locally and cheaply. Homegrown vaccines would also avoid logistical and economic problems posed by having to transport traditional preparations over long distances and keeping them cold while in transit. And since they are edible, they will not need syringes, which are not only an additional expense in the traditional vaccine preparations but also a source of infections if contaminated.[28] In the case of insulin grown in

transgenic plants, it is well-established that the gastrointestinal system breaks the protein down therefore this could not currently be administered as an edible protein. However, it might be produced at significantly lower cost than insulin produced in costly bioreactors. For example, Calgary, Canada-based SemBioSys Genetics, Inc. reports that its safflower-produced insulin will reduce unit costs by over 25% or more and approximates a reduction in the capital costs associated with building a commercial-scale insulin manufacturing facility of over $100 million, compared to traditional biomanufacturing facilities.[29]

[edit]Criticism

There is another side to the agricultural biotechnology issue. It includes increased herbicide usage and resultant herbicide resistance, "super weeds," residues on and in food crops, genetic contamination of non-GM crops which hurt organic and conventional farmers, etc.[30][31]

[edit]Biological engineering

Main article: Bioengineering

Biotechnological engineering or biological engineering is a branch of engineering that focuses on biotechnologies and biological science. It includes different disciplines such as biochemical engineering, biomedical engineering, bioprocess engineering, biosystem engineering and so on. Because of the novelty of the field, the definition of a bioengineer is still undefined. However, in general it is an integrated approach of fundamental biological sciences and traditional engineering principles.

Biotechnologists are often employed to scale up bio processes from the laboratory scale to the manufacturing scale.

Moreover, as with most engineers, they often deal with management, economic and legal issues. Since patents and regulation (e.g., U.S. Food and Drug Administration regulation in the U.S.) are very important issues for biotech enterprises, bioengineers are often required to have knowledge related to these issues.

The increasing number of biotech enterprises is likely to create a need for bioengineers in the years to come. Many universities throughout the world are now providing programs in bioengineering and biotechnology (as independent programs or specialty programs within more established engineering fields).

[edit]Bioremediation and biodegradation

Main article: Microbial biodegradation

Biotechnology is being used to engineer and adapt organisms especially microorganisms in an effort to find sustainable ways to clean up contaminated environments. The elimination of a wide range of pollutants and wastes from the environment is an absolute requirement to promote a sustainable development of our society with low environmental impact. Biological processes play a major role in the removal of contaminants and biotechnology is taking advantage of the astonishing catabolic versatility of microorganisms to degrade/convert such compounds. New methodological breakthroughs in sequencing, genomics, proteomics, bioinformatics and imaging are producing vast amounts of information. In the field of Environmental Microbiology, genome-based global studies open a new era providing unprecedented in silico views of metabolic and regulatory networks, as well as clues to the evolution of degradationpathways and to the molecular adaptation strategies to changing environmental conditions. Functional

genomic and metagenomic approaches are increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds and they will certainly accelerate the development of bioremediation technologies and biotransformation processes.[32]

Marine environments are especially vulnerable since oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult. In addition to pollution through human activities, millions of tons of petroleum enter the marine environment every year from natural seepages. Despite its toxicity, a considerable fraction of petroleum oil entering marine systems is eliminated by the hydrocarbon-degrading activities of microbial communities, in particular by a remarkable recently discovered group of specialists, the so-called hydrocarbonoclastic bacteria (HCCB).[33]

[edit]Biotechnology regulations

The National Institute of Health was the first federal agency to assume regulatory responsibility in the United States.

The Recombinant DNA Advisory Committee of the NIH published guidelines for working with recombinant DNA and recombinant organisms in the laboratory. Nowadays, the agencies that are responsible for the biotechnology regulation are: US Department of Agriculture (USDA) that regulates plant pests and medical preparation from living organisms, Environmental Protection Agency (EPA) that regulates pesticides and herbicides, and the Food and Drug Administration (FDA) which ensures that the food and drug products are safe and effective [2]

[edit]Education

In 1988, after prompting from the United States Congress, the National Institute of General Medical

Sciences (National Institutes of Health) instituted a funding mechanism for biotechnology training. Universities nationwide compete for these funds to establishBiotechnology Training Programs (BTPs). Each successful application is generally funded for five years then must be competitively renewed. Graduate students in turn compete for acceptance into a BTP; if accepted then stipend, tuition and health insurance support is provided for two or three years during the course of their PhD thesis work. Nineteen institutions offer NIGMS supported BTPs.[34]Biotechnology training is also offered at the undergraduate level and in community colleges.

[edit]See also

Biotechnology portal

. Outline of biotechnology

. Bioeconomics

. Bioengineering

. Biopolitics

. Biomimetics

. Bioculture

. Biochemistry

. Lancaster Laboratories

. Pharmaceutical companies

. Pharmaceutical chemistry

. History of biochemistry

. Bionic architecture

. Biotechnology industrial park

. Biotechnology Training Program – University of Virginia

. Competitions and prizes in biotechnology

. Genetic Engineering

. Green Revolution

. International Assessment of Agricultural Science and Technology for Development

. International Service for the Acquisition of Agri-biotech Applications

. Kelvin probe force microscope

. List of biotechnology articles

. List of biotechnology companies

. List of emerging biotechnologies

. NASDAQ Biotechnology Index

. SWORD-financing

. History of Biotechnology

. Technobiology

. National Industrial Biotechnology Facility

Outline of biotechnology

From Wikipedia, the free encyclopedia See also: Index of biotechnology articles

Biotechnology is technology based on biology, especially when used in agriculture, food science, and medicine.

The UN Convention on Biological Diversity has come up with one of many definitions of biotechnology: Biotechnology means any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use.

The following outline is provided as an overview of and topical guide to biotechnology:

[edit]Essence of biotechnology

Main article: Biotechnology

. Bioengineering

. Biology

. Technology [edit]Applications of biotechnology

. Cloning

. Reproductive cloning

. Therapeutic cloning

. Environmental biotechnology

. Genetic engineering

. Recombinant DNA

. Tissue engineering

. Use of biotechnology in pharmaceutical manufacturing [edit]History of biotechnology

Main article: History of biotechnology

. Timeline of biotechnology

. Green Revolution [edit]General biotechnology concepts

. Bioeconomy

. Biotechnology industrial park

. Green Revolution

. Human Genome Project

. Pharmaceutical company

. Stem cell

. Telomere

. Tissue culture

. Biomimetics [edit]Leaders in biotechnology

. Leonard Hayflick

. Michael D. West index of biotechnology articles

From Wikipedia, the free encyclopedia

(Redirected from List of biotechnology articles)

Biotechnology is a technology based on biology, especially when used in agriculture, food science, and medicine.

Of the many different definitions available, the one formulated by the UN Convention on Biological Diversity is one of the broadest:

"Biotechnology means any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use." (Article 2. Use of Terms)

More about Biotechnology...

Template:Biotechnology title 17

See also: Outline of biotechnology

This page provides an alphabetical list of articles and other pages (including categories, lists, etc) about biotechnology. For other overviews of the topic, please see the Biotechnology portal.

[edit]A

Agrobacterium -- Affymetrix -- Alcoholic beverages -- Category:Alcoholic beverages -- Amgen -- AnaSpec -- Antibiotic -- Artificial selection

[edit]B

Biochemical engineering -- Biochip -- Biodiesel -- Bioengineering -- Biofuel -- Biogas -- Biogen Idec --

Bioindicator -- Bioinformatics --Category:Bioinformatics -- Bioleaching -- Biological agent -- Biological warfare -- Bioluminescence -- Biomimetics -- Bionanotechnology -- Bionics --Biopharmacology -- Biophotonics -- Bioreactor -- Bioremediation -- Biostimulation -- Biosynthesis -- Biotechnology --Category:Biotechnology -- Category:Biotechnology companies -- Category:Biotechnology products -- Bt corn -- BioSynergy

[edit]C

Cancer immunotherapy -- Cell therapy -- Chimera (genetics) -- Chinese hamster -- Chinese Hamster Ovary

cell -- Chiron Corp. -- Cloning-- Compost -- Composting -- Convention on Biological Diversity -- Chromatography

[edit]D

Directive on the patentability of biotechnological inventions -- DNA microarray -- Dwarfing

[edit]E

Enzymes -- Electroporation -- Environmental biotechnology -- Eugenics

[edit]F

Fermentation -- Category:Fermented foods

[edit]G

Gene knockout -- Gene therapy -- Genentech -- Genetic engineering -- Genetically modified food -- Genetically modified organisms --Genetics -- Genomics -- Genzyme -- Global Knowledge Center on Crop Biotechnology - Glycomics -- Golden rice -- Green fluorescent protein

[edit]H

Human cloning -- Human Genome Project -- Human Metabolome Project[1]

[edit]I

Immunotherapy -- Immune suppression -- Industrial biotechnology -- Interactomics

[edit]J Competitions and prizes in biotechnology

From Wikipedia, the free encyclopedia

There exist a number of competitions and prizes to reward distinguished contributions and to encourage developments in biotechnology.

[edit]Inducement prizes

. The Archon X Prize for Genomics of US$10,000,000 is to be awarded to "the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 (US) per genome."

. The Prize4Life ALS biomarker prize is a US$1,000,000 award for a reliable way of tracking progression of amyotrophic lateral sclerosis (ALS).

. The Prize4Life ALS treatment prize is a US$1,000,000 award for a therapy that reliably and effectively extends the life of ALS mice by 25%.

. People for Ethical Treatment of Animals (PETA) is offering a US$1,000,000 reward for a method of producing enough meat to be marketed in 10 U.S. states at a price competitive with chicken prices.[1][2] [edit]Recognition prizes

. The Gotham Prize for Cancer Research is a US$1,000,000 prize awarded annually to "encourage new and innovative approaches to cancer research by fostering collaboration among top thinkers in the field--with the goal of leading to progress in the prevention, diagnosis, etiology and treatment of cancer."[3]

. Gruber Prize in Genetics is a US$500,000 prize awarded annually for distinguished contributions in any realm of genetics research.

. The Nobel Prize in Physiology or Medicine is an annual grant worth approximately 10 million SEK. It is routinely awarded for contributions to biotechnology.

Genetic engineering

From Wikipedia, the free encyclopedia (Redirected from Genetic Engineering)

For a non-technical introduction to the topic, see Introduction to Genetics. For the song by Orchestral Manoeuvres in the Dark, seeGenetic Engineering (song).

Part of the Biology series on

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Genetic engineering, also called genetic modification, is the direct human manipulation of an organism'sgenetic material in a way that does not occur under natural conditions. It involves the use of recombinant DNA techniques, but does not include traditional animal and plant breeding or mutagenesis. Any organism that is generated using these techniques is considered to be a genetically modified organism. The first organisms genetically engineered were bacteria in 1973 and then mice in 1974. Insulin producing bacteria were commercialized in 1982 and genetically modified food has been sold since 1994.

The most common form of genetic engineering involves the insertion of new genetic material at an unspecified location in the host genome. This is accomplished by isolating and copying the genetic material of interest, generating a construct containing all the genetic elements for correct expression, and then inserting this construct into the host organism. Other forms of genetic engineering include gene targeting and knocking out specific genes via engineered nucleases such as zinc finger nucleases or engineered homing endonucleases.

Genetic engineering techniques have been applied in numerous fields including research, biotechnology, and medicine. Medicines such as insulin and human growth hormone are now produced in bacteria, experimental mice such as the oncomouse and the knockout mouse are being used for research purposes and insect resistant and/or herbicide tolerant crops have been commercialized. Genetically engineered plants and animals capable of producing biotechnology drugs more cheaply than current methods (called pharming) are also being developed and in 2009 the FDA approved the sale of the pharmaceutical protein antithrombinproduced in the milk of genetically engineered goats.

Definition

Genetic engineering alters the genetic makeup of an organism using techniques that introduce heritable material prepared outside the organism either directly into the host or into a cell that is then fused or hybridized with the host.[1] This involves using recombinant nucleic acid (DNA or RNA) techniques to form new combinations of heritable genetic material followed by the incorporation of that material either indirectly through a vector system or directly through micro-injection, macro-injection and micro-encapsulationtechniques. Genetic engineering does not include traditional animal and plant breeding, in vitro fertilisation, induction of polyploidy,mutagenesis and cell fusion

techniques that do not use recombinant nucleic acids or a genetically modified organism in the process.[1]Cloning and stem cell research, although not considered genetic engineering,[2] are closely related and genetic engineering can be used within them.[3] Synthetic biology is an emerging discipline that takes genetic engineering a step further by introducing artificially synthesized genetic material from raw materials into an organism.[4]

If genetic material from another species is added to the host, the resulting organism is called transgenic. If genetic material from the same species or a species that can naturally breed with the host is used the resulting organism is called cisgenic.[5] Genetic engineering can also be used to remove genetic material from the target organism, creating a knock out organism.[6] In Europe genetic modification is synonymous with genetic engineering while within the United States of America it can also refer to conventional breeding methods.[7] History

Humans have altered the genomes of species for thousands of years through artificial selection and more recently mutagenesis. Genetic engineering as the direct manipulation of DNA by humans outside breeding and mutations has only existed since the 1970s. The term "genetic engineering" was first coined by Jack Williamson in his science fiction novel Dragon's Island, published in 1951,[8] one year before DNA's role in heredity was confirmed by Alfred Hershey and Martha Chase,[9] and two years before James Watson and Francis Crick showed that the DNA molecule has a double-helix structure.

In 1972 Paul Berg created the first recombinant DNA molecules by combined DNA from the monkey virus SV40 with that of the lambda virus.[10] In 1973 Herbert Boyer and Stanley Cohen created the first transgenic organism by inserting antibiotic resistance genes into theplasmid of an E. coli bacterium.[11][12] A year later Rudolf Jaenisch created a transgenic mouse by introducing foreign DNA into its embryo, making it the world’s first transgenic animal.[13] In 1976 Genentech, the first genetic engineering company was founded by Herbert Boyer and Robert Swanson and a year later and the company produced a human protein (somatostatin) in E.coli. Genentech announced the production of genetically engineered human insulin in 1978.[14] In 1980, the U.S. Supreme Court in the Diamond v. Chakrabarty case ruled that genetically altered life could be patented.[15] The insulin produced by bacteria, branded humulin, was approved for release by the Food and Drug Administration in 1982.[16]

The first field trials of genetically engineered plants occurred in France and the USA in 1986, tobacco plants were engineered to be resistant to herbicides.[17] The People’s Republic of China was the first country to commercialize transgenic plants, introducing a virus-resistant tobacco in 1992.[18] In 1994 Calgene attained approval to commercially release the Flavr Savr tomato, a tomato engineered to have a longer shelf life.[19] In 1994, the European Union approved tobacco engineered to be resistant to the herbicide bromoxynil, making it the first genetically engineered crop commercialized in Europe.[20] In 1995, Bt Potato was approved safe by the Environmental Protection Agency, making it the first pesticide producing crop to be approved in the USA.[21] In 2009 11 transgenic crops were grown commercially in 25 countries, the largest of which by area grown were the USA, Brazil, Argentina, India, Canada, China, Paraguay and South Africa.[22]

In 2010, scientists at the J. Craig Venter Institute, announced that they had created the first synthetic bacterial genome, and added it to a cell containing no DNA. The resulting bacterium, named Synthia, was the world's first synthetic life form.[23][24] Process

Isolating the Gene

Elements of genetic engineering

First, the gene to be inserted into the genetically modified organism must be chosen and isolated. Presently, most genes transferred into plants provide protection against insects or tolerance to herbicides.[25] In animals the majority of genes used are growth hormonegenes.[26] Once chosen the genes must be isolated. This typically involves multiplying the gene using polymerase chain reaction (PCR). If the chosen gene or the donor organism'sgenome has been well studied it may be present in a genetic library. If the DNA sequence is known, but no copies of the gene are available, it can be artificially synthesized. Once isolated, the gene is inserted into a bacterial plasmid.

Constructs

The gene to be inserted into the genetically modified organism must be combined with other genetic elements in order for it to work properly. The gene can also be modified at this stage for better expression or effectiveness. As well as the gene to be inserted most constructscontain a promoter and terminator region as well as a selectable marker gene. The promoter region initiates transcription of the gene and can be used to control the location and level of gene expression, while the terminator region ends transcription. The selectable marker, which in most cases confers antibiotic resistance to the organism it is expressed in, is needed to determine which cells are transformed with the new gene. The constructs are made using recombinant DNA techniques, such as restriction digests, ligations andmolecular cloning.[27]

Gene Targeting

Main article: gene targeting

The most common form of genetic engineering involves inserting new genetic material randomly within the host genome. Other techniques allow new genetic material to be inserted at a specific location in the host genome or generate mutations at desired genomic loci capable of knocking out endogenous genes. The technique of gene targeting uses homologous recombination to target desired changes to a specific endogenous gene. This tends to occur at a relatively low frequency in plants and animals and generally requires the use of selectable markers. The frequency of gene targeting can be greatly enhanced with the use of engineered nucleases such aszinc finger nucleases,[28] [29] engineered homing endonucleases,[30] [31] or nucleases created from TAL effectors.[32] [33] In addition to enhancing gene targeting, engineered nucleases can also be used to introduce mutations at endogenous genes that generate a gene knockout[34] [35].

Transformation

Main article: Transformation (genetics)

A. tumefaciens attaching itself to a carrot cell

About 1% of bacteria are naturally able to take up foreign DNA but it can also be induced in other bacteria.[36] Stressing the bacteria for example, with a heat shock or an electric shock, can make the cell membrane permeable to DNA that may then incorporate into their genome or exist asextrachromosomal DNA. DNA is generally inserted into animal cells using microinjection, where it can be injected through the cells nuclear envelope directly into the nucleus or through the use ofviral vectors. In plants the DNA is generally inserted using Agrobacterium-mediated recombinationor biolistics.[37]

In Agrobacterium-mediated recombination the plasmid construct must also contain T-DNA.Agrobacterium naturally inserts DNA from a tumor inducing plasmid into any susceptible plant's genome it infects, causing crown gall disease. The T-DNA region of this plasmid is responsible for insertion of the DNA. The genes to be inserted are cloned into a binary vector, which contains T-DNA and can be grown in both E. Coli and Agrobacterium. Once the binary vector

is constructed the plasmid is transformed into Agrobacterium containing no plasmids and plant cells are infected. The Agrobacterium will then naturally insert the genetic material into the plant cells.[38]

In biolistics particles of gold or tungsten are coated with DNA and then shot into young plant cells or plant embryos. Some genetic material will enter the cells and transform them. This method can be used on plants that are not susceptible to Agrobacterium infection and also allows transformation of plant plastids. Another transformation method for plant and animal cells is electroporation. Electroporation involves subjecting the plant or animal cell to an electric shock, which can make the cell membrane permeable to plasmid DNA. In some cases the electroporated cells will incorporate the DNA into their genome. Due to the damage caused to the cells and DNA the transformation efficiency of biolistics and electroporation is lower than agrobacterial mediated transformation and microinjection.[39]

Selection

Not all the organism's cells will be transformed with the new genetic material; in most cases a selectable marker is used to differentiate transformed from untransformed cells. If a cell has been successfully transformed with the DNA it will also contain the marker gene. By growing the cells in the presence of an antibiotic or chemical that selects or marks the cells expressing that gene it is possible to separate the transgenic events from the non-transgenic. Another method of screening involves using a DNA probe that will only stick to the inserted gene. A number of strategies have been developed that can remove the selectable marker from the mature transgenic plant.[40]

Regeneration

As often only a single cell is transformed with genetic material the organism must be regrown from that single cell. As bacteria consist of a single cell and reproduce clonally regeneration is not necessary. In plants this is accomplished through the use of tissue culture. Each plant species has different requirements for successful regeneration through tissue culture. If successful an adult plant is produced that contains the transgene in every cell. In animals it is necessary to ensure that the inserted DNA is present in the embryonic stem cells. When the offspring is produced they can be screened for the presence of the gene. All offspring from the first generation will beheterozygous for the inserted gene and must be mated together to produce a homozygous animal.

Confirmation

Further tests using PCR, Southern Blots and Bioassays are needed to confirm that the gene is expressed and functions correctly. The organism's offspring are also tested to ensure that the trait can be inherited and that it follows a Mendelian inheritance pattern. Applications

Genetic engineering has applications in medicine, research, industry and agriculture and can be used on a wide range of plants, animals and micro organism.

Medicine

In medicine genetic engineering has been used to mass produce insulin, human growth hormones, follistim (for treating infertility),human albumin, monoclonal antibodies, antihemophilic factors, vaccines and many other

drugs.[41] Vaccination generally involves injecting weak live, killed or inactivated forms of viruses or their toxins into the person being immunized.[42] Genetically engineered viruses are being developed that can still confer immunity, but lack the infectious sequences.[43] Mouse hybridomas, cells fused together to create monoclonal antibodies, have been humanised through genetic engineering to create human monoclonal antibodies.[44]

Genetic engineering is used to create animal models of human diseases. Genetically modified mice are the most common genetically engineered animal model.[45] They have been used to study and model cancer (the oncomouse), obesity, heart disease, diabetes, arthritis, substance abuse, anxiety, aging and Parkinson disease.[46] Potential cures can be tested against these mouse models. Also genetically modified pigs have been bred with the aim of increasing the success of pig to human organ transplantation.[47]

Gene therapy is the genetic engineering of humans by replacing defective human genes with functional copies. This can occur insomatic tissue or germline tissue. If the gene is inserted into the germline tissue it can be passed down to that person's descendants.[48] Gene therapy has been used to treat patients suffering from immune deficiencies (notably Severe combined immunodeficiency) and trials have been carried out on other genetic disorders.[49] The success of gene therapy so far has been limited and a patient (Jesse Gelsinger) has died during a clinical trial testing a new treatment.[50] There are also ethical concerns should the technology be used not just for treatment, but for enhancement, modification or alteration of a human beings' appearance, adaptability, intelligence, character or behavior.[51] The distinction between cure and enhancement can also be difficult to establish.[52]Transhumanists consider the enhancement of humans desirable.

Research

Knockout mice

Human cells in which some proteins are fused with green fluorescent protein to allow them to be visualised

Genetic engineering is an important tool for natural scientists. Genes and other genetic information from a wide range of organisms are transformed into bacteria for storage and modification, creating genetically modified bacteria in the process. Bacteria are cheap, easy to grow, clonal, multiply quickly, relatively easy to transform and can be stored at - 80°C almost indefinitely. Once a gene is isolated it can be stored inside the bacteria providing an unlimited supply for research.

Organisms are genetically engineered to discover the functions of certain genes. This could be the effect on the phenotype of the organism, where the gene is expressed or what other genes it interacts with. These experiments generally involve loss of function, gain of function, tracking and expression.

. Loss of function experiments, such as in a gene knockout experiment, in which an organism is engineered to

lack the activity of one or more genes. A knockout experiment involves the creation and manipulation of a DNA construct in vitro, which, in a simple knockout, consists of a copy of the desired gene, which has been altered

such that it is non-functional. Embryonic stem cells incorporate the altered gene, which replaces the already present functional copy. These stem cells are injected into blastocysts, which are implanted into surrogate mothers. This allows the experimenter to analyze the defects caused by this mutation and thereby determine the

role of particular genes. It is used especially frequently in developmental biology. Another method, useful in organisms such as Drosophila (fruit fly), is to induce mutations in a large population and then screen the progeny for the desired mutation. A similar process can be used in both plants andprokaryotes.

. Gain of function experiments, the logical counterpart of knockouts. These are sometimes performed in

conjunction with knockout experiments to more finely establish the function of the desired gene. The process is much the same as that in knockout engineering, except that the construct is designed to increase the function of the gene, usually by providing extra copies of the gene or inducing synthesis of the protein more frequently.

. Tracking experiments, which seek to gain information about the localization and interaction of the desired

protein. One way to do this is to replace the wild-type gene with a 'fusion' gene, which is a juxtaposition of the

wild-type gene with a reporting element such as green fluorescent protein (GFP) that will allow easy visualization of the products of the genetic modification. While this is a useful technique, the manipulation can destroy the function of the gene, creating secondary effects and possibly calling into question the results of the experiment. More sophisticated techniques are now in development that can track protein products without mitigating their function, such as the addition of small sequences that will serve as binding motifs to monoclonal antibodies.

. Expression studies aim to discover where and when specific proteins are produced. In these experiments, the

DNA sequence before the DNA that codes for a protein, known as a gene's promoter, is reintroduced into an organism with the protein coding region replaced by a reporter gene such as GFP or an enzyme that catalyzes the production of a dye. Thus the time and place where a particular protein is produced can be observed.

Expression studies can be taken a step further by altering the promoter to find which pieces are crucial for the proper expression of the gene and are actually bound by transcription factor proteins; this process is known as promoter bashing. Industrial

By engineering genes into bacterial plasmids it is possible to create a biological factory that can produce proteins and enzymes.[53]Some genes do not work well in bacteria, so yeast, a eukaryote, can also be used.[54] Bacteria and yeast factories have been used to produce medicines such as insulin, human growth hormone, and vaccines, supplements such as tryptophan, aid in the production of food (chymosin in cheese making) and fuels.[55] Other applications involving genetically engineered bacteria being investigated involve making the bacteria perform tasks outside their natural cycle, such as cleaning up oil spills, carbon and other toxic waste.[56]

Agriculture

Bt-toxins present in peanut leaves (bottom image) protect it from extensive damage caused by European corn borerlarvae (top image).[57]

One of the best-known and controversial applications of genetic engineering is the creation ofgenetically modified food. There are three generations of genetically modified crops.[58] First generation crops have been commercialized and most provide protection from insects and/or resistance to herbicides. There are also fungal and virus resistant crops developed or in development.[59][60] They have been developed to make the insect and weed management of crops easier and can indirectly increase crop yield.[61]

The second generation of genetically modified crops being developed aim to directly improve yield by improving salt, cold or drought tolerance and to increase the nutritional value of the crops.[62] The third generation consists of pharmaceutical crops, crops that contain edible vaccines and other drugs.[63] Some agriculturally important animals have been genetically modified with growth hormones to increase their size[64] while others have been engineered to express drugs and other proteins in their milk.[65][66][67]

The genetic engineering of agricultural crops can increase the growth rates and resistance to different diseases caused by pathogens and parasites.[68] This is beneficial as it can greatly increase the production of food sources with the usage of fewer resources that would be required to host the world's growing populations. These modified crops would also reduce the usage of chemicals, such as fertilizers and pesticides, and therefore decrease the severity and frequency of the damages produced by these chemical pollution.[68]

Ethical and safety concerns have been raised around the use of genetically modified food.[69]A major safety concern relates to the human health implications of eating genetically modified food, in particular whether toxic or allergic

reactions could occur.[70] Gene flow into related non-transgenic crops, off target effects on beneficial organisms and the impact onbiodiversity are important environmental issues.[71] Ethical concerns involve religious issues,corporate control of the food supply, intellectual property rights and the level of labeling needed on genetically modified products.

Other uses

In materials science, a genetically modified virus has been used to construct a more environmentally friendly lithium- ion battery.[72][73]Some bacteria have been genetically engineered to create black and white photographs[74] while others have potential to be used as sensors by expressing a fluorescent protein under certain environmental conditions.[75] Genetic engineering is also being used to createBioArt[76] and novelty items such as blue roses,[77] and glowing fish.[78] Opposition and criticism

This section requires expansion.

A 2010 study of Canola found transgenes in 80% of wild (uncultivated or "feral") varieties in North Dakota, meaning 80% of the plants which had established themselves in the area were genetically engineered varieties. The researchers stated that "we found the highest densities of [such transgene-containing] plants near agricultural fields and along major freeways, but we were also finding plants in the middle of nowhere" adding that "over time,..the build-up of different types of herbicide resistance in feral [natural] canola and closely related weeds, like field mustard, could make it more difficult to manage these plants using herbicides."[79]

See also: Human genetic engineering, GM food controversy, and Genetically modified organism See also

. Biological engineering

. Marker assisted selection a way to select suitable offspring without using genetic engineering

. Paratransgenesis

Biological engineering, biotechnological engineering or bioengineering(including biological systems engineering) is the application of concepts and methods of physics and mathematics to solve problems in life sciences, usingengineering's own analytical and synthetical methodologies. In this context, while traditional engineering applies physical and mathematical sciences to analyze, designand manufacture inanimate tools, structures and processess, bioengineering uses the same sciences to study many aspects of living organisms. Usually it is used to analyze and solve problems related to human health.

Biological engineering is a science based discipline founded upon the biological sciences in the same way that chemical engineering, electrical engineering, and mechanical engineering are based upon chemistry, electricity and magnetism, and statics, respectively. [1]

Biological Engineering can be differentiated from its roots of pure biology or classical engineering in the following way. Biological studies often follow a reductionist approach in viewing a system on its smallest possible scale which naturally leads toward tools such as functional genomics. Engineering approaches, using classical design perspectives, are constructionist, building new devices, approaches, and technologies from component concepts. Biological engineering utilizes both of these methods in concert relying on reductionist approaches to define the fundamental units which are then commingled to generate something new. [2] Although engineered biological systems have been used to manipulate information, construct materials, process chemicals, produce energy, provide food, and help maintain or enhance human health and our environment, our ability to quickly and reliably engineer biological systems that behave as expected remains less well developed than our mastery over mechanical and electrical systems. [3]

The differentiation between Biological Engineering and overlap with Biomedical Engineering can be unclear, as many universities now use the terms "bioengineering" and "biomedical engineering" interchangeably [4]. Some contend that Biological Engineering (likebiotechnology) has a broader base which spans molecular methods (tends to emphasize the using of biological substances - applying engineering principles to molecular biology, biochemistry, microbiology, pharmacology, protein chemistry, cytology, immunology,neurobiology and neuros cience, cellular and tissue based methods (including devices and sensors), whole organisms (plants, animals), and up increasing length scales to ecosystems. Neither biological engineering nor biomedical engineering is wholly contained within the other, as there are non-biological products for medical needs and biological products for non- medical needs.

ABET [5], the U.S. based accreditation board for engineering B.S. programs, makes a distinction between Biomedical

Engineering and Biological Engineering; however, the differences are quite small. Biomedical engineers must have life science courses that include human physiology and have experience in performing measurements on living systems while biological engineers must have life science courses (which may or may not include physiology) and experience in making measurements not specifically on living systems. Foundational engineering courses are often the same and include thermodynamics, fluid and mechanical dynamics, kinetics, electronics, and materials properties. [6] [7]

The word bioengineering was coined by British scientist and broadcaster Heinz Wolff in 1954. [8] The term bioengineering is also used to describe the use of vegetation in civil engineering construction. The term bioengineering may also be applied to environmental modifications such as surface soil protection, slope stabilisation, watercourse and shoreline protection, windbreaks, vegetation barriers including noise barriers and visual screens, and the ecological enhancement of an area. The first biological engineering program was created at Mississippi State University in 1967, making it the first Biological Engineering curriculum in the United States.[9] More recent programs have been launched at MIT [10] and Utah State University [11].

Biological Engineers or bioengineers are engineers who use the principles of biology and the tools of engineering to create usable, tangible products. Biological Engineering employs knowledge and expertise from a number of pure and applied sciences, such as mass and heat transfer, kinetics, biocatalysts, biomechanics, bioinformatics,

separation and purification processes, bioreactor design, surface science, fluid mechanics, thermodynamics, and polymer science. It is used in the design of medical devices, diagnostic equipment, biocompatible materials, renewable bioenergy, ecological engineering, and other areas that improve the living standards of societies.

In general, biological engineers attempt to either mimic biological systems in order to create products or modify and control biological systems so that they can replace, augment, or sustain chemical and mechanical processes. Bioengineers can apply their expertise to other applications of engineering and biotechnology, including genetic modification of plants and microorganisms, bioprocess engineering, and biocatalysis.

Because other engineering disciplines also address living organisms (e.g., prosthetics in mechanical engineering), the term biological engineering can be applied more broadly to include agricultural engineering and biotechnology. In fact, many old agricultural engineering departments in universities over the world have rebranded themselves as agricultural and biological engineering or agricultural and biosystems engineering. Biological engineering is also called bioengineering by some colleges and Biomedical engineering is called Bioengineering by others, and is a rapidly developing field with fluid categorization. The Main Fields of Bioengineering may be categorised as:

. Bioprocess Engineering: Bioprocess Design, Biocatalysis, Bioseparation, Bioinformatics, Bioenergy

. Genetic Engineering: Synthetic Biology, Horizontal gene transfer.

. Cellular Engineering: Cell Engineering, Tissue Culture Engineering, Metabolic Engineering.

. Biomedical Engineering: Biomedical technology, Biomedical Diagnostics, Biomedical Therapy, Biomechanics, Biomaterials.

Biochemistry

From Wikipedia, the free encyclopedia For the journal, see Biochemistry (journal).

"Biological Chemistry" redirects here. For the journal formerly named Biological Chemistry Hoppe-Seyler, see Biological Chemistry (journal).

Biochemistry, sometimes abbreviated as "BioChem", is the study of chemical processes in living organisms.

Biochemistry governs all living organisms and living processes. By controlling information flow through biochemical signalling and the flow of chemical energy through metabolism; biochemical processes give rise to the seemingly magical phenomenon of life. Much of biochemistry deals with thestructures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules although increasingly processes rather than individual molecules are the main focus. Over the last 40 years biochemistry has become so successful at explaining living processes that now almost all areas of the life sciences from botany to medicine are engaged in biochemical research. Today the main focus of pure biochemistry is in understanding how biological molecules give rise to the processes that occur within living cells which in turn relates greatly to the study and understanding of whole organisms.

Among the vast number of different biomolecules, many are complex and large molecules (called polymers), which are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types.[1] For example, a protein is a polymer whose subunits are selected from a set of 20 or more amino acids. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions.

The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include thegenetic code (DNA, RNA), protein synthesis, cell membrane transport, and signal transduction.

[edit]History

Main article: History of biochemistry

Originally, it was generally believed that life was not subject to the laws of science the way non-life was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.[2][3]

The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term ―biochemistry‖ seems to have been first used in 1882, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuberg, a German chemist. Previously, this area would have been referred to as physiological chemistry. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy,radioisotopic labeling, electron microscopy and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle).

Another significant historic event in biochemistry is the discovery of the gene and its role in the transfer of information in the cell. This part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to growth of forensic science. More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi), in the silencing of gene expression

Today, there are three main types of biochemistry. Plant biochemistry involves the study of the biochemistry of autotrophic organisms such as photosynthesis and other plant specific biochemical processes. General

biochemistry encompasses both plant and animal biochemistry. Human/medical/medicinal biochemistry focuses on the biochemistry of humans and medical illnesses.{{Citation needed|date=April 2010}

[edit]Monomers and polymers

Main articles: Monomer and Polymer

The four main classes of molecules in biochemistry are carbohydrates, lipids, proteins, and nucleic acids. Many biological moleculesare polymers: in this terminology, monomers are relatively small micromolecules that are linked together to create largemacromolecules, which are known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis.

[edit]Carbohydrates

Main articles: Carbohydrates, Monosaccharides, Disaccharides, and Polysaccharides

A molecule ofsucrose (glucose + fructose), adisaccharide.

Carbohydrates are made from monomers called monosaccharides. Some of these monosaccharides includeglucose (C6H12O6), fructose (C6H12O6), and deoxyribose (C5H10O4). When two monosaccharides undergo dehydration synthesis, water is produced, as two hydrogen atoms and one oxygen atom are lost from the two monosaccharides' hydroxyl group.

[edit]Lipids

Main articles: Lipids, Glycerol, and Fatty acids

A triglyceride with a glycerol molecule on the left and three fatty acids coming off it.

Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).

Lipids, especially phospholipids, are also used in various pharmaceutical products, either as co-solubilisers (e.g. in parenteral infusions) or else as drug carrier components (e.g. in a liposome ortransfersome).

[edit]Proteins

Main articles: Proteins and Amino Acids

The general structure of an α-amino acid, with theamino group on the left and thecarboxyl group on the right.

Proteins are very large molecules – macro-biopolymers – made from monomers called amino acids. There are

20standard amino acids, each containing a carboxyl group, an amino group, and a side chain (known as an "R" group). The "R" group is what makes each amino acid different, and the properties of the side chains greatly influence the overall three-dimensional conformation of a protein. When amino acids combine, they form a special bond called a peptide bond through dehydration synthesis, and become a polypeptide, or protein.

To determine if two proteins are related or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods. Methods like Sequence Alignments and Structural Alignments are powerful tools that help scientist identify homologies between related molecules. The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of protein families. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.

[edit]Nucleic acids

Main articles: Nucleic acid, DNA, RNA, and Nucleotides

The structure of deoxyribonucleic acid (DNA), the picture shows the monomers being put together.

Nucleic acids are the molecules that make up DNA, an extremely important substance which all cellular organisms use to store their genetic information. The most common nucleic acids aredeoxyribonucleic acid and ribonucleic acid. Their monomers are called nucleotides. The most common nucleotides are adenine, cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil; thymine only binds with adenine; and cytosine and guanine can only bind with each other.

[edit]Carbohydrates

Main article: Carbohydrate

The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.

[edit]Monosaccharides

Glucose

The simplest type of carbohydrate is amonosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar commonly associated with the sweet taste of fruits.[4][a] Some carbohydrates (especially after condensation to oligo- and polysaccharides) contain less carbon relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can be grouped intoaldoses (having an aldehyde group at the end of the chain, e. g. glucose) and ketoses (having a keto group in their chain; e. g. fructose). Both aldoses and ketoses occur in an equilibrium(starting with chain lengths of C4) cyclic forms. These are generated by bond formation between one of the hydroxyl groups of the sugar chain with the carbon of the aldehyde or keto group to form a hemiacetal bond. This leads to saturated five-membered (in furanoses) or six-membered (in pyranoses) heterocyclic rings containing one O as heteroatom.

[edit]Disaccharides

Sucrose: ordinary table sugar and probably the most familiar carbohydrate.

Two monosaccharides can be joined together using dehydration synthesis, in which a hydrogen atom is removed from the end of one molecule and a hydroxyl group (—OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The H—OH or H2O is then released as a molecule of water, hence the term dehydration. The new molecule, consisting of two monosaccharides, is called adisaccharide and is conjoined together by a glycosidic or ether bond. The reverse reaction can also occur, using a

molecule of water to split up a disaccharide and break the glycosidic bond; this is termed hydrolysis. The most well- known disaccharide is sucrose, ordinary sugar(in scientific contexts, called table sugar or cane sugar to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production oflactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called lactose intolerance.

Sugar polymers are characterised by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom which can be in equilibrium with the open-chain aldehyde or keto form. If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

[edit]Oligosaccharides and polysaccharides

Cellulose as polymer of β-D-glucose

When a few (around three to six) monosaccharides are joined together, it is called anoligosaccharide (oligo- meaning

"few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined together make apolysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers.

. Cellulose is made by plants and is an important structural component of their cell walls.Humans can neither manufacture nor digest it.

. Glycogen, on the other hand, is an animal carbohydrate; humans and other animals use it as a form of energy storage.

[edit]Use of carbohydrates as an energy source

Main article: Carbohydrate metabolism

Glucose is the major energy source in most life forms. For instance, polysaccharides are broken down into their monomers (glycogen phosphorylase removes glucose residues from glycogen). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides.

[edit]Glycolysis (anaerobic)

Glucose is mainly metabolized by a very important ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate; this also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents in the form of converting NAD+ to NADH. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e. g. in humans) or to ethanol plus carbon dioxide (e. g. in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.

[edit]Aerobic

In aerobic cells with sufficient oxygen, like most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two more molecules of ATP, six moreNADH molecules and two reduced (ubi)quinones

(via FADH2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thereby, oxygen is reduced to water and the original electron acceptors NAD+ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.

[edit]Gluconeogenesis

Main article: Gluconeogenesis

In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate.

The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle.[citation needed]

[edit]Proteins

Main article: Protein

A schematic ofhemoglobin. The red and blue ribbons represent the proteinglobin; the green structures are the heme groups.

Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These molecules recognize specific reactant molecules called substrates; they then catalyze the reaction between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

In essence, proteins are chains of amino acids. An amino acid consists of a carbon atom bound to four groups. One

+ is an amino group, —NH2, and one is a carboxylic acid group, —COOH (although these exist as —NH3 and — COO−under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "—R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter.

Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined together as a dipeptide.

Amino acids can be joined together via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic

acid group. The resulting molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than around thirty) are called peptides or polypeptides. Longer stretches merit the title proteins. As an example, the important bloodserum protein albumin contains 585 amino acid residues.

The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate- asparagine-glycine-lysine-…". Secondary structure is concerned with local morphology (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an α-helix or into a sheet called a β-sheet; some α-helixes can be seen in the hemoglobin schematic above.Tertiary structure is the entire three- dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of theglutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.

Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathwaycan be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can only synthesize half of them. They cannot synthesize isoleucine, leucine, lysine,methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline,serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.

If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes calledtransaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α- keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein.

A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids.

+ Free ammonia (NH3), existing as the ammonium ion (NH4 ) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Similarly, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.

[edit]Lipids

Main article: Lipid

The term lipid comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolarcompounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids and terpenoids(e.g. retinoids and steroids). Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid.

Most lipids have some polar character in addition to being largely nonpolar. Generally, the bulk of their structure is nonpolar orhydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.

Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc., are composed of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids.

[edit]Nucleic acids

Main article: Nucleic acid

A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate, the primary energy-carrier molecule found in all living organisms.

Nucleic acid, so called because of its prevalence in cellular nuclei, is the generic name of the family of biopolymers. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentosesugar, and a phosphate group. Different nucleic acid types differ in the specific sugar found in their chain (e.g. DNA or deoxyribonucleic acid contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, andguanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.

[edit]Relationship to other "molecular-scale" biological sciences

Schematic relationship between biochemistry, genetics and molecular biology

Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas from genetics, molecular biologyand biophysics. There has never been a hard-line between these disciplines in terms of content and technique. Today the terms molecular biology and biochemistry are nearly interchangeable. The following figure is a schematic that depicts one possible view of the relationship between the fields:

Simplistic overview of the chemical basis of love, one of many applications that may be described in terms of biochemistry.

. Biochemistry is the study of the chemical substances and vital processes occurring in

living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.

. Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms which lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" studies.

. Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biologywhere genetic material is transcribed

into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA.

. Chemical Biology seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules). [edit]See also Utline of biochemistry

From Wikipedia, the free encyclopedia (Redirected from List of biochemistry topics)

See also: Index of biochemistry articles

Biochemistry is the study of the chemical processes and transformations in living organisms, including the structure and function ofcellular components, such as proteins, carbohydrates, lipids, nucleic acids, and other biomolecules.

The following outline is provided as an overview of and topical guide to biochemistry:

[edit]Essence of biochemistry

Main article: Biochemistry

Biochemistry is the science deals with chemical composition and its reactions, happening in the living cells of organisms, such as mammals, vertebrates, plants and all living organisms.

[edit]Branches of biochemistry

[edit]Main Branches

. Animal Biochemistry

. Plant Biochemistry

. Molecular Biology

. Cell Biology

. Metabolism

. Immunology

. Genetics

. Enzymatic biology

[edit]Other branches

Biotechnology, Bioluminescence, Molecular chemistry, Enzymatic Chemistry, Genetic engineering, Pharmaceuticals, Endocrinology,Cytology, Hematology, Nutrition and Photosynthesis

[edit]History of biochemistry

Main article: History of biochemistry [edit]General biochemistry concepts

. Major categories of bio-compounds:

. Carbohydrates : sugar -- disaccharide -- polysaccharide -- starch -- glycogen

. Lipids : fatty acid -- fats -- essential oils -- oils -- waxes -- cholesterol

. Nucleic acids : DNA -- RNA -- mRNA -- tRNA -- rRNA -- codon -- adenosine -- cytosine -- guanine -- thymine -- uracil

. Proteins :

. amino acid -- glycine -- arginine -- lysine

. peptide -- primary structure -- secondary structure -- tertiary structure -- conformation -- protein folding

. Chemical properties:

. molecular bond -- covalent bond -- ionic bond -- hydrogen bond -- ester -- ethyl

. molecular charge -- hydrophilic -- hydrophobic -- polar

. pH -- acid -- alkaline -- base

. oxidation -- reduction -- hydrolysis

. Structural compounds:

. In cells: flagellin -- peptidoglycan -- myelin -- actin -- myosin

. In animals: chitin -- keratin -- collagen -- silk

. In plants: cellulose -- lignin -- cell wall

. Enzymes and enzyme activity:

. enzyme kinetics -- enzyme inhibition

. proteolysis -- ubiquitin -- proteasome

. kinase -- dehydrogenase

. Membranes : fluid mosaic model -- diffusion -- osmosis

. phospholipids -- glycolipid -- glycocalyx -- antigen -- isoprene

. ion channel -- proton pump -- electron transport -- ion gradient -- antiporter -- symporter -- quinone -- riboflavin

. Energy pathways :

. pigments : chlorophyll -- carotenoids -- xanthophyll -- cytochrome -- phycobilin -- bacteriorhodopsin -- hemoglobin -- myoglobin --absorption spectrum -- action spectrum -- fluorescence

. Photosynthesis : light reaction -- dark reaction

. Fermentation : Acetyl-CoA -- lactic acid

. Cellular respiration : Adenosine triphosphate (ATP) -- NADH -- pyruvate -- oxalate -- citrate

. Chemosynthesis

. Regulation

. hormones : auxin

. signal transduction -- growth factor -- transcription factor -- protein kinase -- SH3 domain

. Malfunctions : tumor -- oncogene -- tumor suppressor gene

. Receptors : Integrin -- transmembrane receptor -- ion channel

. Techniques : electrophoresis -- chromatography -- mass spectrometry -- x-ray diffraction -- Southern blot -- fractionation -- Gram stain-- Surface Plasmon Resonance Green Revolution (agriculture)

From Wikipedia, the free encyclopedia (Redirected from Green Revolution)

"Green Revolution" redirects here. For other uses, see Green Revolution (disambiguation).

Green Revolution refers to a series of research, development, and technology transfer initiatives, occurring between

1943 and the late 1970s, that increased industrialized agriculture production in India; however, the yield increase has also occurred world wide.

The initiatives involved the development of high-yielding varieties of cereal grains, expansion of irrigation infrastructure, and distribution of hybridized seeds, synthetic fertilizers, and pesticides to farmers.

The term "Green Revolution" was first used in 1968 by former USAID director William Gaud, who noted the spread of the new technologies and said,

"These and other developments in the field of agriculture contain the makings of a new revolution. It is not a violent Red Revolution like that of the Soviets, nor is it a White Revolution like that of the Shah of Iran. I call it the Green Revolution."[1]

[edit]History

With the experience of agricultural development begun in Mexico by Norman Borlaug in 1943 judged as a success, the Rockefeller Foundation sought to spread it to other nations. The Office of Special Studies in Mexico became an informal international research institution in 1959, and in 1963 it formally became CIMMYT, The International Maize and Wheat Improvement Center.

In 1961 India was on the brink of mass famine.[2] Borlaug was invited to India by the adviser to the Indian minister of agriculture M. S. Swaminathan. Despite bureaucratic hurdles imposed by India's grain monopolies, the Ford

Foundation and Indian government collaborated to import wheat seed from CIMMYT. Punjab was selected by the Indian government to be the first site to try the new crops because of its reliable water supply and a history of agricultural success. India began its own Green Revolution program of plant breeding, irrigation development, and financing of agrochemicals.[3]

India soon adopted IR8 - a semi-dwarf rice variety developed by the International Rice Research Institute (IRRI) that could produce more grains of rice per plant when grown with certain fertilizers and irrigation. In 1968, Indian agronomist S.K. De Datta published his findings that IR8 rice yielded about 5 tons per hectare with no fertilizer, and almost 10 tons per hectare under optimal conditions. This was 10 times the yield of traditional rice.[4] IR8 was a success throughout Asia, and dubbed the "Miracle Rice". IR8 was also developed intoSemi-dwarf IR36.

In the 1960s, rice yields in India were about two tons per hectare; by the mid-1990s, they had risen to six tons per hectare. In the 1970s, rice cost about $550 a ton; in 2001, it cost under $200 a ton.[5] India became one of the world's most successful rice producers, and is now a major rice exporter, shipping nearly 4.5 million tons in 2006.

[edit]IR8 and the Philippines

In 1960, the Government of the Republic of the Philippines with Ford and Rockefeller Foundations established IRRI

(International Rice Research Institute). A rice crossing between Dee-Geo-woo-gen and Peta was done at IRRI in 1962. In 1966, one of the breeding lines became a new cultivar, IR8.[6] IR8 required the use of fertilizers and pesticides, but produced substantially higher yields than the traditional cultivars. Annual rice production in the Philippines increased from 3.7 to 7.7 million tonnes in two decades.[7] The switch to IR8 rice made the Philippines a rice exporter for the first time in the 20th century.[8] But the heavy pesticide use reduced the number of fish and frog species found in rice paddies.[9]

[edit]CGIAR

In 1970, foundation officials proposed a worldwide network of agricultural research centers under a permanent secretariat. This was further supported and developed by the World Bank; on May 19, 1971, the Consultative Group on International Agricultural Researchwas established, co-sponsored by the FAO, IFAD and UNDP. CGIAR, has added many research centers throughout the world.

CGIAR has responded, at least in part, to criticisms of Green Revolution methodologies. This began in the 1980s, and mainly was a result of pressure from donor organizations.[10] Methods like Agroecosystem Analysis and Farming

System Research have been adopted to gain a more holistic view of agriculture. Methods like Rapid Rural Appraisal and Participatory Rural Appraisal have been adopted to help scientists understand the problems faced by farmers and even give farmers a role in the development process.

[edit]Problems in Africa

There have been numerous attempts to introduce the successful concepts from the Mexican and Indian projects into Africa.[11] These programs have generally been less successful. Reasons cited include widespread corruption, insecurity, a lack of infrastructure, and a general lack of will on the part of the governments. Yet environmental

factors, such as the availability of water for irrigation, the high diversity in slope and soil types in one given area are also reasons why the Green Revolution is not so successful in Africa.[12]

A recent program in western Africa is attempting to introduce a new high-yield variety of rice known as "New Rice for Africa"(NERICA). NERICAs yield about 30% more rice under normal conditions, and can double yields with small amounts of fertilizer and very basic irrigation. However the program has been beset by problems getting the rice into the hands of farmers, and to date the only success has been in Guinea where it currently accounts for 16% of rice cultivation.[13]

After a famine in 2001 and years of chronic hunger and poverty, in 2005 the small African country of Malawi launched the Agricultural Input Subsidy Program by which vouchers are given to smallholder farmers to buy subsidized nitrogen fertilizer and maize seeds. Within its first year, the program was reported with extreme success, producing the largest maize harvest of the country's history; enough to feed the country with tons of maize left over. The program has advanced yearly ever since. Various sources claim that the program has been an unusual success, hailing it as a "miracle".[14]

[edit]Agricultural production and food security

[edit]Technologies

The Green Revolution spread technologies that had already existed before, but had not been widely used outside industrialized nations. These technologies included pesticides, irrigation projects, synthetic nitrogen fertilizer and improved crop varieties developed through the conventional, science-based methods available at the time.

The novel technological development of the Green Revolution was the production of novel wheat cultivars. Agronomists bred cultivars ofmaize, wheat, and rice that are generally referred to as HYVs or ―high-yielding varieties‖. HYVs have higher nitrogen-absorbing potential than other varieties. Since cereals that absorbed extra nitrogen would typically lodge, or fall over before harvest, semi-dwarfing geneswere bred into their genomes. A Japanese dwarf wheat cultivar (Norin 10 wheat), which was sent to Washington, D.C. by Cecil Salmon, was instrumental in developing Green Revolution wheat cultivars. IR8, the first widely implemented HYV rice to be developed by IRRI, was created through a cross between an Indonesian variety named ―Peta‖ and a Chinese variety named ―Dee-geo-woo-gen.‖

With advances in molecular genetics, the mutant genes responsible for Arabidopsis thaliana genes (GA 20- oxidase,[15] ga1,[16] ga1-3[17]), wheat reduced-height genes (Rht)[18] and a rice semidwarf gene (sd1)[19] were cloned.

These were identified as gibberellinbiosynthesis genes or cellular signaling component genes. Stem growth in the mutant background is significantly reduced leading to thedwarf phenotype. Photosynthetic investment in the stem is reduced dramatically as the shorter plants are inherently more stable mechanically. Assimilates become redirected to grain production, amplifying in particular the effect of chemical fertilizers on commercial yield.

HYVs significantly outperform traditional varieties in the presence of adequate irrigation, pesticides, and fertilizers. In the absence of these inputs, traditional varieties may outperform HYVs. Therefore, several authors have challenged

the apparent superiority of HYVs not only compared to the traditional varieties alone, but by contrasting the monocultural system asssociated with HYVs with the polycultural system associated with traditional ones.[20]

[edit]Production increases

Cereal production more than doubled in developing nations between the years 1961–1985.[21] Yields of rice, maize, and wheat increased steadily during that period.[21] The production increases can be attributed roughly equally to irrigation, fertilizer, and seed development, at least in the case of Asian rice.[21]

While agricultural output increased as a result of the Green Revolution, the energy input to produce a crop has increased faster,[22] so that the ratio of crops produced to energy input has decreased over time. Green Revolution techniques also heavily rely on chemicalfertilizers, pesticides and herbicides, some of which must be developed from fossil fuels, making agriculture increasingly reliant onpetroleum products.[23] Proponents of the Peak Oil theory fear that a future decline in oil and gas production would lead to a decline in food production or even a Malthusian catastrophe.[24]

[edit]Effects on food security

Main article: Food security

The effects of the Green Revolution on global food security are difficult to assess because of the complexities involved in food systems.

The world population has grown by about four billion since the beginning of the Green Revolution and many believe that, without the Revolution, there would have been greater famine and malnutrition. India saw annual wheat production rise from 10 million tons in the 1960s to 73 million in 2006.[25] The average person in the developing world consumes roughly 25% more calories per day now than before the Green Revolution.[21] Between 1950 and 1984, as the Green Revolution transformed agriculture around the globe, world grain production increased by over 250%[26]

The production increases fostered by the Green Revolution are often credited with having helped to avoid widespread famine, and for feeding billions of people.[citation needed]

There are also claims that the Green Revolution has decreased food security for a large number of people. One claim involves the shift of subsistence-oriented cropland to cropland oriented towards production of grain for export or animal feed. For example, the Green Revolution replaced much of the land used for pulses that fed Indian peasants for wheat, which did not make up a large portion of the peasant diet.[27]

[edit]Criticisms

[edit]Food security

[edit]Malthusian criticism

Some criticisms generally involve some variation of the Malthusian principle of population. Such concerns often revolve around the idea that the Green Revolution is unsustainable,[28] and argue that humanity is now in a state of overpopulation with regards to the sustainable carrying capacity and ecological demands on the Earth.

Although 36 million people die each year as a direct or indirect result of hunger and poor nutrition,[29] Malthus' more extreme predictions have frequently failed to materialize. In 1798 Thomas Malthus made his prediction of impending famine.[30] The world's population had doubled by 1923 and doubled again by 1973 without fulfilling Malthus' prediction. Malthusian Paul R. Ehrlich, in his 1968 book The Population Bomb, said that "India couldn't possibly feed two hundred million more people by 1980" and "Hundreds of millions of people will starve to death in spite of any crash programs."[30] Ehrlich's warnings failed to materialize when India became self-sustaining in cereal production in 1974 (six years later) as a result of the introduction of Norman Borlaug's dwarf wheat varieties.[30]

[edit]Is food production related to famine?

To some modern Western sociologists and writers, increasing food production is not synonymous with increasing food security, and is only part of a larger equation. For example, Harvard professor Amartya Sen claimed large historic famines were not caused by decreases in food supply, but by socioeconomic dynamics and a failure of public action.[31] However, economist Peter Bowbrick refutes that Sen's theory is incorrect as Sen relies on inconsistent arguments, and contradicting available information, including sources that Sen himself cited.[32] Bowbrick further argues that Sen's views coincide with that of the Bengal government at the time of the Bengal famine of 1943 and the policies Sen advocates failed to relieve the famine.[32]

[edit]Quality of diet

Some have challenged the value of the increased food production of Green Revolution agriculture. Miguel A. Altieri,

(a pioneer of agroecology and peasant-advocate), writes that the comparison between traditional systems of agriculture and Green Revolution agriculture has been unfair, because Green Revolution agriculture produces monocultures of cereal grains, while traditional agriculture usually incorporates polycultures.[citation needed]

These monoculture crops are often used for export, feed for animals, or conversion into biofuel. According to Emile Frison of Bioversity International, the Green Revolution has also led to a change in dietary habits, as less people are affected by hunger and die from starvation, but many are affected by malnutrition such as iron or vitamin-A deficiencies.[12] Frison further asserts that almost 60% of yearly deaths of children under age five in developing countries are related to malnutrition.[12]

High-yield rice (HYR), introduced since 1964 to poverty-ridden Asian countries, (such as the Philippines), was found to have inferior flavor and be more glutinous and less savory than their native varieties.[citation needed] This caused its price to be lower than the average market value.[33]

In the Philippines the introduction of heavy pesticides to rice production, in the early part of the green revolution, poisoned and killed off fish and weedy green vegetables that traditionally coexisted in rice paddies. These were nutritious food sources for many poor Filipino farmers prior to the introduction of pesticides, further impacting the diets of locals.[34]

[edit]Political impacts

A major critic[citation needed] of the Green Revolution, U.S. investigative journalist Mark Dowie, writes:[citation needed]

The primary objective of the program was geopolitical: to provide food for the populace in undeveloped countries and so bring social stability and weaken the fomenting of communist insurgency.

Citing internal Foundation documents, Dowie states that the Ford Foundation had a greater concern than Rockefeller in this area.[35]

There is significant evidence that the Green Revolution weakened socialist movements in many nations. In countries such as India, Mexico, and the Philippines, technological solutions were sought as an alternative to expanding agrarian reform initiatives, the latter of which were often linked to socialist politics.[36]

Adversely, a similar logic can be applied against Mark Dowie's own argument, such that his politicized argument against the Green Revolution implies the advocation of and need to starve a nation's population into submission if a Communist or socialist government is to be considered a viable alternative within the eyes of a desperate population.

[edit]Socioeconomic impacts

The transition from traditional agriculture, in which inputs were generated on-farm, to Green Revolution agriculture, which required the purchase of inputs, led to the widespread establishment of rural credit institutions. Smaller farmers often went into debt, which in many cases results in a loss of their farmland.[10][37] The increased level of mechanization on larger farms made possible by the Green Revolution removed a large source of employment from the rural economy.[10] Because wealthier farmers had better access to credit and land, the Green Revolution increased class disparities. The rich - poor gap widened due to that. Because some regions were able to adopt Green Revolution agriculture more readily than others (for political or geographical reasons), interregional economic disparities increased as well. Many small farmers are hurt by the dropping prices resulting from increased production overall.[citation needed]However, large-scale farming companies only account for less than 10% of the total farming capacity.

The new economic difficulties of small holder farmers and landless farm workers led to increased rural-urban migration. The increase in food production led to a cheaper food for urban dwellers, and the increase in urban population increased the potential for industrialization.[citation needed]

[edit]Globalization

In the most basic sense, the Green Revolution was a product of globalization as evidenced in the creation of international agricultural research centers that shared information, and with transnational funding from groups like the

Rockefeller Foundation, Ford Foundation, and United States Agency for International Development (USAID). Additionally, the inputs required in Green Revolution agriculture created new markets for seed and chemical corporations, many of which were based in the United States. For example, Standard Oil of New Jersey established hundreds of distributors in the Philippines to sell agricultural packages composed of HYV seed, fertilizer, and pesticides.[citation needed]

[edit]Environmental impact

[edit]Pesticides

Green Revolution agriculture relies on extensive use of pesticides, which are necessary to limit the high levels of pest damage that inevitably occur in monocropping - the practice of producing or growing one single crop over a wide area.

[edit]Water

Industrialized agriculture with its high yield varieties are extremely water intensive. In the US, agriculture consumes

70% of all fresh water resources. For example, the Southwest uses 36% of the nation's water while at the same time only receiving 6% of the country's rainfall.[citation needed] Only 60% of the water used for irrigation comes from surface water supplies. The other 40% comes from underground aquifers that are being used up in a way similar to topsoil that makes the aquifers,[citation needed] as Pfeiffer says, ―for all intents and purposes non renewable resources.‖[citation needed] The Ogallala Aquifer is essential to a huge portion of central and southwest plain states, but has been at annual overdrafts of 130-160% in excess of replacement. This irrigation source for America's bread basket will become entirely unproductive in another 30 years or so.[citation needed]

Likewise, rivers are drying up at an alarming rate. In 1997, the lower parts of China’s Yellow River were dry for a record 226 days. Over the past ten years, it has gone dry an average of 70 days a year.[citation needed] Famous lifelines such as the Nile and Ganges along with countless other rivers are sharing in the same fate.[citation needed] The Aral

Sea has lost half its area and two-thirds its volume due to river diversion for cotton production.

Also the water quality is being compromised. In the Aral Sea, water salinization has wiped out all native fish, leaving an economy even more dependent on the agricultural model that originated the problem.[citation needed]

Fish are disappearing through another form of agricultural run off as well.[citation needed] When nitrogen- intensive fertilizers wash into waterways it results in an explosion of algae and other microorganisms that lead to oxygen depletion resulting in ―dead zones‖, killing off fish and other creatures.

[edit]Biodiversity

The spread of Green Revolution agriculture affected both agricultural biodiversity and wild biodiversity.[38] There is little disagreement that the Green Revolution acted to reduce agricultural biodiversity, as it relied on just a few high- yield varieties of each crop.

This has led to concerns about the susceptibility of a food supply to pathogens that cannot be controlled by agrochemicals, as well as the permanent loss of many valuable genetic traits bred into traditional varieties over thousands of years. To address these concerns, massive seed banks such as Consultative Group on International Agricultural Research’s (CGIAR) International Plant Genetic Resources Institute (now Bioversity International) have been established (see Svalbard Global Seed Vault).

There are varying opinions about the effect of the Green Revolution on wild biodiversity. One hypothesis speculates that by increasing production per unit of land area, agriculture will not need to expand into new, uncultivated areas to feed a growing human population.[39]However, land degradation and soil nutrients depletion have forced farmers to clear up formerly forested areas in order to keep up with production.[40] A counter-hypothesis speculates that biodiversity was sacrificed because traditional systems of agriculture that were displaced sometimes incorporated

practices to preserve wild biodiversity, and because the Green Revolution expanded agricultural development into new areas where it was once unprofitable or too arid. For example, the development of wheat varieties tolerant to acid soil conditions with high aluminium content, permitted the introduction of agriculture in the Amazonian Cerrado ecosystem in Brazil.[39]

Nevertheless, the world community has clearly acknowledged the negative aspects of agricultural expansion as the 1992 Rio Treaty, signed by 189 nations, has generated numerous national Biodiversity Action Plans which assign significant biodiversity loss to agriculture's expansion into new domains.

[edit]Health impact

The consumption of the chemicals and pesticides used to kill pests by humans in some cases may be increasing the likelihood ofcancer in some of the rural villages using them. Poor farming practices including non-compliance to usage of masks and over-usage of the chemicals compound this situation.[41] In 1989, WHO and UNEP estimated that there were around 1 million human pesticide poisonings annually. Some 20000 (mostly in developing countries) ended in death, as a result of poor labeling, loose safety standards etc. [42]

[edit]Pesticides and cancer

Long term exposure to pesticides such as organochlorines, creosote, and sulfallate have been correlated with higher cancer rates and organochlorines DDT, chlordane, and lindane as tumor promoters in animals.[citation needed] Contradictory epidemiologic studies in humans have linked phenoxy acid herbicides or contaminants in them with soft tissue sarcoma (STS) and malignant lymphoma, organochlorine insecticides with STS, non-Hodgkin's lymphoma (NHL), leukemia, and, less consistently, with cancers of the lung andbreast, organophosphorous compounds with NHL and leukemia, and triazine herbicides with ovarian cancer.[43][44]

However, additional comprehensive studies in 2009 have been unable to link any human health issues to the use of DDT. It is estimated that as many as 60 million people have died of malaria specifically because DDT was banned from use in their country. Within first-world nations, such as the United States, cancer rates among farmers are actually much lower than the general United States population.[45]

[edit]Punjab case