BIOTECH STUDIES

Mesothelioma

2008-10-08T23:05:00.006+05:30

Mesothelioma: Questions and Answers

Mesothelioma is a rare form of cancer in which malignant (cancerous) cells are found in the mesothelium, a protective sac that covers most of the body�??s internal organs. Most people who develop mesothelioma have worked on jobs where they inhaled asbestos particles.

What is the mesothelium?

The mesothelium is a membrane that covers and protects most of the internal organs of the body. It is composed of two layers of cells: One layer immediately surrounds the organ; the other forms a sac around it. The mesothelium produces a lubricating fluid that is released between these layers, allowing moving organs (such as the beating heart and the expanding and contracting lungs) to glide easily against adjacent structures.

The mesothelium has different names, depending on its location in the body. The peritoneum is the mesothelial tissue that covers most of the organs in the abdominal cavity. The pleura is the membrane that surrounds the lungs and lines the wall of the chest cavity. The pericardium covers and protects the heart. The mesothelial tissue surrounding the male internal reproductive organs is called the tunica vaginalis testis. The tunica serosa uteri covers the internal reproductive organs in women.

What is mesothelioma?

Mesothelioma (cancer of the mesothelium) is a disease in which cells of the mesothelium become abnormal and divide without control or order. They can invade and damage nearby tissues and organs. Cancer cells can also metastasize (spread) from their original site to other parts of the body. Most cases of mesothelioma begin in the pleura or peritoneum.

How common is mesothelioma?

Although reported incidence rates have increased in the past 20 years, mesothelioma is still a relatively rare cancer. About 2,000 new cases of mesothelioma are diagnosed in the United States each year. Mesothelioma occurs more often in men than in women and risk increases with age, but this disease can appear in either men or women at any age.

What are the risk factors for mesothelioma?

Working with asbestos is the major risk factor for mesothelioma. A history of asbestos exposure at work is reported in about 70 percent to 80 percent of all cases. However, mesothelioma has been reported in some individuals without any known exposure to asbestos.

Asbestos is the name of a group of minerals that occur naturally as masses of strong, flexible fibers that can be separated into thin threads and woven. Asbestos has been widely used in many industrial products, including cement, brake linings, roof shingles, flooring products, textiles, and insulation. If tiny asbestos particles float in the air, especially during the manufacturing process, they may be inhaled or swallowed, and can cause serious health problems. In addition to mesothelioma, exposure to asbestos increases the risk of lung cancer, asbestosis (a noncancerous, chronic lung ailment), and other cancers, such as those of the larynx and kidney.

Smoking does not appear to increase the risk of mesothelioma. However, the combination of smoking and asbestos exposure significantly increases a person�??s risk of developing cancer of the air passageways in the lung.

Who is at increased risk for developing mesothelioma?

Asbestos has been mined and used commercially since the late 1800s. Its use greatly increased during World War II. Since the early 1940s, millions of American workers have been exposed to asbestos dust. Initially, the risks associated with asbestos exposure were not known. However, an increased risk of developing mesothelioma was later found among shipyard workers, people who work in asbestos mines and mills, producers of asbestos products, workers in the heating and construction industries, and other tradespeople. Today, the U.S. Occupational Safety and Health Administration (OSHA) sets limits for acceptable levels of asbestos exposure in the workplace. People who work with asbestos wear personal protective equipment to lower their risk of exposure.

The risk of asbestos-related disease increases with heavier exposure to asbestos and longer exposure time. However, some individuals with only brief exposures have developed mesothelioma. On the other hand, not all workers who are heavily exposed develop asbestos-related diseases.

There is some evidence that family members and others living with asbestos workers have an increased risk of developing mesothelioma, and possibly other asbestos-related diseases. This risk may be the result of exposure to asbestos dust brought home on the clothing and hair of asbestos workers. To reduce the chance of exposing family members to asbestos fibers, asbestos workers are usually required to shower and change their clothing before leaving the workplace.

What are the symptoms of mesothelioma?

Symptoms of mesothelioma may not appear until 30 to 50 years after exposure to asbestos. Shortness of breath and pain in the chest due to an accumulation of fluid in the pleura are often symptoms of pleural mesothelioma. Symptoms of peritoneal mesothelioma include weight loss and abdominal pain and swelling due to a buildup of fluid in the abdomen. Other symptoms of peritoneal mesothelioma may include bowel obstruction, blood clotting abnormalities, anemia, and fever. If the cancer has spread beyond the mesothelium to other parts of the body, symptoms may include pain, trouble swallowing, or swelling of the neck or face.

These symptoms may be caused by mesothelioma or by other, less serious conditions. It is important to see a doctor about any of these symptoms. Only a doctor can make a diagnosis.

How is mesothelioma diagnosed?

Diagnosing mesothelioma is often difficult, because the symptoms are similar to those of a number of other conditions. Diagnosis begins with a review of the patient�??s medical history, including any history of asbestos exposure. A complete physical examination may be performed, including x-rays of the chest or abdomen and lung function tests. A CT (or CAT) scan or an MRI may also be useful. A CT scan is a series of detailed pictures of areas inside the body created by a computer linked to an x-ray machine. In an MRI, a powerful magnet linked to a computer is used to make detailed pictures of areas inside the body. These pictures are viewed on a monitor and can also be printed.

A biopsy is needed to confirm a diagnosis of mesothelioma. In a biopsy, a surgeon or a medical oncologist (a doctor who specializes in diagnosing and treating cancer) removes a sample of tissue for examination under a microscope by a pathologist. A biopsy may be done in different ways, depending on where the abnormal area is located. If the cancer is in the chest, the doctor may perform a thoracoscopy. In this procedure, the doctor makes a small cut through the chest wall and puts a thin, lighted tube called a thoracoscope into the chest between two ribs. Thoracoscopy allows the doctor to look inside the chest and obtain tissue samples. If the cancer is in the abdomen, the doctor may perform a peritoneoscopy. To obtain tissue for examination, the doctor makes a small opening in the abdomen and inserts a special instrument called a peritoneoscope into the abdominal cavity. If these procedures do not yield enough tissue, more extensive diagnostic surgery may be necessary.

If the diagnosis is mesothelioma, the doctor will want to learn the stage (or extent) of the disease. Staging involves more tests in a careful attempt to find out whether the cancer has spread and, if so, to which parts of the body. Knowing the stage of the disease helps the doctor plan treatment.

Mesothelioma is described as localized if the cancer is found only on the membrane surface where it originated. It is classified as advanced if it has spread beyond the original membrane surface to other parts of the body, such as the lymph nodes, lungs, chest wall, or abdominal organs.

How is mesothelioma treated?

Treatment for mesothelioma depends on the location of the cancer, the stage of the disease, and the patient�??s age and general health. Standard treatment options include surgery, radiation therapy, and chemotherapy. Sometimes, these treatments are combined.

Surgery is a common treatment for mesothelioma. The doctor may remove part of the lining of the chest or abdomen and some of the tissue around it. For cancer of the pleura (pleural mesothelioma), a lung may be removed in an operation called a pneumonectomy. Sometimes part of the diaphragm, the muscle below the lungs that helps with breathing, is also removed.
Radiation therapy, also called radiotherapy, involves the use of high-energy rays to kill cancer cells and shrink tumors. Radiation therapy affects the cancer cells only in the treated area. The radiation may come from a machine (external radiation) or from putting materials that produce radiation through thin plastic tubes into the area where the cancer cells are found (internal radiation therapy).

Chemotherapy is the use of anticancer drugs to kill cancer cells throughout the body. Most drugs used to treat mesothelioma are given by injection into a vein (intravenous, or IV). Doctors are also studying the effectiveness of putting chemotherapy directly into the chest or abdomen (intracavitary chemotherapy).

To relieve symptoms and control pain, the doctor may use a needle or a thin tube to drain fluid that has built up in the chest or abdomen. The procedure for removing fluid from the chest is called thoracentesis. Removal of fluid from the abdomen is called paracentesis. Drugs may be given through a tube in the chest to prevent more fluid from accumulating. Radiation therapy and surgery may also be helpful in relieving symptoms.

bacteria

2008-04-25T20:56:00.001+05:30

Wikipedia: bacteria

Bacteria
Fossil range: Archean or earlier - Recent

Escherichia coli cells magnified 25,000 times

Scientific classification

Domain:

Bacteria

Phyla

Actinobacteria
Aquificae
Chlamydiae
Bacteroidetes/Chlorobi
Chloroflexi
Chrysiogenetes
Cyanobacteria
Deferribacteres
Deinococcus-Thermus
Dictyoglomi
Fibrobacteres/Acidobacteria
Firmicutes
Fusobacteria
Gemmatimonadetes
Lentisphaerae
Nitrospirae
Planctomycetes
Proteobacteria
Spirochaetes
Thermodesulfobacteria
Thermomicrobia
Thermotogae
Verrucomicrobia

Bacteria (singular: bacterium) are unicellular microorganisms. Typically a few micrometres spheres to rods to spirals. Bacteria are ubiquitous in every habitat on Earth, growing in soil, acidic hot springs, radioactive waste,^[1] seawater, and deep in the Earth's crust. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five nonillion (5�?10³⁰) bacteria in the world.^[2] Bacteria are vital in recycling nutrients, and many important steps in nutrient cycles depend on bacteria, such as the fixation of nitrogen from the atmosphere. However, most of these bacteria have not been characterised, and only about half of the phyla of bacteria have species that can be cultured in the laboratory.^[3] The study of bacteria is known as bacteriology, a branch of microbiology. in length, individual bacteria have a wide-range of shapes, ranging from

There are approximately 10 times as many bacterial cells as human cells in the human body, with large numbers of bacteria on the skin and in the digestive tract.^[4] Although the vast majority of these bacteria are rendered harmless or beneficial by the protective effects of the immune system, a few pathogenic bacteria cause infectious diseases, including cholera, syphilis, anthrax, leprosy and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people a year, mostly in sub-Saharan Africa.^[5] In developed countries, antibiotics are used to treat bacterial infections and in various agricultural processes, so antibiotic resistance is becoming common. In industry, bacteria are important in processes such as wastewater treatment, the production of cheese and yoghurt, and the manufacture of antibiotics and other chemicals.^[6]

Bacteria are prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteriascientific classification changed after the discovery in the 1990s that prokaryotic life consists of two very different groups of organisms that evolved evolutionary domains are called Bacteria and Archaea.^[7] traditionally included all prokaryotes, the independently from an ancient common ancestor. These

History of bacteriology

Further information: Microbiology

The existence of microorganisms was hypothesized during the late Middle Ages. In The Canon of Medicine (1020), Abū Alī ibn Sīn�? (Avicenna) stated that bodily secretions are contaminated by "foul foreign earthly bodies" before a person becomes infected, but he did not view these bodies as primary causes of disease. When the Black Death bubonic plague reached al-Andalus in the 14th century, Ibn Khatima and Ibn al-Khatib wrote of infectious diseases being caused by contagious entities that enter the human body.^[8]^[9] These ideas about the contagious nature of some diseases became more popular in Europe during the Renaissance, particularly through the writing of Girolamo Fracastoro.^[10]

Antonie van Leeuwenhoek, the first person to observe bacteria using a microscope.

Bacteria were first observed by Anton van Leeuwenhoek in 1676, using a single-lens microscope^[11] He called them "animalcules" and published his observations in a series of letters to the Royal Society.^[12]^[13]^[14] The name bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1828, and is derived from the Greek word βακ�?ή�?ιον -α , bacterion -a , meaning "small staff".^[15] of his own design.

Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary, Robert Koch, Pasteur was an early advocate of the germ theory of disease.^[16]cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in 1905.^[17] In Koch's postulates, he set out criteria to test if an organism is the cause of a disease; these postulates are still used today.^[18] Robert Koch was a pioneer in medical microbiology and worked on

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available.^[19] In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum�??the spirochete that causes syphilis�??into compounds that selectively killed the pathogen.^[20] Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl-Neelsen stain.^[21]

A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that archaea have a separate line of evolutionary descent from bacteria.^[22] This new phylogenetic taxonomy was based on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains as part of the three-domain system.^[23]

Origin and early evolution

Further information: Timeline of evolution

The ancestors of modern bacteria were single-celled microorganisms that were the first forms of life to develop on earth, about 4 billion years ago. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life.^[24]^[25] Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the past history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.^[26] The most recent common ancestor of bacteria and archaea was probably a hyperthermophile that lived about 2.5 billion�??3.2 billion years ago.^[27]^[28]

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into endosymbiotic^[29]^[30] This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still being found in all known Eukarya (sometimes in highly reduced form, e. g. in ancient "amitochondrial" protozoa). Later on, an independent second engulfment by some mitochondria-containing eukaryotes of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants. There are even some algal groups known that clearly originated from subsequent events of endosymbiosis by heterotrophic eukaryotic hosts engulfing a eukaryotic algae that developed into "second-generation" plastids.^[31]^[32] associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea.

Morphology

Bacteria display a large diversity of cell morphologies and arrangements.

Bacteria display a wide diversity of shapes and sizes, called morphologies. Bacterial cells are about 10 times smaller than eukaryotic cells and are typically 0.5�??5.0 micrometres in length. However, a few species�??for example Thiomargarita namibiensis and Epulopiscium fishelsoni�??are up to half a millimetre long and are visible to the unaided eye.^[33] Among the smallest bacteria are members of the genus Mycoplasma, which measure only 0.3 micrometres, as small as the largest viruses.^[34]

Most bacterial species are either spherical, called cocci (sing. coccus, from Greek kókkos, grain, seed) or rod-shaped, called bacilli (sing. bacillus, from Latin baculus, stick). Some rod-shaped bacteria, called vibrio, are slightly curved or comma-shaped; others, can be spiral-shaped, called spirilla, or tightly coiled, called spirochetes. A small number of species even have tetrahedral or cuboidal shapes.^[35] This wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the ability of bacteria to acquire nutrients, attach to surfaces, swim through liquids and escape predators.^[36]^[37]

Many bacterial species exist simply as single cells, others associate in characteristic patterns: Neisseria form diploids (pairs), Streptococcus form chains, and Staphylococcus group together in "bunch of grapes" clusters. Bacteria can also be elongated to form filaments, for example the Actinobacteria. Filamentous bacteria are often surrounded by a sheath that contains many individual cells; certain types, such as species of the genus Nocardia, even form complex, branched filaments, similar in appearance to fungal mycelia.^[38]

The range of sizes shown by prokaryotes, relative to those of other organisms and biomolecules

Bacteria often attach to surfaces and form dense aggregations called biofilms or microbial mats. These films can range from a few micrometers in thickness to up to half a meter in depth, and may contain multiple species of bacteria, protists and archaea. Bacteria living in biofilms display a complex arrangement of cells and extracellular components, forming secondary structures such as microcolonies, through which there are networks of channels to enable better diffusion of nutrients.^[39]^[40] In natural environments, such as soil or the surfaces of plants, the majority of bacteria are bound to surfaces in biofilms.^[41] Biofilms are also important for chronic bacterial infections and infections of implanted medical devices, as bacteria protected within these structures are much harder to kill than individual bacteria.^[42]

Even more complex morphological changes are sometimes possible. For example, when starved of amino acids, Myxobacteria detect surrounding cells in a process known as quorum sensing, migrate towards each other, and aggregate to form fruiting bodies up to 500 micrometres long and containing approximately 100,000 bacterial cells.^[43] In these fruiting bodies, the bacteria perform separate tasks; this type of cooperation is a simple type of multicellular organisation. For example, about one in 10 cells migrate to the top of these fruiting bodies and differentiate^[44] into a specialised dormant state called myxospores, which are more resistant to desiccation and other adverse environmental conditions than are ordinary cells.

Cellular structure

Further information: Bacterial cell structure

Diagram of the cellular structure of a typical bacterial cell

Intracellular structures

The bacterial cell is surrounded by a lipid membrane, or cell membrane, which encompasses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. As they are prokaryotes, bacteria do not have membrane-bound organelles in their cytoplasm and thus contain few intracellular structures. They consequently lack a nucleus, mitochondria, chloroplasts and the other organelles present in eukaryotic cells, such as the Golgi apparatus and endoplasmic reticulum.^[45]

Many important biochemical reactions, such as energy generation, occur due to concentration gradients across membranes, creating a potential difference analogous to a battery. The absence of internal membranes in bacteria means these reactions, such as electron transport, occur across the cell membrane, between the cytoplasm and the periplasmic space.^[46] Additionally, while some transporter proteins consume chemical energy, others harness concentration gradients to import nutrients across the cell membrane or to expel undesired molecules from the cytoplasm.

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular chromosome located in the cytoplasm in an irregularly shaped body called the nucleoid.^[47] The nucleoid contains the chromosome with associated proteins and RNA. Like all living organisms, bacteria contain ribosomes for the production of proteins, but the structure of the bacterial ribosome is different from those of eukaryotes and Archaea.^[48] The order Planctomycetes are an exception to the general absence of internal membranes in bacteria, because they have a membrane around their nucleoid and contain other membrane-bound cellular structures.^[49]

Some bacteria produce intracellular nutrient storage granules, such as glycogen,^[50]polyphosphate,^[51] sulfur^[52] or polyhydroxyalkanoates.^[53] These granules enable bacteria to store compounds for later use. Certain bacterial species, such as the photosynthetic Cyanobacteria, produce internal gas vesicles, which they use to regulate their buoyancy - allowing them to move up or down into water layers with different light intensities and nutrient levels.^[54]

Extracellular structures

Further information: Cell envelope

Around the outside of the cell membrane is the bacterial cell wall. Bacterial cell walls are made of peptidoglycan (called murein in older sources), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids.^[55] Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively.^[56] The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.^[56]

There are broadly speaking two different types of cell wall in bacteria, called Gram-positive and Gram-negative. The names originate from the reaction of cells to the Gram stain, a test long-employed for the classification of bacterial species.^[57]

Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Most bacteria have the Gram-negative cell wall, and only the Firmicutes and Actinobacteria (previously known as the low G+C and high G+C Gram-positive bacteria, respectively) have the alternative Gram-positive arrangement.^[58]vancomycin can kill only Gram-positive bacteria and is ineffective against Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa.^[59] These differences in structure can produce differences in antibiotic susceptibility; for instance,

In many bacteria an S-layer of rigidly arrayed protein molecules covers the outside of the cell.^[60] This layer provides chemical and physical protection for the cell surface and can act as a macromolecular diffusion barrier. S-layers have diverse but mostly poorly understood functions, but are known to act as virulence factors in Campylobacter and contain surface enzymes in Bacillus stearothermophilus.^[61]

Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface

Flagella are rigid protein structures, about 20 nanometres in diameter and up to 20 micrometres in length, that are used for motility. Flagella are driven by the energy released by the transfer of ions down an electrochemical gradient across the cell membrane.^[62]

Fimbriae are fine filaments of protein, just 2�??10 nanometres in diameter and up to several micrometers in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells and are essential for the virulence of some bacterial pathogens.^[63]Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation (see bacterial genetics, below).^[64]

Capsules or slime layers are produced by many bacteria to surround their cells, and vary in structural complexity: ranging from a disorganised slime layer of extra-cellular polymer, to a highly structured capsule or glycocalyx. These structures can protect cells from engulfment by eukaryotic cells, such as macrophages.^[65] They can also act as antigens and be involved in cell recognition, as well as aiding attachment to surfaces and the formation of biofilms.^[66]

The assembly of these extracellular structures is dependent on bacterial secretion systems. These transfer proteins from the cytoplasm into the periplasm or into the environment around the cell. Many types of secretion systems are known and these structures are often essential for the virulence of pathogens, so are intensively studied.^[67]

Endospores

Further information: Endospores

Bacillus anthracis (stained purple) growing in cerebrospinal fluid

Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter and Heliobacterium, can form highly resistant, dormant structures called endospores.^[68] In almost all cases, one endospore is formed and this is not a reproductive process, although Anaerobacter can make up to seven endospores in a single cell.^[69]cytoplasm containing DNA and ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat. Endospores have a central core of

Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, pressure and desiccation.^[70] In this dormant state, these organisms may remain viable for millions of years,^[71]^[72] and endospores even allow bacteria to survive exposure to the vacuum^[73] Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus.^[74] and radiation in space.

Metabolism

Further information: Microbial metabolism

Fillaments of photosynthetic cyanobacteria

In contrast to higher organisms, bacteria exhibit an extremely wide variety of metabolic^[75] The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications.^[76] Bacterial metabolism is classified on the basis of three major criteria: the kind of energy used for growth, the source of carbon, and the electron donors used for growth. An additional criterion of respiratory microorganisms are the electron acceptors used for aerobic or anaerobic respiration.^[77] types.

Carbon metabolism in bacteria is either heterotrophic, where organic carbon compounds are used as carbon sources, or autotrophic, meaning that cellular carbon is obtained by fixing carbon dioxide. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-bacteria and some purple bacteria, but also many chemolithotrophic species, e. g. nitrifying or sulfur-oxidising bacteria.^[78] Energy metabolism of bacteria is either based on phototrophy, the use of light through photosynthesis, or on chemotrophy, the use of chemical substances for energy, which are mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic respiration).

Finally, bacteria are further divided into lithotrophs that use inorganic electron donors and organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the respective electron donors for energy conservation (by aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g. carbon dioxide fixation), whereas phototrophic organisms use them only for biosynthetic purposes. Respiratory organisms use chemical compounds as a source of energy by taking electrons from the reduced substrate and transferring them to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to synthesise ATP and drive metabolism. In aerobic organisms, oxygen anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically important processes of denitrification, sulfate reduction and acetogenesis, respectively. is used as the electron acceptor. In

Another way of life of chemotrophs in the absence of possible electron acceptors is fermentation, where the electrons taken from the reduced substrates are transferred to oxidised intermediates to generate reduced fermentation products (e. g. lactate, ethanol, hydrogen, butyrate). Fermentation is possible, because the energy content of the substrates is higher than that of the products, which allows the organisms to synthesise ATP and drive their metabolism.^[79]^[80]

These processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury methyl- and dimethylmercury) in the environment.^[81] Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves. (

Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic electron donors are hydrogen, carbon monoxide, ammonia (leading to nitrification), ferrous iron sulfur compounds. Unusually, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism.^[82] In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, while under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic. and other reduced metal ions, and several reduced

In addition to fixing carbon dioxide in photosynthesis, some bacteria also fix nitrogen gas (nitrogen fixation) using the enzyme nitrogenase. This environmentally important trait can be found in bacteria of nearly all the metabolic types listed above, but is not universal.^[83]

Growth and reproduction

Further information: Bacterial growth

Unlike multicellular organisms, increases in the size of bacteria (cell growth) and their reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction.^[84] Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes.^[85] In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that facilitate the dispersal of the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and arial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.

A growing colony of Escherichia coli^[86] cells.

In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media such as agar plates are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.^[87]

Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer.^[88] Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms.^[89] In nature, many organisms live in communities (e.g. biofilms) which may allow for increased supply of nutrients and protection from environmental stresses.^[41] These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).^[90]

Bacterial growth follows three phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to fast growth. The lag phase has high biosynthesis rates, as enzymes and nutrient transporters are produced.^[91] The second phase of growth is the logarithmic phase (log phase), also known as the exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The final phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport.^[92]

Genetics

Further information: Plasmid, Genome

Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii,^[93] to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum.^[94] Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome.^[95] Bacteria may also contain plasmids, which are small extra-chromosomal DNAs that may contain genes for antibiotic resistance or virulence factors. Another type of bacterial DNA are integrated viruses (bacteriophages). Many types of bacteriophage exist, some simply infect and lyse their host bacteria, while others insert into the bacterial chromosome. A bacteriophage can contain genes that contribute to its host's phenotype: for example, in the evolution of Escherichia coli O157:H7 and Clostridium botulinum, the toxin genes in an integrated phage converted a harmless ancestral bacteria into a lethal pathogen.^[96]

Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are clonal). However, all bacteria can evolve by selection on changes to their genetic material DNA genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria.^[97] Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.^[98] caused by

Some bacteria also transfer genetic material between cells. This can occur in three main ways. Firstly, bacteria can take up exogenous DNA from their environment, in a process called transformation. Genes can also be transferred by the process of transduction, when the integration of a bacteriophage introduces foreign DNA into the chromosome. The third method of gene transfer is bacterial conjugation, where DNA is transferred through direct cell contact. This gene acquisition from other bacteria or the environment is called horizontal gene transfer and may be common under natural conditions.^[99] Gene transfer is particularly important in antibiotic resistance as it allows the rapid transfer of resistance genes between different pathogens.^[100]

Movement

Further information: Chemotaxis, Flagella, Pilus

The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous;

Motile bacteria can move using flagella, bacterial gliding, twitching motility or changes of buoyancy.^[101] In twitching motility, bacterial use their type IV pili as a grappling hook, repeatedly extending it, anchoring it and then retracting it with remarkable force (>80 pN).^[102]

Bacterial species differ in the number and arrangement of flagella on their surface; some have a single flagellum (monotrichous), a flagellum at each end (amphitrichous), clusters of flagella at the poles of the cell (lophotrichous), while others have flagella distributed over the entire surface of the cell (peritrichous). The bacterial flagella is the best-understood motility structure in any organism and is made of about 20 proteins, with approximately another 30 proteins required for its regulation and assembly.^[101] The flagellum is a rotating structure driven by a motor at the base that uses the electrochemical gradient across the membrane for power. This motor drives the motion of the filament, which acts as a propeller. Many bacteria (such as E. coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and makes their movement a three-dimensional random walk.^[103] (See external links below for link to videos.) The flagella of a unique group of bacteria, the spirochaetes, are found between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves.^[101]

Motile bacteria are attracted or repelled by certain stimuli in behaviors called taxes: these include chemotaxis, phototaxis and magnetotaxis.^[104]^[105] In one peculiar group, the myxobacteria, individual bacteria move together to form waves of cells that then differentiate to form fruiting bodies containing spores.^[106] The myxobacteria move only when on solid surfaces, unlike E. coli which is motile in liquid or solid media.

Several Listeria and Shigella species move inside host cells by usurping the cytoskeleton, which is normally used to move organelles inside the cell. By promoting actin polymerization at one pole of their cells, they can form a kind of tail that pushes them through the host cell's cytoplasm.^[107]

Classification and identification

Streptococcus mutans visualized with a Gram stain

Further information: Taxonomy, Clinical pathology

Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA, fatty acids, pigments, antigens and quinones.^[87] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species.^[108] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasizes molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridization, as well as sequencing genes that have not undergone extensive lateral gene transfer, such as the rRNA gene.^[109] Classification of bacteria is determined by publication in the International Journal of Systematic Bacteriology,^[110] and Bergey's Manual of Systematic Bacteriology.^[111]

The term "bacteria" was traditionally applied to all microscopic, single-celled prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea^[112] that evolved independently from an ancient common ancestor. These two domains, along with Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in bacteriology.^[113] However, due to the relatively recent introduction of molecular systematics and the analysis of genome sequences, bacterial classification remains a changing and expanding field.^[3]^[114] For example, a few biologists argue that Archaea evolved from Gram-positive bacteria.^[115]

Identification of bacteria in the laboratory is particularly relevant in medicine, where the correct treatment is determined by the bacterial species causing an infection. Consequently, the need to identify human pathogens was a major impetus for the development of techniques to identify bacteria.

Phylogenetic tree showing the incredible diversity of bacteria, compared to other organisms.^[116] Eukaryotes archaea green and bacteria blue. are colored red,

The Gram stain, developed in 1884 by Hans Christian Gram, characterises bacteria based on the structural characteristics of their cell walls.^[57] The thick layers of peptidoglycan in the "Gram-positive" cell wall stain purple, while the thin "Gram-negative" cell wall appears pink. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of four groups (Gram-positive cocci, Gram-positive bacilli, Gram-negative cocci and Gram-negative bacilli). Some organisms are best identified by stains other than the Gram stain, particularly mycobacteria or Nocardia, which show acid-fastness on Ziehl�??Neelsen or similar stains.^[117] Other organisms may need to be identified by their growth in special media, or by other techniques, such as serology.

Culture techniques are designed to promote the growth and identify particular bacteria, while restricting the growth of the other bacteria in the sample. Often these techniques are designed for specific specimens; for example, a sputum sample will be treated to identify organisms that cause pneumonia, while stool specimens are cultured on selective media to identify organisms that cause diarrhoea, while preventing growth of non-pathogenic bacteria. Specimens that are normally sterile, such as blood, urine or spinal fluid, are cultured under conditions designed to grow all possible organisms.^[118]^[87] Once a pathogenic organism has been isolated, it can be further characterised by its morphology, growth patterns such as (aerobic or anaerobic growth, patterns of hemolysis) and staining.

As with bacterial classification, identification of bacteria is increasingly using molecular methods. Diagnostics using such DNA-based tools, such as polymerase chain reaction, are increasingly popular due to their specificity and speed, compared to culture-based methods.^[119] These methods also allow the detection and identification of "viable but nonculturable" cells that are metabolically active but non-dividing.^[120] However, even using these improved methods, the total number of bacterial species is not known and cannot even be estimated with any certainty. Attempts to quantify bacterial diversity have ranged from 10⁷ to 10⁹ total species, but even these diverse estimates may be out by many orders of magnitude.^[121]^[122]

Interactions with other organisms

Despite their apparent simplicity, bacteria can form complex associations with other organisms. These symbiotic associations can be divided into parasitism, mutualism and commensalism. Due to their small size, commensal bacteria are ubiquitous and grow on animals and plants exactly as they will grow on any other surface. However, their growth can be increased by warmth and sweat, and large populations of these organisms in humans are the cause of body odor.

Mutualists

Certain bacteria form close spatial associations that are essential for their survival. One such mutualistic association, called interspecies hydrogen transfer, occurs between clusters of anaerobic bacteria that consume organic acids such as butyric acid or propionic acid and produce hydrogen, and methanogenic Archaea that consume hydrogen.^[123] The bacteria in this association are unable to consume the organic acids as this reaction produces hydrogen that accumulates in their surroundings. Only the intimate association with the hydrogen-consuming Archaea keeps the hydrogen concentration low enough to allow the bacteria to grow.

In soil, microorganisms which reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking) carry out nitrogen fixation, converting nitrogen gas to nitrogenous compounds.^[124] This serves to provide an easily absorbable form of nitrogen for many plants, which cannot fix nitrogen themselves. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of over 1,000 bacterial species in the normal human gut flora of the intestines can contribute to gut immunity, synthesise vitamins such as folic acid, vitamin K and biotin, convert milk protein to lactic acidLactobacillus), as well as fermenting complex undigestible carbohydrates.^[125]^[126]^[127]competitive exclusion) and these beneficial bacteria are consequently sold as probiotic dietary supplements.^[128] (see The presence of this gut flora also inhibits the growth of potentially pathogenic bacteria (usually through

Pathogens

Further information: Bacteria and human health, Pathogen

Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

If bacteria form a parasitic association with other organisms, they are classed as pathogens. Pathogenic bacteria are a major cause of human death and disease and cause infections such as tetanus, typhoid fever, diphtheria, syphilis, cholera, food-borne illness, leprosy and tuberculosis. A pathogenic cause for a known medical disease may only be discovered many years after, as was the case with Helicobacter pylori and peptic ulcer disease. Bacterial diseases are also important in agriculture, with bacteria causing leaf spot, fireblight and wilts in plants, as well as Johne's disease, mastitis, salmonella and anthrax in farm animals.

Each species of pathogen has a characteristic spectrum of interactions with its human hosts. Some organisms, such as Staphylococcus or Streptococcus, can cause skin infections, pneumonia, meningitis and even overwhelming sepsis, a systemic inflammatory response producing shock, massive vasodilation and death.^[129] Yet these organisms are also part of the normal human flora and usually exist on the skin or in the nose without causing any disease at all. Other organisms invariably cause disease in humans, such as the Rickettsia, which are obligate intracellular parasites able to grow and reproduce only within the cells of other organisms. One species of Rickettsia causes typhus, while another causes Rocky Mountain spotted fever. Chlamydia, another phylum of obligate intracellular parasites, contains species that can cause pneumonia, or urinary tract infection and may be involved in coronary heart disease.^[130] Finally, some species such as Pseudomonas aeruginosa, Burkholderia cenocepacia, and Mycobacterium avium are opportunistic pathogens and cause disease mainly in people suffering from immunosuppression or cystic fibrosis.^[131]^[132]

Bacterial infections may be treated with antibiotics, which are classified as bacteriocidal if they kill bacteria, or bacteriostatic if they just prevent bacterial growth. There are many types of antibiotics and each class inhibits a process that is different in the pathogen from that found in the host. An example of how antibiotics produce selective toxicity are chloramphenicol and puromycin, which inhibit the bacterial ribosome, but not the structurally different eukaryotic ribosome.^[133] Antibiotics are used both in treating human disease and in intensive farming to promote animal growth, where they may be contributing to the rapid development of antibiotic resistance in bacterial populations.^[134] Infections can be prevented by antiseptic measures such as sterilizating the skin prior to piercing it with the needle of a syringe, and by proper care of indwelling catheters. Surgical and dental instruments are also sterilized to prevent contamination and infection by bacteria. Disinfectants such as bleach are used to kill bacteria or other pathogens on surfaces to prevent contamination and further reduce the risk of infection.

Significance in technology and industry

Further information: Economic importance of bacteria

Bacteria, often Lactobacillus in combination with yeasts and molds, have been used for thousands of years in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine and yoghurt.^[135]^[136]

The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills.^[137] Fertilizer was added to some of the beaches in Prince William Sound in an attempt to promote the growth of these naturally occurring bacteria after the infamous 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic wastes.^[138] In the chemical industry, bacteria are most important in the production of enantiomerically pure chemicals for use as pharmaceuticals or agrichemicals.^[139]

Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide.^[140] Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects.^[141]^[142]

Because of their ability to quickly grow and the relative ease with which they can be manipulated, bacteria are the workhorses for the fields of molecular biology, genetics and biochemistry. By making mutations in bacterial DNA and examining the resulting phenotypes, scientists can determine the function of genes, enzymes and metabolic pathways in bacteria, then apply this knowledge to more complex organisms.^[143] This aim of understanding the biochemistry of a cell reaches its most complex expression in the synthesis of huge amounts of enzyme kinetic and gene expression data into mathematical models of entire organisms. This is achievable in some well-studied bacteria, with models of Escherichia coli metabolism now being produced and tested.^[144]^[145] This understanding of bacterial metabolism and genetics allows the use of biotechnology to bioengineer bacteria for the production of therapeutic proteins, such as insulin, growth factors, or antibodies.^[146]^[147]

2008-04-25T20:53:00.000+05:30

Genetics Encyclopedia: Escherichia coli

Escherichia coli (E. coli) is a very common bacterium that normally inhabits the digestive tract of animals, including humans. It is widespread in the natural world and can also be found in soil and water. It is a member of the bacterial family Enterobacteriaciae, which also includes the bacteria Shigella, Salmonella, and Yersinia, among others. Some of these organisms, including E. coli, can cause serious diseases under certain conditions.

Attributes of E. Coli

E. coli is important to human health because it is a source of vitamins B12 and K, which it manufactures from undigested food in the large intestine. Unlike many other intestinal bacteria, E. coli can survive and grow in the presence of oxygen (although it can also grow without oxygen), which makes it a useful experimental model organism in the laboratory.

Even though E. coli is a single species of bacteria, many different varieties (called strains) of the species exist. Each has different characteristics, and while some are safe model organisms, others can cause potentially deadly disease. This is the case with E. coli 0157:H7, which is considered a dangerous pathogen which can infect humans. This strain is significantly different from the commonly used laboratory strains, which do not cause disease.

Importance in Laboratory Studies

E. coli is the most well-understood bacterium in the world, and is an extremely important model organism in many fields of research, particularly molecular biology, genetics, and biochemistry. It is easy to grow under laboratory conditions, and research strains are very safe to work with. As with many bacteria, E. coli grows quickly, which allows many generations to be studied in a short time. In fact, under ideal conditions, E. coli cells can double in number after only 20 minutes.

Furthermore, a very large number of E. coli bacteria can be grown in a small space�??many millions in a drop of broth, for example. These are important characteristics in genetic experiments, which often involve selecting a single bacterial cell from among millions of candidates, then allowing it to reproduce into high numbers again to perform additional experiments.

Many vital techniques, such as molecular cloning and overexpression of cloned genes, were initially developed in E. coli and are still simpler and more effective in the bacterium. Crucial experiments that illuminated the details of fundamental biological processes such as DNA replication, transcription, and translation were performed for the first time or with greatest success in E. coli. The bacterium is still a primary resource in many modern laboratories. Even research efforts that focus on other organisms, including humans or crop plants, often use E. coli extensively as a tool to facilitate cloning and DNA sequencing.

Discoveries Made in E. Coli

Some of the discoveries made in E. coli have provided an invaluable framework for understanding biological processes in more complex organisms. As mentioned above, many fundamental processes that are shared by all living things are most easily studied in this simple bacterial model. Furthermore,E. coli has served as a model for understanding the biology of other bacteria.

The ways in which E. coli interacts with the human body are in many cases very similar to the ways that other disease-causing organisms act. Therefore, this model organism has been important in the study of human health, and has allowed researchers to ask questions about bacteria in general (for example, how antibiotics stop infections, or how the immune system fights off disease).

Genome Sequenced Early

Sequencing of the E. coli K-12 strain genome (a popular model strain) was completed in 1997; subsequently, at least two collections of the pathogenic 0157:H7 strain have been completely sequenced. The bacterium has a genome of approximately 4.3 million base pairs of DNA, and carries about 4,400 genes. Interestingly, only about 50 percent of the predicted genes have been described and characterized, a surprisingly low percentage for such a well-understood organism. For this and other reasons, E. coli remains one of the most significant model organisms used today.

Bibliography

Madigan, Michael T., John M. Martinko, and Jack Parker. Brock Biology of Micro-organisms, 9th ed. Upper Saddle River, NJ: Prentice Hall, 2000.

�??Daniel J. Tomso

apoptosis

2008-04-25T20:24:00.000+05:30

Genetics Encyclopedia: Apoptosis

Did You Know?

Apoptosis Genes in C. Elegans

Much of our understanding of what causes apoptosis comes from genetic studies in Caenorhabditis elegans. Several cell death proteins (CED) proteins were identified in C. elegans by studying apoptosis-defective mutants. The main executioner is CED-3, a caspase, which becomes activated by CED-4, another caspase. The central guardian protecting cells against apoptosis is CED-9, which inhibits the actions of CED-4 and CED-3. CED-9 has a mammalian homolog, called BCL-2, which serves a similar role in mammals.

Caspase inhibitors are being investigated as a possible means to slow the progress of Huntington's disease, a degenerative brain disease.

Death is an inevitable fact of life for organisms. Increasingly, biologists have come to realize that death is also, in many cases, an important and predestined fate of individual cells of organisms. Apoptosis is a process by which cells in a multicellular organism commit suicide. While cells can die as a result of necrosis, apoptosis is a form of death that the cell itself initiates, regulates, and executes using an elaborate arsenal of cellular and molecular machinery. For this reason, the term apoptosis is often used interchangeably with the term "programmed cell death," or PCD (although technically, apoptosis is but one particular form of programmed cell death). There is some disagreement on the origins of the word. The word apoptosis has ancient Greek origins, referring to the falling of leaves, or possibly "dropping of scabs" or "falling off of bones." There is even less agreement on its proper pronunciation, and even specialists in the field seem to use every possible way to say the word. "A-pop-TOE-sis" and "AP-oh-TOE-sis" are both common.

Why Cells Commit Suicide

Why do cells commit apoptosis? There seem to be two major reasons. First, apoptosis is one means by which a developing organism shapes its tissues and organs. For instance, a human fetus has webbed hands and feet early on its development. Later, apoptosis removes skin cells, revealing individual fingers and toes. A fetus's eyelids form an opening by the process of apoptosis. During metamorphosis, tadpoles lose their tails through apoptosis. In young children, apoptosis is involved in the processes that literally shape the connections between brain cells, and in mature females, apoptosis of cells in the uterus causes the uterine lining to slough off at each menstrual cycle.

Cells may also commit suicide in times of distress, for the good of the organism as a whole. For example, in the case of a viral infection, certain cells of the immune system, called cytotoxic T lymphocytes, bind to infected cells and trigger them to undergo apoptosis. Also, cells that have suffered damage to their DNA, which can make them prone to becoming cancerous, are induced to commit apoptosis.

The Regulatory Mechanism

The cellular mechanisms that regulate and cause apoptosis were first elucidated by genetic studies of the roundworm, Caenorhabditis elegans. Normally, in the development of a C. elegansuncontrolled cell proliferation, can result either from too much cell division or not enough apoptosis. Because of this important finding, apoptosis has become the subject of intense medical research, and molecules that regulate apoptosis are being studied as potential targets for anti-cancer drug therapies. worm, one out of every eight body cells produced is eliminated by programmed cell death. By studying mutants in which either too many or too few cells died, worm geneticists identified many of the proteins that control apoptosis. Subsequently, the critical medical relevance of apoptosis became clear when biologists discovered that mammals contain many of the same genes that control apoptosis in worms. More strikingly, they found that many of these genes were mutated in tumors from cancer patients. Other genes often found to be mutated in cancers are those which regulate the cell cycle, which is the complex set of processes controlling how and when cells divide. These two findings led cancer researchers to recognize that cancer, a disease of

A cell can be triggered to undergo apoptosis either by external signaling molecules, such as so-called "death activator" proteins, or through molecules that reside within the cell and monitor events that might commit the cell to suicide, such as damage to DNA. There are several biochemical pathways that lead to apoptosis. One of the major pathways involves inducing mitochondria to leak one of their proteins, cytochrome c, into the cystosol. This in turn activates a set of related proteases (enzymes that degrade proteins) called caspases. Ultimately, the caspases degrade proteins in the cell and activate enzymes that degrade other cell constituents, such as the DNA. Cells undergoing apoptosis exhibit characteristic morphological and biochemical traits, which can be recognized by microscopic examination or biochemical assays. Apoptosis can occur in as little as twenty minutes, after which the cell "corpse" typically becomes engulfed and completely degraded by neighboring phagocytic cells that are present in the tissue and attracted to the apoptotic cell.

Bibliography

Lodish, Harvey, et al. Molecular Cell Biology, 4th ed. New York: W. H. Freeman, 2000.

Nature 407, no. 12 (Oct., 2000). (Issue devoted to review articles on apoptosis).

Internet Resource

The WWW Virtual Library of Cell Biology. "Apoptosis." http://vlib.org/Science/Cell_Biology/apoptosis.shtml.

�??Paul J. Muhlrad

exons

2008-04-25T15:42:00.001+05:30

Sci-Tech Encyclopedia: Exon

In split genes, a portion that is included in the ribonucleic acid (RNA) transcript of a gene and survives processing of the RNA in the cell nucleus to become part of a spliced messenger RNA (mRNA) or structural RNA in the cell cytoplasm. Split genes are those in which regions that are represented in mature mRNAs or structural RNAs (exons) are separated by regions that are transcribed along with exons in the primary RNA products of genes, but are removed from within the primary RNA molecule during RNA processing steps (introns). See also Intron; Ribonucleic acid (RNA).

Exons comprise three distinct regions of a protein-coding gene. The first is a portion that is not translated into protein, but contains the signal for the beginning of RNA synthesis, and sequences that direct the mRNA to ribosomes for protein synthesis. The second is a set of exons containing information that is translated into the amino acid sequence of a protein. The third region of a gene that becomes part of an mRNA is an untranslated end portion that contains signals for transcription termination and for the addition of a polyadenylate tract at the end of a transcript.

The mechanism by which the exons are joined in RNA copies of genes is called RNA splicing, and it is part of the maturation of mRNAs and some transfer and ribosomal RNAs (tRNAs and rRNAs) from primary transcripts of genes. Three different RNA splicing processes have been identified. One involves mRNA precursors in nuclei, and specific sequences at exon-intron junctions that are recognized by certain nuclear ribonucleoprotein particles that facilitate the cleavage and ligation of RNA. Another applies to nuclear precursors of tRNA, where splice sites are determined by structural features of the folded RNA molecules. The third form of splicing was discovered in studies of protozoan rRNA synthesis, and has also been shown to be a part of the maturation of both rRNA yeast mitochondria; it is an autocatalytic process that requires neither an enzyme nor added energy such as from adenosine triphosphate. See also Gene; Genetic code; Protein; Ribosomes. and mRNA in

introns

2008-04-25T14:56:00.001+05:30

Sci-Tech Encyclopedia: Intron

In split genes, a portion that is included in ribonucleic acid (RNA) transcripts but is removed from within a transcript during RNA processing and is rapidly degraded. Split genes are those in which portions appearing in messenger RNAs (mRNAs) or in structural RNAs, termed exons, are not contiguous in a gene but are separated by lengths of deoxyribonucleic acid (DNA) encoding parts of transcripts that do not survive the maturation of RNA (introns). Most genes in eukaryotes, and a few in prokaryotes, are split. These include not just a large number of different protein-coding genes but also genes encoding transfer RNAs (tRNAs) in such diverse eukaryotes as yeast and frogs, and genes encoding structural RNAs of ribosomes in some protozoa. Introns are also found in mitochondrial genes of lower eukaryotes and in some chloroplast genes. See also Exon.

The number of introns in a gene varies greatly, from 1 in the case of structural RNA genes to more than 50 in collagen. The lengths, locations, and compositions of introns also vary greatly among genes. However, in general, sizes and locations�??but not DNA sequence�??are comparable in homologous genes in different organisms. The implication is that introns became established in genes early in the evolution of eukaryotes, and while their nucleotide sequence is not very important, their existence, positions, and sizes are significant.

Speculation on the roles and the evolution of introns is mostly based on correlations that have been seen between domains of protein structure and the exons of genes that are defined by intervening introns. For example, the enzyme alcohol dehydrogenase (ADH) has two domains, one portion of the protein that binds alcohol, and another that binds the enzyme cofactor adenine dinucleotide (NAD). The ADH gene has an intron that cleanly separates the nucleotide sequences which encode each domain, and gene-sequence arrangements such as this are not uncommon. It has been suggested that introns became established in the genes of eukaryotes (and to a limited extent in bacteria) because they facilitate a genetic shuffling or rearrangement of portions of genes which encode various units of function, thus creating new genes with new combinations of properties. The introns allow genetic recombination to occur between the coding units rather than within them, thus providing a means of genetic evolution via wholesale reassortments of functional subunits or building blocks, rather than by fortuitousSee also Gene; Genetic code; Recombination (genetics). nicotinamide recombinations of actual protein-coding DNA sequences.

transgenic plants

2008-04-17T15:24:00.000+05:30

Transgenic plants possess a gene or genes that have been transferred from a different species. Although DNA of another species can be integrated in a plant genome by natural processes, the term "transgenic plants" refers to plants created in a laboratory using recombinant DNA technology. The aim is to design plants with specific characteristics by artificial insertion of genes from other species or sometimes entirely different kingdoms. See also Genetics, List of genetic engineering topics.

Varieties containing genes of two distinct plant species are frequently created by classical breeders who deliberately force hybridization between distinct plant species when carrying out interspecific or intergeneric wide crosses with the intention of developing disease resistant crop varieties. Classical plant breeders use a number of in vitro techniques such as protoplast fusion, embryo rescue or mutagenisis to generate diversity and produce plants that would not exist in nature (see also Plant breeding, Heterosis, New Rice for Africa).

Such traditional techniques (used since about 1930 on) have never been controversial, or been given wide publicity except among professional biologists, and have allowed crop breeders to develop varieties of basic food crop, wheat in particular, which resist devastating plant diseases such as rusts. Hope is one such wheat variety bred by E. S. McFadden with a gene from a wild grass. Hope saved American wheat growers from devastating stem rust outbreaks in the 1930s.

Methods used in traditional breeding that generate plants with DNA from two species by non-recombinant methods are widely familiar to professional plant scientists, and serve important roles in securing a sustainable future for agriculture by protecting crops from pests and helping land and water to be used more efficiently. (see also Food security, International Fund for Agricultural Development, International development)

Natural movements of genes between species.

Natural movement of genes between species, often called horizontal gene transfer or lateral gene transfer, can occur because of gene transfer mediated by natural processes.

This natural gene movement between species has been widely detected during genetic investigation of various natural mobile genetic elements, such as transposons, and retrotransposons that naturally translocate to new sites in a genome, and often move to new species over an evolutionary time scale. There are many types of natural mobile DNAs, and they have been detected abundantly in food crops such as rice ^[1].

These various mobile genes play a major role in dynamic changes to chromosomes during evolution [2], [3], and have often been given whimsical names, such as Mariner, Hobo, Trans-Siberian Express (Transib), Osmar, Helitron, Sleeping Princess, MITE and MULE, to emphasize their mobile and transient behavior.

Genetically mobile DNA contitututes a major fraction of the DNA of many plants, and the natural dynamic changes to crop plant chromosomes caused by this natural transgenic DNA mimics many of the features of plant genetic engineering currently pursued in the laboratory, such as using transposons as a genetic tool, and molecular cloning. See also transposon, retrotransposon, integron, provirus, endogenous retrovirus, heterosis, Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize.

There is new scientific literature about natural transgenic events in plants, through movement of natural mobile DNAs called MULEs between rice and Setaria millet [4].

It is becoming clear that natural rearrangements of DNA and horizontal gene transfer play a pervasive role in natural evolution. Importantly many, if not most, flowering plants evolved by transgenesis - that is, the creation of natural interspecies hybrids in which chromosome sets from different plant species were added together. There is also the long and rich history of interspecies cross-breeding with traditional methods.

Deliberate creation of transgenic plants during breeding

Production of transgenic plants in wide-crosses by plant breeders has been a vital aspect of conventional plant breeding for about a century. Without it, security of our food supply against losses caused by crop pests such as rusts and mildews would be severely compromised. The first historically recorded interpecies transgenic cereal hybrid was actually between wheat and rye (Wilson, 1876).

In the 20^th century, the introduction of alien probing into common foods was repeatedly achieved by traditional crop breeders by artificially overcoming fertility barriers. Novel genetic rearrangements of plant chromosomes, such as insertion of large blocks of rye (Secale) genes into wheat chromosomes ('translocations'), has also been exploited widely for many decades [5].

By the late 1930s with the introduction of colchicine, perennial grasses were being hybridized with wheat with the aim of transferring aids resistance and perenniality into annual crops, and large-scale practical use of hybrids was well established, leading on to development of Triticosecale and other new transgenic cereal crops. In 1985 Plant Genetic Systems (Ghent, Belgium), founded by Marc Van Montagu and Jeff Schell, was the first company to develop genetically engineered (tobacco) plants with insect tolerance by expressing genes encoding for insecticidal proteins from Bacillus thuringiensis (Bt). ^[2]

Transgenic resistance traits in bread wheat varieties

Important transgenic pathogen and parasite resistance traits in current bread wheat varieties (gene, eg "Lr9" followed by the source species) are:

Disease resistance

Leaf rust
- Lr9 (from Aegilops umbellulata)
- Lr18 Triticum timopheevi
- Lr19 Thinopyrum
- Lr23 T. turgidum
- Lr24 Ag. elongatum
- Lr25 Secale cereale
- Lr29 Ag. elongatum
- Lr32 T. tauschii
Stem rust
- Sr2 T. turgidum ("Hope" ) McFadden, E. S. (1930) J. Am. Soc. Agron. 22, 1020-1031 .
- Sr22 Triticum monococcum
- Sr36 Triticum timopheevii
Stripe rust
- Yr15 Triticum dicoccoides
Powdery mildew
- Pm12 Aegilops speltoides
- Pm21 Haynaldia villosa
- Pm25 T. monococcum
Wheat streak mosaic virus
- Wsm1 Ag. elongatum

Pest resistance

Hessian fly
- H21 S. cereale H23,
- H24 T. tauschii
- H27 Aegilops ventricosa
Cereal cyst nematode
- Cre3 (Ccn-D1) T. tauschii
Lepidoptera
- Bt Bacillus thuringiensis

Genetically engineered plants

The intentional creation of transgenic plants by laboratory based recombinant DNA methods is more recent (from the mid-80s on) and has been a controversial development opposed vigorously by many NGOs, and several governments, particularly within the European Community. These transgenic recombinant plants (= biotech crops, modern transgenics) are transforming agriculture in those regions that have allowed farmers to adopt them, and the area sown to these crops has continued to grow globally in every years since their first introduction in 1996.

Transgenic recombinant plants are generated in a laboratory by adding one or more genes to a plant's genome,and the techniques frequently called transformation. Transformation is usually achieved using gold particle bombardment or a soil bacterium (Agrobacterium tumefaciens) carrying an engineered plasmid vector, or carrier of selected extra genes.

Transgenic recombinant plants are identified as a class of genetically modified organism(GMO); usually only transgenic plants created by direct DNA manipulation are given much attention in public discussions.

Transgenic plants have been deliberately developed for a variety of reasons: longer shelf life, disease resistance, herbicide resistance, pest resistance, non-biological stress resistances, such as to drought or nitrogen starvation, and nutritional improvement (see Golden rice). The first modern recombinant crop approved for sale in the US, in 1994, was the FlavrSavr tomato, which was intended to have a longer shelf life. The first conventional transgenic cereal created by scientific breeders was actually a hybrid between wheat and rye in 1876 (Wilson, 1876). The first transgenic cereal may have been wheat, which itself is a natural transgenic plant derived from at least three different parenteral species.

Commercial factors, especially high regulatory and research costs, have so far restricted modern transgenic crop varieties to major traded commodity crops, but recently R&D projects to enhance crops that are locally important in developing counties are being pursued, such as insect protected cow-pea for Africa. [6], and insect protected Brinjal eggplant for India [7].

Regulation of transgenic plants

In the United States the Coordinated Framework for Regulation of Biotechnology governs the regulation of transgenic organisms, including plants. The three agencies involved are:

USDA Animal and Plant Health Inspection Service - who state that

The Biotechnology Regulatory Services (BRS) program of the U.S. Department of Agriculture�??s (USDA) Animal and Plant Health Inspection Service (APHIS) is responsible for regulating the introduction (importation, interstate movement, and field release) of genetically engineered (GE) organisms that may pose a plant pest risk. BRS exercises this authority through APHIS regulations in Title 7, Code of Federal Regulations, Part 340 under the Plant Protection Act of 2000. APHIS protects agriculture and the environment by ensuring that biotechnology is developed and used in a safe manner. Through a strong regulatory framework, BRS ensures the safe and confined introduction of new GE plants with significant safeguards to prevent the accidental release of any GE material. APHIS has regulated the biotechnology industry since 1987 and has authorized more than 10,000 field tests of GE organisms. In order to emphasize the importance of the program, APHIS established BRS in August 2002 by combining units within the agency that dealt with the regulation of biotechnology. Biotechnology, Federal Regulation, and the U.S. Department of Agriculture, February 2006, USDA-APHIS Fact Sheet

EPA - evaluates potential environmental impacts, especially for genes which encode for pesticide production
DHHS, Food and Drug Administration (FDA) - evaluates human health risk if the plant is intended for human consumption

Ecological risks

The potential impact on nearby ecosystems is one of the greatest concerns associated with transgenic plants.

Transgenes have the potential for significant ecological impact if the plants can increase in frequency and persist in natural populations. These concerns are similar to those surrounding conventionally bred plant breeds. Several risk factors should be considered:

Is the transgenic plant capable of growing outside a cultivated area?
Can the transgenic plant pass its genes to a local wild species, and are the offspring also fertile?
Does the introduction of the transgene confer a selective advantage to the plant or to hybrids in the wild?

Many domesticated plants can mate and hybridise with wild relatives when they are grown in proximity, and whatever genes the cultivated plant had can then be passed to the hybrid. This applies equally to transgenic plants and conventionally bred plants, as in either case there are advantageous genes that may have negative consequences to an ecosystem upon release. This is normally not a significant concern, despite fears over 'mutant superweeds' overgrowing local wildlife: although hybrid plants are far from uncommon, in most cases these hybrids are not fertile due to polyploidy, and will not multiply or persist long after the original domestic plant is removed from the environment. However, this does not negate the possibility of a negative impact.

In some cases, the pollen from a domestic plant may travel many miles on the wind before fertilising another plant. This can make it difficult to assess the potential harm of crossbreeding; many of the relevant hybrids are far away from the test site. Among the solutions under study for this concern are systems designed to prevent transfer of transgenes, such as Terminator Technology, and the genetic transformation of the chloroplast only, so that only the seed of the transgenic plant would bear the transgene. With regard to the former, there is some controversy that the technologies may be inequitable and might force dependence upon producers for valid seed in the case of poor farmers, whereas the latter has no such concern but has technical constraints that still need to be overcome. Solutions are being developed by EU funded research programmes such as Co-Extra and Transcontainer.

There are at least three possible avenues of hybridization leading to escape of a transgene:

Hybridization with non-transgenic crop plants of the same species and variety.
Hybridization with wild plants of the same species.
Hybridization with wild plants of closely related species, usually of the same genus.

However, there are a number of factors which must be present for hybrids to be created.

The transgenic plants must be close enough to the wild species for the pollen to reach the wild plants.
The wild and transgenic plants must flower at the same time.
The wild and transgenic plants must be genetically compatible.

In order to persist, these hybrid offspring:

Must be viable, and fertile.
Must carry the transgene.

Studies suggest that a possible escape route for transgenic plants will be through hybridization with wild plants of related species.

It is known that some crop plants have been found to hybridize with wild counterparts.
It is understood, as a basic part of population genetics, that the spread of a transgene in a wild population will be directly related to the fitness effects of the gene in addition to the rate of influx of the gene to the population. Advantageous genes will spread rapidly, neutral genes will spread with genetic drift, and disadvantageous genes will only spread if there is a constant influx.
The ecological effects of transgenes are not known, but it is generally accepted that only genes which improve fitness in relation to abiotic factors would give hybrid plants sufficient advantages to become weedy or invasive. Abiotic factors are parts of the ecosystem which are not alive, such as climate, salt and mineral content, and temperature. Genes improving fitness in relation to biotic factors could disturb the (sometimes fragile) balance of an ecosystem. For instance, a wild plant receiving a pest resistance gene from a transgenic plant might become resistant to one of its natural pests, say, a beetle. This could allow the plant to increase in frequency, while at the same time animals higher up in the food chain, which are at least partly dependent on that beetle as food source, might decrease in abundance. However, the exact consequences of a transgene with a selective advantage in the natural environment are almost impossible to predict reliably.

It is also important to refer to the demanding actions that government of developing countries had been building up among the last decades.

Agricultural impact of transgenic plants

Outcrossing of transgenic plants not only poses potential environmental risks, it may also trouble farmers and food producers. Many countries have different legislations for transgenic and conventional plants as well as the derived food and feed, and consumers demand the freedom of choice to buy GM-derived or conventional products. Therefore, farmers and producers must separate both production chains. This requires coexistence measures on the field level as well as traceability measures throughout the whole food and feed processing chain. Research projects such as Co-Extra, SIGMEA and Transcontainer investigate how farmers can avoid outcrossing and mixing of transgenic and non-transgenic crops, and how processors can ensure and verify the separation of both production chains.

dna fingerprinting

2008-04-17T15:21:00.001+05:30

DNA profiling is a molecular testing method used to uniquely identify people and other organisms. In many ways, it is similar to blood typing and fingerprinting, and it is sometimes called "DNA fingerprinting." Because every organism's DNA is unique, DNA can be examined to identify people who might be related to each other, to compare suspected criminals to DNA left at the scene of a crime, or even to identify certain strains of disease-causing bacteria.

Blood Typing and the Abo Groupings

Before the development of the molecular biology tools that make DNA testing possible, investigators identified people through blood typing. This method hails from 1900, when Karl Landsteiner first discovered that people inherited different blood types. Several decades later, researchers determined that the basis for those blood types was a set of proteins on the surface of red blood cells.

The main proteins on the surface of red blood cells used in blood typing come in two varieties: A and B. Every person inherits from their parents either the genes for the A protein, the B protein, both, or neither. Someone who inherits the A gene from one parent and neither gene from the other parent has blood type A. If a person inherits both genes, they are AB. A person who inherits neither is type O. Another protein group found on red blood cells is referred to collectively as the Rh factor. People either have the Rh factor or they do not, regardless of which of the A and B genes they inherited. To type a person's blood, antibodies against these various proteins (A, B, and Rh) are mixed with a blood sample. If the proteins are present, the blood cells will stick together and the sample will get cloudy.

Blood typing can be used to exclude the possibility that a blood sample came from a particular person, if the person's type does not match that of the sample. However, it cannot be used to claim that any particular person is the source of the sample, because there are so few blood types, and they are shared by so many people. About 45 percent of people in the United States are type O, and another 40 percent are type A. If four people were physically present at the scene of a murder, and the candlestick found nearby had type O blood spilled on it, chances are good that two of those individuals could be found guilty of the crime, based solely on the blood typing evidence. Most court cases, however, rely on more evidence than just blood or DNA typing, such as whose fingerprints are also found on the candlestick (see Statistics and the Prosecutor's Fallacy, below).

Dna Polymorphism Offers High Resolution

DNA is the molecule that contains all the genetic information of an individual. One person's DNA is made up of about three billion building blocks known as nucleotides or bases. Every organism in the world has a unique DNA sequence except for identical twins. Although identical twins accrue changes as they develop, they generally do not accumulate enough genetic differences for DNA typing to be useful. Portions of the DNA, called genes, encode proteins within the sequence of bases. Genes are separated by long stretches of noncoding DNA. Because these sequences do not have to code for functional proteins, they are free to accumulate more differences over time, and thus provide more variation than genes. Thus, they are more useful than gene sequences in distinguishing individuals.

Polymorphisms are differences between individuals that occur in DNA sequences which occupy the same locus in the chromosome. An individual will have only one sequence at a particular polymorphic locus in each chromosome, but if the population bears several to dozens of different possible sequences at the site in question, then the locus is considered "highly variable" within the population. DNA profiling determines which polymorphisms a person has at a small number of these highly variable loci. Because of this, DNA profiling can provide high resolution in distinguishing different individuals. The chances of one person having the same DNA profile as another are typically much less than the chances of winning a lottery.

Str Analysis

The technology of DNA profiling has advanced from its beginnings in the 1980s. Today, DNA profiling primarily examines "short tandem repeats," or STRs. STRs are repetitive DNA elements between two and six bases long that are repeated in tandem, like GATAGATAGATAGATA. These repeat sequences often exist in a chromosomal region called heterochromatin, a largely unused portion of DNA found in each chromosome.

Different STR sequences (also called genetic markers) occur at different loci. While their positions are fixed, the number of repeated units varies within the population, from four to forty depending on the STR. Therefore, one genetic marker may have between four and forty different variations, and each variation is referred to as an allele of that marker. Each person has at most two alleles of each marker, one inherited from each parent. The two alleles for a particular marker may be identical, if both parents had the same form.

The United States Federal Bureau of Investigation has designated thirteen of these sequences to use with STR analysis. These thirteen markers are all four-base repeats, and were chosen because multiple alleles of each exist throughout the population. The FBI system, called CODIS (Combined DNA Indexing System), has become the standard DNA profiling system in use today.

STR analysis begins with sample collection. Because of the often small samples involved and the legal weight that will be given to them, it is vital that the sample not be contaminated by other DNA. This may occur for instance if skin cells from the person collecting the sample are mixed with skin cells under the fingernails of a victim. Once the sample is collected, it must be kept secure at all times, to prevent any possibility of tampering.

In the laboratory, the DNA is isolated and purified, and then multiple copies of it are made using the polymerase chain reaction (PCR). Technicians can specify which DNA sequences to multiply, so that only the thirteen core STR sequences will be amplified (multiple copies produced), leaving the rest of the billions of irrelevant bases alone.

In order to specify which DNA to amplify, "primers" are used. The primers are DNA sequences that recognize a nonrepeated sequence in the genetic markers, and which are used by the DNA polymerase that does the actual copying. After the DNA has been copied, the new DNA molecules are separated by size, by gel electrophoresis. A fluorescent molecule previously attached to each primer will send a light signal to the machine that measures the length of the molecule, or allele.

Vntr Analysis

An early form of DNA profiling, rarely used today, is based on VNTRs, or "variable number of tandem repeats." VNTRs requires extensive sample processing: The DNA is chopped up with restriction enzymes, separated by size, and probes are applied to the fragmented DNA to view only the relevant DNA pieces. In the DNA of two different individuals, different spacing between two cut sites for the restriction enzymes gives a unique pattern of DNA size fragments, called "restriction fragment length polymorphisms," or RFLPs.

Making a Match

To understand how DNA profiling is used to identify a person, imagine a sample of blood collected at a crime scene that doesn't match the victim's blood, and is presumably from the unknown perpetrator. DNA from the blood is isolated and its set of STRs are analyzed. The results will be a list of the alleles found at each of the markers (for example, VWA-12, 13; TH01-6, 7, and so on), where the initial symbol is the abbreviation for the markers and the last two are the numbers of the alleles found in the sample for that marker. The full set of thirteen markers may or may not be analyzed in each case. When a suspect is identified, his or her DNA can be analyzed for these same markers. If the set of alleles are different, the investigators can be sure that the two DNAs came from different sources, and the suspect is not the source of the blood. Since the introduction of DNA profiling, an absence of matching DNA has been used to free dozens of wrongly convicted prisoners.

If the samples do match, the question becomes whether the blood is actually from the suspect, or from someone else with the same set of alleles. As with blood typing, this is a matter of statistics, and depends on how frequently each allele occurs in the population. This information has been tabulated and is kept on file in the FBI CODIS database. If two samples share a very rare allele, that increases the likelihood they came from the same source.

Matching multiple alleles increases the certainty they came from the same source. Since the thirteen STRs are inherited independently of each other, the likelihood that one person's DNA will include specific alleles of all thirteen STR sites is the product of the individual allele frequencies. For example, if each allele a person carries occurs in 25 percent of the population, then the probability that all thirteen alleles will occur in one individual is (0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25 �? 0.25) or 1 in more than 67 million. This analysis can discriminate between millions of people, far better than is possible using the four blood groups. Since many alleles are even rarer than 25 percent, their presence in both samples further increases the probability that they came from the same source.

Statistics and the Prosecutor's Fallacy

Despite the persuasiveness of such figures, it is quite possible to misuse DNA evidence to incorrectly argue that an innocent suspect must be the perpetrator of the crime, or that a guilty suspect should go free. Both defense and prosecution attorneys can�??accidentially or otherwise�??misinterpret data to make a highly likely event seem improbable, or a highly unlikely event seem probable. Jurors can be confused because DNA testing reveals the probability that an innocent person's DNA profile matches the sample at the scene of the crime. Jurors must decide, however, what the probability is that a person is innocent, if his DNA matches that sample. The prosecutor's fallacy occurs when investigators focus on the existence of the match, rather than the possibility that the match could be a coincidence.

Let's assume the DNA profile found at the crime scene�??and the matching DNA of the suspect�??is expected to occur once in every million people. The correct statement of probability arising from these facts is, "If the suspect is innocent, there is a one-in-one-million chance of obtaining this DNA match." The fallacy is to reverse these clauses, and state, "If the DNA matches, there is a one in one million chance that the suspect is innocent." To understand the logical fallacy, imagine the statement, "If it's Tuesday, it must be a school day." The reverse is not true�??there are other school days besides Tuesday.

Similarly, there are other ways of misusing statistics in DNA profiling. Let's assume the suspect in the above case is actually guilty. If the suspect hails from a city with a population of ten million, there are ten people in the city whose DNA matches the DNA at the crime scene. Therefore, his defense lawyers could argue there is a 90 percent chance that the suspect is innocent, because he is 1 out of 10 individuals with that same DNA profile. If the defense can convince the jury to ignore other incriminating evidence, such as the suspect's bloody glove left behind at the scene, then the attorney may introduce reasonable doubt. Only by considering DNA typing within the context of other evidence can the probability of a DNA match improve the integrity of the justice system.

Dna Profiling Comes of Age

Although DNA profiling was viewed with some skepticism when it first made its way into the courts, DNA typing is now used routinely, in and out of the courthouse. It is commonly used in rape and murder cases, where the assailant generally leaves behind some personal evidence such as hair, blood, or semen. In paternity tests, the child's DNA profile will be a combination of the profiles of both parents. DNA profiling has also been used to identify victims in disasters where large numbers of people died at once, such as in airplane crashes, large fires, or military conflicts.

DNA testing can also used in organisms other than humans. For instance, it has been used to type cattle in a cattle-stealing case. It can also be used to identify pathogenic strains of bacteria to track the outbreak of disease epidemics.

Bibliography

Bloom, Mark V., Greg A. Freyer, and David A. Micklos. Laboratory DNA Science: An Introduction to Recombinant DNA Techniques and Methods of Genome Analysis. Menlo Park, CA: Addison-Wesley, 1996.

Evert, Ian W., and Bruce S. Weir. Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists. Sunderland, MA: Sinauer Associates, 1998.

Steward, Ian. "The Interrogator's Fallacy." Scientific American (September 1996): 172-175.

Internet Resources

"13 CODIS Core STR Loci with Chromosomal Positions." National Institute of Standards and Technology. http://www.cstl.nist.gov/biotech/strbase/images/codis.jpg.

The Biology Project. The University of Arizona. http://www.biology.arizona.edu/human_bio/activities/blackett2/gifs/sample2.gif.

FBI Core STR Markers.http://www.cstl.nist.gov/biotech/strbase/fbicore.htm.

The Innocence Project.http://www.innocenceproject.org/.

�??Mary Beckman

genome

2008-04-17T15:18:00.001+05:30

Genetics Encyclopedia: Genome

A genome is the complete collection of hereditary information for an individual organism. In cellular life forms, the hereditary information exists as DNA. There are two fundamentally distinct types of cells in the living world, prokaryotic and eukaryotic, and the organization of genomes differs in these two types of cells.

Prokaryotes comprise the bacteria and archaea. The latter were originally designated "extremophiles" because they favor such extreme environments as high acidity, salinity, or temperature. Prokaryotic cells tend to be very small, have few or no cytoplasmic organelles, and have the cellular DNA arranged in a "nucleoid region" that is not separated from the remainder of the cell by any membrane. Eukaryotes exist as unicellular or multicellular organisms. Among the unicellular eukaryotes are the protozoa, some types of algae, and a few forms of fungi, while the multicellular organisms include animals, plants, and most fungi.

Eukaryotic cells are larger than prokaryotic cells, have a complex array of cytoplasmic structures, and have a prominent nucleus that communicates with components in the cytoplasm through an elaborate nuclear envelope. The hereditary information occurs principally in the nucleus of eukaryotic cells; in addition, minuscule (but essential) amounts of hereditary information occur in some cytoplasmic organelles (specifically, in chloroplasts for plants and algae, and in mitochondria for all eukaryotic groups).

Eukaryotic cells pass through a "cycle," progressing from a newly formed cell to a cell that is dividing to produce the next generation of progeny cells. Prior to division, the cell is in an "interphase"; during division, the cell is in a "division phase." During interphase, the nuclear DNA is organized in a dispersed network of chromatin, which is a complex consisting of nucleic acid and basic proteins. Immediately prior to and during division, the chromatin condenses to a series of discrete, compact structures called chromosomes. Thus, the physical organization of the genome varies from inter-phase to division phase. Finally, viruses (which are noncellular, parasitic "life forms") have genomes of double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA.

Eukaryotes

In sexually reproducing eukaryotes, progeny organisms receive a portion of their genetic information from each parent, receiving half the information from each. These parental contributions are designated haploid complements. The haploid complement can be represented as a "C value," which expresses the haploid complement as an amount of DNA measured in base pairs. Alternatively, the haploid complement can be expressed as the number of chromosomes contributed by each parent: This number of chromosomes is characteristic of each species. Finally, the haploid complement can be expressed as the number of genes on the haploid set of chromosomes.

Chromosome Number

Each species has a characteristic number of chromosomes. For species with genetically determined sexes, the haploid set is composed of autosomes plus a sex chromosome. Homo sapiens, for example, have 22 autosomes plus an X chromosome or Y chromosome. The haploid DNA content of chimpanzees is nearly identical, but is organized into 23 autosomes plus a sex chromosome.

The record for minimum number of chromosomes belongs to a sub-species of the ant, Myrmecia pilosula. The females have a single pair of chromosomes, while males have only a single chromosome. Like some other members of the insect class, these ants reproduce by a process called haplodiploidy, in which diploid fertilized eggs develop into females, while haploid unfertilized eggs develop into males.

The record for maximum number of chromosomes is found in the plant kingdom, due to a condition known as polyploidy. In polyploidy, many extra sets of chromosomes beyond the normal diploid number may accumulate over time. Cultivars of wheat exist with diploid numbers of chromosomes equaling 14, 28, or 42 (multiples of the haploid number, which is 7). Polyploids exist for many cultivated plants, including potatoes, strawberries, and cotton, as well as in wild plants such as dandelions. Polyploidy has led to striking numbers, and the known record is held by the fern Ophioglossum reticulatum, which has approximately 630 pairs.

Genome Size or C Value

The C value is the amount of DNA in a haploid complement. Currently, the amount is reported as the total number of base pairs. Generally, more complex organisms have more DNA. For example, the haploid complement of Homo sapiens DNA contains between 3.12 and 3.2 gigabases (the prefix "giga" denotes billions), while the haploid complement of yeast (Saccharomyces cerevisiae) DNA contains 12,057,500 base pairs.

Unexpected genomic sizes occur, however, in a condition called the C value paradox. Two closely related species can have widely divergent amounts of DNA. For example, Paramecium caudatum has a C value of 8,600,000 kilobases (where the prefix "kilo" denotes thousands) while its near relative P. aurelia has a C value of just 190,000 kilobases. Another paradoxical circumstance occurs when a simpler organism has a C value higher than a more complex organism. For example, Amphiuma means (a newt) and Amoeba dubia (an amoeba) have, respectively, C values that are 26 and 209 times the C value of humans.

Number of Nuclear Genes, "Gene Density," and Intergenic Sequences

An important trend in genome evolution has been the accumulation, both within the genes (intragenic) and between genes (intergenic), of DNA that does not code for any gene products. Homo sapiens have between 31,000 and 70,000 genes; mice have 24,780; Caenorhabditis elegans (a roundworm) has more than 19,099; fruit flies have 13,601; and yeast approximately 6,000. A ratio of gene number to C value indicates that lower organisms have both smaller genes and lower numbers of nongene base pairs between adjacent genes. Higher eukaryotes have a larger number of intragenic inserts (introns), greater intergenic distances, and more abundant repeated sequences.

In higher eukaryotes, only a small portion of the genome is organized into genes. For example, in humans less than 2 percent of the genome specifies protein products. Another portion (about 20 percent in humans) is present as gene fragments, pseudogenes (sequences that resemble genes but are not expressed as proteins), and surrounding stretches of nucleotides. The vast majority of nucleotides (approximately 75 percent in humans) constitute extragenic sequences. Two forms of extragenic sequences are prominent: unique sequences and repetitive sequences.

For repetitive sequences, two types of organization occur: short tandem repeats (called satellite sequences) and widely distributed, interspersed repeats. Satellites are recurrent short sequences present in essential chromosomal structures such as centromeres and telomeres. Interspersed repeats are generated from transposons, which are nucleotide sequences that can replicate themselves and become distributed throughout the genome. An example of interspersed repeats that occurs in humans is a sequence of a few hundred nucleotides called Alu, which occurs approximately a million times. In higher plants, satellites and interspersed sequences constitute the bulk of the genome.

Ploidy

Ploidy reflects the reproductive mechanisms of an organism. Animals commonly have both a maternal and a paternal parent. Through meiosis, the former forms a haploid gamete called an ovum (or egg); the latter forms a haploid gamete called a sperm. During fertilization, the egg and sperm unite to form a diploid zygote that matures to an adult organism. Thus, the genome of adult animals is diploid, while the genome of their gametes is haploid.

Plants exhibit an alternation of generations; sporophytes (the mature, visible plant) are diploid; through meiosis, they produce spores that germinate into gametophytes; the gametophytes are haploid and produce gametes that fuse to reestablish the diploid state. Fungi also exhibit an alternation of generations. They commonly exist as multinucleate tubes of cytoplasm called hyphae. The individual nuclei are most often haploid (though may be diploid in the lower fungi).

Hyphae of different members of a fungal species sometimes fuse; in this circumstance (called heterokaryosis) the genome becomes the sum of the two (dikaryotic) haploid complements. Unicellular protistan organisms, a group that includes protozoans and most algae, exhibit many variations. For example, the ciliates (such as paramecia) have diploid micronuclei and polyploid macronuclei; the former are the basis of inheritance; the latter establish the genetic character of an existing organism.

Mitochondrial and Chloroplast Genomes

Two cytoplasmic organelles responsible for the production of energy are the mitochondria (present in nearly all eukaryotic cells) and chloroplasts (present only in photosynthetic organisms). Both contain small, circular DNA molecules that constitute the nonnuclear portion of a eukaryotic genome. These organelles are descended from formerly free-living bacteria that took up residence in the first eukaryotes.

The human mitochondrial genome contains 16,569 base pairs specifying 13 protein products and 24 RNA products. In both lower eukaryotes and especially plants, larger mitochondrial genomes are present. In extreme cases, mitochondrial genomes may be several hundred thousand or millions of base pairs. Chloroplast genomes contain between 100 and 200 kilobases. It is thought that each was once larger, but over time their genes have been moved to the nucleus.

Prokaryotes

Prokaryotic genomes are composed of a chromosome plus various accessory elements. The former is most commonly a circular double-stranded DNA molecule but may be a linear molecule in some major groups, such as Streptomyces and Borrelia (the causative agent of Lyme disease). Accessory elements most prominently include plasmids (commonly circular but linear in Actinomycetes and some Proteobacteria) as well as insertion sequence (IS) elements, transposons, and prophages (derived from viruses). Other variations in chromosomal geometry exist: multiple circular chromosomes are found in some organisms; combinations of circular and linear chromosomes occur in others; and, in the extreme (observed in Streptomyces), circular and linear chromosomes can convert between those two topologies.

The smallest bacterial chromosome, with only 580 kilobase pairs (kbp) occurs in Mycoplasma genitalium, and the largest, with 9,200 kbp, occurs in Myxococcus xanthus. Representative sizes cluster between 2,000 and 5,000 kbp (e.g., Escherichia coli MG1655 has 4,649,221 bp). A typical bacterial gene contains approximately a thousand base pairs. M. genitalium has approximately 470 genes, while M. xanthus has more than 10,000, and E. coli has approximately 4,288.

By 2002 the nucleotide sequences of more than seventy-five prokaryotic chromosomes had been mapped. One goal of these sequencing projects is gene annotation: establishing the location, function, and allelic variation for each gene. In E. coli MG1655, for example, the positions of the 4,288 protein-coding genes have been identified; the average distance between genes is 118 base pairs; and the noncoding sequences (some of which may function as regulatory sites) constitute less than 11 percent of the genome. The function of approximately 40 percent of the genes, however, remains unknown. Notably, the chromosomal size and gene content of another isolate of E. coli, the pathogenic H157:O7 strain, are quite different. The H157:O7 chromosome is 20 percent larger, while MG1655 and H157:O7 share 4.1 million base pairs (mbp) in common. H157:O7 has 1.34 mbp that are not found in MG1655 and MG1655 has 0.53 mbp that are not found in H157:O7.

The genomes of closely related prokaryotes often have different organizations. These differences arise from rearrangements (such as inversions) between repeated elements, IS elements, and transposons and from the "horizontal transfer" of nucleotide sequences between cells. The latter phenomenon is mediated most commonly by conjugative plasmids, which are nonessential, autonomous accessory genetic elements that can acquire genes (such as antibiotic resistance genes) and then move them from a donor organism to a recipient. The dynamic character of genomic organization in prokaryotes is often designated as "genomic plasticity."

A series of repeated elements exist in the chromosomes of prokaryotes. In some instances the repeats are redundant copies of essential, long nucleotide sequences, as is seen in ribosomal RNA loci. Other repeats are small and have known functions (as in the Chi sequences in E. coli that facilitate genetic crossing over) or unknown functions (as in the REP [repeated extragenic palindromic] sequences in E. coli).

Viruses

Viral genomes are composed of single-stranded or double-stranded DNA or RNA. Single-stranded RNAs are either positive (capable of being immediately translated into protein) or negative. Double-stranded RNA genomes are most often segmented, with each segment being a single gene, while the other genomes are single circular or linear molecules. The Retroviridae have single-stranded RNA genomes that are converted by an enzyme (reverse transcriptase) into double-stranded DNA that becomes incorporated into the genome of the host.

The smallest known virus, containing 5,386 bases, is a member of the Microviridae, which infects bacteria and is designated fX174. The largest viral genomes occur in Poxviridae, which can possess as many as 309 kbp.

Viruses are extraordinarily efficient in using the coding capacity of their genomes. The virus known as fX174 contains ten genes, and the end of one gene commonly overlaps with the beginning of the following gene. In addition, two smaller genes are nested within larger genes (this compaction being achieved by having the two genes expressed in alternate "reading frames"). As a consequence of this efficiency, only 36 bases are not translated into an amino acid sequence. At the opposite extreme, the various pox viruses share more than 100 similar genes and may have an equal number of unique genes.

Bibliography

Brown, T. A. Genomes. New York: Wiley-Liss, 1999.

Casjens, Sherwood. "The Diverse and Dynamic Structure of Bacterial Genomes." Annual Review of Genetics 32 (1998): 339-377.

Gould, Stephen J. "The Ant and the Plant." In Bully for Brontosaurus. New York:

W. W. Norton, 1991.

�??Steven Krawiec

bioinformatics

2008-04-17T15:13:00.001+05:30

Genetics Encyclopedia: Bioinformatics

Bioinformatics is the use of mathematical, statistical and computer methods to analyze biological, biochemical, and biophysical data. Because bioinformatics is a young, rapidly evolving field, however, it also has a number of other credible definitions. It can also be defined as the science and technology of learning, managing, and processing biological information. Bioinformatics is often focused on obtaining biologically oriented data, organizing this information into databases, developing methods to get useful information from such databases, and devising methods to integrate related data from disparate sources. The computer databases and algorithms are developed to speed up and enhance biological research.

Bioinformatics can help answer such questions as whether a newly analyzed gene is similar to any previously known gene, whether a protein's sequence can suggest how the protein functions, and whether the genes turned on in a cancer cell are different from those turned on in a healthy cell.

Databases and Analysis Programs

A good deal of the early work in bioinformatics focused on processing and analyzing gene and protein sequences catalogued in databases such as GenBank, EMBL, and SWISS-PROT. Such databases were developed in academia or by government-sponsored groups and served as repositories where scientists could store and share their sequence data with other researchers. With the start of the Human Genome Project in 1990, efforts in bioinformatics intensified, rising to the challenge of handling the large amounts of DNA sequence data being generated at an unprecedented rate. By the midto late-1990s, much of the efforts in bioinformatics centered around genomic data, generated by the Human Genome Project and by private companies, and around proteomic data.

Early analysis of sequence information focused on looking for similarities between genes and between proteins. Algorithms were developed to help researchers rapidly identify similar gene or protein sequences. Such tools were extremely useful for determining whether a newly sequenced piece of DNA was at all similar to sequences already entered in a database. To determine how multiple sequences align and to view their similarities, multiplealignment programs were developed. Such programs helped scientists compare the sequences of closely related genes or compare the sequence of a particular gene or protein as it appears in several species.

To better understand the functional roles of new nucleotide and amino acid sequences, researchers developed algorithms to look for particular sequence "domains." Domains are regions where a particular sequence of nucleotides or amino acids is indicative of function in the protein. For example, a protein may have a domain that binds to ATP or GTP, two important protein regulators.

In addition, these algorithms can detect sequences that denote a region involved in particular types of post-translational modifications, such as tyrosine phosphorylation. Tools such as prosite, blocks, prints, and Pfam can be used to detect and predict such protein domains in sequence data.

Structure is central to protein function, and another set of tools, including SWISS-MODEL, allows researchers to use gene and protein sequence data to predict a protein's three-dimensional structure. Such tools can help predict how mutations in a gene sequence could alter the three-dimensional structure of the corresponding protein. They accomplish such molecular modeling by comparing a novel sequence to the sequences of genes whose protein structures are known.

The majority of tools were developed as academic freeware distributed on the Internet. In the early-to mid-1990s, commercial companies began to develop their own proprietary algorithms and tools, as well as their own proprietary databases. Those databases were then marketed to pharmaceutical and biotech companies as well as to academic research groups. The most commercially viable and profitable businesses focused on the production and sale of proprietary DNA-and gene-sequence databases in the mid-to late-1990s. These databases primarily contained genetic information that were not in the public domain databases, such as GenBank, and they thus offered potential competitive advantages to the drug discovery groups of large pharmaceutical and biotech companies.

Applications of Bioinformatics to Drug Discovery

The application of bioinformatics to genomics data could be a huge potential boon for the discovery of new drugs. During the 1990s many pharmaceutical companies and biotech companies became convinced that they could speed up their drug-discovery pipelines by taking advantage of the data from the Human Genome Project as well as by funding their own internal genomics programs and by collaborating with third-party genomics companies.

The goal in such practical applications is to use such data as DNA sequence information and gene expression levels to help discover new drug targets. The vast majority of drugs target proteins, but there are a handful of drugs, such as some chemotherapeutic agents, that bind to DNA. In cases where the target is a protein, the drugs themselves are primarily small chemical molecules or, in some cases, small proteins, such as hormones, that bind to a larger protein in the body. Some drugs are therapeutic proteins delivered to the site of the disease.

The extent to which genomics will actually be able to help identify validated drug targets is uncertain. Genomics and bioinformatics are still young areas, and the drug development cycle can take up to ten years. As of 2001 relatively few of the drugs on the market or in the late stages of clinical trials were discovered via genomics or bioinformatics programs.

Specialists

Bioinformatics is applied to at least five major types of activities: data acquisition, database development, data analysis, data integration, and analysis of integrated data.

Data Acquisition

Data acquisition is primarily concerned with accessing and storing data generated directly off of laboratory instruments. Many of these instruments are either automated or semi-automated high-throughput instruments that generate large volumes of data. The Human Genome Project utilized hundreds of DNA sequencers, producing enormous amounts of data. The data had to be captured in the appropriate format, and it had to be capable of being linked to all the information related to the DNA samples, such as the species, tissue type, and quality parameters used in the experiments. This area of bioinformatics primarily relates to the use of "laboratory information management systems," which are the computer systems used to manage the information needs of a particular laboratory.

Database Development

Many laboratories generate large volumes of such data as DNA sequences, gene expression information, three-dimensional molecular structure, and high-throughput screening. Consequently, they must develop effective databases for storing and quickly accessing data. For each type of data, it is likely that a different database organization must be used. A database must be designed to allow efficient storage, search, and analysis of the data it contains. Designing a high-quality database is complicated by the fact that there are several formats for many types of data and a wide variety of ways in which scientists may want to use the data. Many of these databases are best built using a relational database architecture, often based on Oracle or Sybase.

A strong background in relational databases is a fundamental requirement for working in database development. Having some background in the molecular biology techniques used to generate the data is also important. Most critical for the bioinformatics specialist is to have a strong working relationship with the researchers who will be using the database and the ability to understand and interpret their needs into functional database capabilities.

Data Analysis

Being able to analyze data efficiently requires having a good database design, allowing researchers to query the database effectively and letting them quickly obtain the types of information they need to begin their data analysis. If queries cannot be performed, or if performance is tediously slow, the whole system breaks down, since scientists will not be inclined to use the database. Once data is obtained from the database, the user must be able to easily transform it into the format appropriate for the desired analysis tools.

This can be challenging, since researchers often use a combination of publicly available tools, tools developed in-house, and third-party commercial tools. Each tool may have different input and output formats. Starting in the late 1990s, there have been both commercial and in-house efforts at pharmaceutical and biotech companies to reduce the formatting complexities. Such simplification efforts focus on building analysis systems with a number of tools integrated within them such that the transfer of data between tools appears seamless to the end user.

Bioinformatics analysts have a broad range of opportunities. They may write specific algorithms to analyze data, or they may be expert users of analysis tools, helping scientists understand how the tools analyze the data and how to interpret results. A knowledge of various programming languages, such as Java, PERL, C, C++, and Visual Basic, is very useful, if not required, for those working in this area.

Data Integration

Once information has been analyzed, a researcher often needs to associate or integrate it with related data from other databases. For example, a scientist may run a series of gene expression analysis experiments and observe that a particular set of 100 genes is more highly expressed in cancerous lung tissue than in normal lung tissue. The scientist might wonder which of the genes is most likely to be truly related to the disease. To answer the question, the researcher might try to find out more information about those 100 genes, including any associated gene sequence, protein, enzyme, disease, metabolic pathways, or signal transduction pathway data.

Such information will help the researcher narrow the list down to a smaller set of genes. Finding this information, however, requires connections or links between the different databases and a good way to present and store the information. An understanding of database architectures and the relationship between the various biological concepts in the databases is key to doing effective data integration.

Analysis of Integrated Data

Once various types of data are integrated, users need a good way to present these various pieces of data so they can be interpreted and analyzed. The information should be capable of being stored and retrieved so that, over time, various pieces of information can be combined to form a "knowledge base" that can be extended as more experiments are run and additional data are integrated from other sources. This type of work requires skills related to database design and architecture. It also requires specific programming skills in various computer languages, as well as expertise in developing interfaces between a computer and its user.

Bibliography

Howard, Ken. "The Bioinformatics Gold Rush." Scientific American 283, no. 1 (2000): 58-64.

Internet Resources

"EID V3 N3: Host Genes and HIV." Centers for Disease Control and Prevention. http://www.cdc.gov/ncidod/eid/vol3no3/smith.htm.

EMBL Nucleotide Sequence Database. Release 69. December 2001. European Bioinformatics Institute. http://www.ebi.ac.uk/.

GenBank. National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/.

SWISS-PROT. Swiss Institute of Bioinformatics. http://www.expasy.org/sprot/.

�??Anthony J. Recupero

vectors

2008-04-17T15:11:00.000+05:30

Columbia Encyclopedia: vector,

quantity having both magnitude and direction; it may be represented by a directed line segment. Many physical quantities are vectors, e.g., force, velocity, and momentum. Thus, in specifying a force, one must state not only how large it is but also in what direction it acts.

Representation and Reference Systems

The simplest representation of a vector is as an arrow connecting two points. Thus, AB designates the vector represented by an arrow from point A to point B, while BA designates a vector of equal magnitude in the opposite direction, from B to A. In order to compare vectors and to operate on them mathematically, however, it is necessary to have some reference system that determines scale and direction. Cartesian coordinates are often used for this purpose. In the plane, two axes and unit lengths along each axis serve to determine magnitude and direction throughout the plane. For example, if the point A mentioned above has coordinates (2,3) and the point B coordinates (5,7), the size and position of the vector are thus determined. The size of the vector in the x-direction is found by projecting the vector onto the x-axis, i.e., by dropping perpendicular line segments to the x-axis. The length of this projection is simply the difference between the x-coordinates of the two points A and B, or 5�??2=3. This is called the x-component of the vector. Similarly, the y-component of the vector is found to be 7�??3=4. A vector is frequently expressed by giving its components with respect to the coordinate axes; thus, our vector becomes [3,4].

The components of the vector AB �?? are given by its projections on each of the coordinate axes.

Knowledge of the components of a vector enables one to compute its magnitude�??in this case, 5, from the Pythagorean theorem [(3²+4²)^1/2=5)]�??and its direction from trigonometry, once the lengths of the sides of the right triangle formed by the vector and its components are known. (Trigonometry can also be used to find the component of the vector as projected in some direction other than the x-axis or y-axis.) Since the vector points from A to B, both its components are positive; if it pointed from B to A, its components would be [�??3,�??4] but its magnitude and orientation would be the same.

It is obvious that an infinite number of vectors can have the same components [3,4], since there are an infinite number of pairs of points in the plane with x- and y-coordinates whose respective differences are 3 and 4. All these vectors have the same magnitude and direction, being parallel to one another, and are considered equal. Thus, any vector with components a and b can be considered as equal to the vector [a,b] directed from the origin (0,0) to the point (a,b). The concept of a vector can be extended to three or more dimensions.

Addition and Multiplication of Vectors

The addition, or composition, of two vectors can be accomplished either algebraically or graphically. For example, to add the two vectors U [�??3,1] and V [5,2], one can add their corresponding components to find the resultant vector R [2,3], or one can graph U and V on a set of coordinate axes and complete the parallelogram formed with U and V as adjacent sides to obtain R as the diagonal from the common vertex of U and V.

Addition, or composition, of the vectors U [-3,1] and V [5,2] to form the resultant vector R [2,3].

Two different kinds of multiplication are defined for vectors in three dimensions. The scalar, or dot, product of two vectors, A and B, is a scalar, or quantity that has a magnitude but no direction, rather than a vector, and is equal to the product of the magnitudes of A and B and the cosine of the angle θ between them, or AB=|A||B| cos θ. The vector, or cross, product of A and B is a vector, A�?B, whose magnitude is equal to |A||B| sin θ and whose orientation is perpendicular to both A and B and pointing in the direction in which a right-hand screw would advance if turned from A to B through the angle θ. The vector product is an example of a kind of multiplication that does not follow the commutative law, since A�?B=�??B�?A.

Vector Analysis and Vector Space

The components of a vector need not be constants but can also be variables and functions of variables. For example, the position of a body moving through space can be described by a vector whose x, y, and z components are each functions of time. The methods of the calculus may be applied to such vector functions, leading to the branch of mathematics known as vector analysis.

The more general extension of vectors leads to the concept of a vector space. A vector space is a set of elements, A, B, C,..., called vectors, for which the operations of addition of vectors and multiplication of a vector by a scalar are defined and which satisfies ten axioms relating to such properties as closure under both operations, associativity, commutativity, and existence of a zero vector, an additive inverse (negative of a vector), and a unit scalar.

Bibliography

See P. Gustyatnikov and S. Reznichenko, Vector Algebra (1988); J. E. Marsden and A. Tromba, Vector Calculus (1988).

plasmid

2008-04-17T15:09:00.000+05:30

Genetics Encyclopedia: Plasmid

Plasmids are naturally occurring, stable genetic elements found in bacteria, fungi, and even in the mitochondria of some plants. They may be composed of DNA or RNA, double-stranded or single-stranded, linear or circular. Plasmids almost always exist and replicate independently of the chromosome of the cell in which they are found.

Types of Plasmids

Plasmids are not usually required by their host cell for its survival. Instead, they carry genes that confer a selective advantage on their host, such as resistance to heavy metals or resistance to naturally made antibiotics carried by other organisms. Alternatively, they may produce antibiotics (toxins) that help the host to compete for food or space. For instance, antibiotic resistance genes produced by a plasmid will allow its host bacteria to grow even in the presence of competing bacteria or fungi that produce these antibiotics.

Plasmids are subgrouped into five main types based on phenotypic function. R plasmids carry genes encoding resistance to antibiotics. Col plasmids confer on their host the ability to produce antibacterial polypeptides called bacteriocins that are often lethal to closely related or other bacteria. The col proteins of E. coli are encoded by plasmids such as ColE1. F plasmids contain the F or fertility system required for conjugation (the transfer of genetic information between two cells). These are also known as episomes because, under some circumstances, they can integrate into the host chromosome and thereby promote the transfer of chromosomal DNA between bacterial cells. Degradative or catabolic plasmids allow a host bacterium to metabolize normally undegradable or difficult compounds such as various pesticides. Finally, virulence plasmids confer pathogenicity on a host organism by the production of toxins or other virulence factors.

Replication

One common feature of all plasmids is a specific sequence of nucleotides termed an origin of replication (ori). This sequence, together with other regulatory sequences, is referred to as a replicon. The replicon allows a plasmid to replicate within a host cell independently of the host cell's own replication cycle. If the plasmid makes many copies of itself per cell, it is termed a "relaxed" plasmid. If it maintains itself in fewer numbers within the cell it is termed a "stringent" plasmid. Two different plasmids can coexist in the same cell only if they share the same replication elements. If they do not, they will be unable to be propagated stably in the same cell line, and are termed incompatible.

In nature, plasmid inheritance can occur through a variety of mechanisms. During conjugation between two bacterial strains, plasmids can be transferred along with the bacterial DNA, and this activity is controlled by a set of transfer (tra) genes that are located on the plasmid and not on the bacterial chromosome. The proteins produced by these transfer genes bind to the DNA at the ori site to form a DNA-protein complex known as a relaxosome. This complex makes a nick, or break, in one of the two strands of the double-stranded plasmid DNA molecule. The place where this break occurs is called the "nic" site, and the nicked DNA is said to be "relaxed" because the DNA unwinds as a result of the nick in one of the strands. The single-stranded DNA that is generated by the nick is thought to be unwound and transferred through the pilus, or mating bridge, that connects the two bacteria entering the recipient bacteria. The other strand is left in the donor bacteria. It acts as a template for the synthesis of a new complementary DNA strand forming a double-stranded plasmid DNA molecule.

Some nonconjugative plasmids can also be transferred into bacteria by means of a process called mobilization, as long as they carry the necessary (mob) genes. Others are taken up by bacterial cells during the process known as transformation. Finally, plasmids that exist in a host cell that undergoes fission (cell division) are simply divided between the resultant two daughter cells.

Use in Research and Technology

Because of their ability to move genes from cell to cell, plasmids have become versatile tools for both research and biotechnology. In the laboratory, researchers use plasmids to carry marker genes, allowing them to trace the plasmid's inheritance across host cells. Transferred or "cloned" genes are used to produce a variety of important medical, agricultural, or environmental products that can be economically used by humans.

Researchers have also engineered plasmids to be extremely efficient cloning vectors. To be used in this way, the plasmid must contain at least one origin of replication, a multiple cloning site (called a polylinker) where a variety of restriction enzymes can cut so that foreign DNA can be inserted, a selectable genetic marker, and transcription and translation signals recognized by the host cell, so that the expression of a cloned gene can be easily identified.

The foreign DNA is often inserted in such a way that the expression of the foreign gene is tied to the expression of a marker gene. For example, one of the most popular methods to show that a foreign DNA has been inserted and expressed in the host is by the insertional inactivation of the lac Z gene. In this case, the foreign DNA is inserted in the middle of the lac Z gene so that the gene becomes defective and the enzyme it codes for no longer works. The damaged enzyme therefore cannot cleave the artificial substrate Xgal to produce a blue color or blue colony, as it normally would, and white colonies of bacteria are produced. Therefore, the white colonies indicate that artificial DNA has been successfully cloned or recombined into the plasmid in the lac Z gene, whereas nonrecombinant colonies are blue. The white colonies can thus be easily isolated for further expansion and experimentation.

Under certain circumstances, recombinant DNA experiments using plasmids are considered to be hazardous, and the ease with which plasmids are acquired by bacteria has led them to be classed as biohazards. They are therefore subject to guidelines and may require registration and approval. A publication produced by the National Institutes of Health, titled Guidelines for Research Involving Recombinant DNA Molecules, is the definitive reference for recombinant DNA research in the United States and should be consulted when considering research, particularly biomedical research, involving plasmids.

Bibliography

Alberts, Bruce, et al. Molecular Biology of the Cell, 4th ed. New York: Garland Science,2002.

Bloom, Mark V., Greg A. Freyer, and David A. Micklos. Laboratory DNA Science: An Introduction to Recombinant DNA Techniques and Methods of Genome Analysis. Menlo Park, CA: Addison-Wesley, 1996.

Alcamo, I. Edward. DNA Technology: The Awesome Skill, 2nd ed. Burlington, MA: Harcourt Press, 2000.

Lodish, Harvey, et al. Molecular Cell Biology, 4th ed. New York: W. H. Freeman,1999.

�??Linnea Fletcher

BIOTECH COMPONIES

2008-04-12T20:16:00.004+05:30

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bitech books

2008-04-11T22:47:00.003+05:30

here u can get many books related to biotechnology,

Anatomia Color Atlas and Textbook of Human Anatomy Volume 3 2003 Thieme

Plant Biotechnology and Molecular Markers

Food Lipids: Chemistry, Nutrition, and Biotechnology, Third Edition (Food Science & Technology)

Natural Products from Plants

books of ncbi

The Construction And Operation Of Clandestine Drug Laboratories
Nimble

The Global Genome: Biotechnology, Politics, and Culture (Leonardo Books)

Science and Ethics

Isolation and Purification of Proteins (Biotechnology and Bioprocessing Series)
By: Rajni Hatti-Kaul(Editor), Bo Mattiasson(Editor)

The Biotechnology of Ethanol : Classical and Future Applications
password for above book

Genomics, Proteomics and Vaccines

Handbook of Pharmaceutical Manufacturing Formulations vol 1

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ARTIFICIAL SKIN

2008-04-10T22:13:00.004+05:30

The skin produced in vitro is,in fact , only the epidermis portion of skin; when the epidermis applied to the burnt area , it leads to the regeneration of dermis (the remaining part of skin) underneath.but improvement in the techniques have permitted the reconstitution of vvirtually complete skin(both epidermis and dermis) , called living skin equivalent(LSE); this technology emloys a collagen matrix as a support for groth of tissue .the skin explants used for obtaining artificial skinmay be either obtained from the patient concerned or from the foreskin (loose skin from the tip of penis) of newborn babies. Skin cells of new-borns grow without scars.Artificial skin from newborn skin explants is used to cover the wound till the patient's skin is cultured and artificial skin obtained for grafting.
the production of artificial skin , in simple term is as follows and is essentially cell or not organ culture . The bulk (Ca 90%) of epidermis is constituted by cells called keratinocytes , which produce the dead cells (corneocytes) making up the outer most cornfied layers of skin. The keratinocytes are dissociated by treating the skin explant with trypsin . These cells are cultured in vessels the bottom of which is coverd with irradiated 3T3 fibroblast cell lines;this is because certain products from fibroblast cells facillitate the proliferation of keratinocytes . Keratinocytes grow tofrom colonies ,which are again disociated into single cells and cultured in the same manner. The process is repeted ill a confluent sheet of pure epithilium is formed ;this sheet is detached from the culture vessels, cleaned and used for grafting. The explant for preparing artificial skin for the graft must come from the patient himself to avoid rejection. A 3cm2 skin explant can yield about 1.7 m2 artificial skin in 3-4 weeks representing a 5000-fold increase. In about 5 years after grafting of he artificial skin , all the essential components of skin are regenrated . Artificial skin grafts have been used to succesfully types of skin repair several types of skin defects including chronic skin ulcers.

Biophysics of cell membranes

2008-04-07T20:56:00.001+05:30

Biophysics of cell membranes

The plasma membrane endows the mammalian cell with unique mechanical properties which, it has been recognised for many years, are essential to the functioning and survival of the cell. It is now becoming increasingly apparent that the physical properties of the membrane are also important in a much wider context, for example in the processes of signalling, transport, vesiculation, adhesion, migration, mitosis and apoptosis. The plasma membrane consists of a bilayer of phospholipids with protein inclusions which on its inner surface is covered by a network of proteins constituting the membrane cytoskeleton and on its outer surface by a dense, polyanionic glycocalyx. Our research is directed towards understanding the relationships both in normal cells and in disease. In the latter there is growing evidence of abnormalities in membrane structure and composition but little understanding of their functional significance.
Current projects involve:

Analysis of the relationships between membrane lipid composition and rheoviscous properties.
Characterisation of the interactions between membrane lipids and the cytoskeletal protein, spectrin.
Investigation of the changes in the mechanical and rheological properties of blood cells in diabetes.
Investigation of the mechanics and rheological properties of the cammelid erythrocyte.
Characterisation of the physical properties of the endothelial cell glycocalyx.
The development of theoretical models of membrane mechanics.
the role of endothelial cells in mechanotransduction

In this research we employ a variety of approaches ranging from micropipette aspiration and fluctuation spectroscopy of cells and vesicles to the study of Langmuir monolayers using classical approaches, microscopy and glancing angle X-ray diffraction.

bichemistry abbreviations

2008-04-07T19:48:00.000+05:30

Abbreviations
ACAT acyl CoA�??cholesterol acyl transferase
ACTH -adrenocorticotropic hormone
ADP -adenosine diphosphate
AMP- adenosine monophosphate
ATP -adenosine triphosphate
ATPase- adenosine triphosphatase
CAP - catabolite activator protein
CDP - diphosphate
CMP- cytidine monophosphate (cytidylic acid)
CoA -coenzyme A
cyclic AMP -adenosine 3�?�,5�?�-cyclic monophosphate (3�?�,5�?�-cyclic
adenylic acid)
DHAP -dihydroxyacetone phosphate
DNA -deoxyribonucleic acid
DNP 2,4-dinitrophenol
DPG -diphosphoglycerate
dTMP -deoxythymidine monophosphate
dUMP -deoxyuridine monophosphate
EF- elongation factor
FAD- (FADH) flavin adenine dinucleotide (reduced form)
FMN- flavin mononucleotide
FSH -follicle-stimulating hormone
GDP- guanosine diphosphate
GMP- guanosine 5�?�-monophosphate (guanylic acid)
GTP -guanosine triphosphate
hCG- human chorionic gonadotropin
HDL -high-density lipoprotein
HGPRT- hypoxanthine-guanine phosphoribosyltransferase
HMG CoA -3-hydroxy-3-methylglutaryl coenzyme A
hnRNA -heterogeneous RNA of the nucleus
IDL -intermediate-density lipoprotein
IMP -inosine 5�?�-monophosphate (inosinic acid)
IP3- inositol 1,4,5-triphosphate
LDH- lactate dehydrogenase
LDL- low-density lipoprotein
LH -luteinizing hormone
mRNA- messenger RNA
MSH- melanocyte-stimulating hormone
NAD -(NADH) -nicotinamide adenine dinucleotide (reduced
form)
NADP (NADPH) -nicotinamide adenine dinucleotide phosphate
(reduced form)
PGH- pituitary growth hormone
Pi -inorganic orthophosphate
PPi -inorganic pyrophosphate
PRPP- 5-phosphoribosylpyrophosphate
RNA -ribonucleic acid
RQ -respiratory quotient
rRNA -ribosomal RNA
TMP- thymidine monophosphate
TPP- thymidine pyrophosphate
tRNA -transfer RNA
TSH- thyroid-stimulating hormone
TTP -thymidine triphosphate
UDP- uridine diphosphate
UMP- uridine monophosphate
UTP- uridine triphosphate
VLDL -very-low-density lipoprotein

Antibiotics Kill Your Body's Good Bacteria

2008-04-07T17:16:00.000+05:30

Antibiotics Kill Your Body's Good Bacteria, Too, Leading to
Serious Health Risks
Dr. Mercola's Comment:
The information that follows is a two-part article taken directly from Doug Kaufmann and Dave
Holland, MD's new book, �??The Fungus Link, Volume 2.�?? Inside this follow-up to the Fungus Link,
published in 2000, you'll not only learn about the dangers of antibiotics. You'll also learn about the
ins and outs of natural and prescriptive antifungals. Additionally, Doug and Dave share with you the
role fungi and their mycotoxins play in what are unfortunately everyday diseases such as prostatitis,
ear-nose-throat disorders, weight problems (including obesity and anorexia), autoimmune diseases,
hormonal disorders, neurologic diseases, hair loss, and eye problems.
To preorder this or any of Doug Kaufmann's books, you can call Doug's office at 972-772-0990, M-F
8:00 AM to 5:00 PM Central.
You can also get books in person and learn about the role of fungi and mycotoxins in cancer and
diabetes as Doug and Dave talk with you live at their next interactive seminar in Ft. Worth, TX, June
28th at Pantego Bible Church, 8001 Anderson Blvd. Ft. Worth, TX 76120. Click here for directions.
You can register for the seminar by also calling the office or visiting the website.
by Doug Kaufmann
�??It is ironic that this humbled fungus, hailed as a benefactor of mankind, may by its very success prove to
be a deciding factor in the decline of the present civilization.�??
�?? Dr. John I. Pitt, The Genus Penicillum, Academic Press, 1979
Simply put, antibiotics are poisons that are used to kill. Only licensed physicians can prescribe them. The
drugs are used to kill bacteria. Certainly, many people have benefited from using them. However, if bacteria
were the only organisms that antibiotics killed, much of this book would be unnecessary. In fact, I contend
that poisons that kill small organisms in small doses �?? organism-specific varieties notwithstanding �?? can
also kill big organisms, when they are taken in big doses. You, my friend, are a big organism.
We�??ve talked about the link between fungus and human disease. This chapter addresses the possibility that
antibiotics may help fungi to proliferate within the human body.
As an adult human, you have three to four pounds of beneficial bacteria and yeast living within your
intestines. These microbes compete for nutrients from the food you eat. Usually, the strength in numbers
beneficial bacteria enjoy both keeps the ever-present yeasts in check and causes them to produce nutrients
such as the B vitamins.
However, every time you swallow antibiotics, you kill the beneficial bacteria within your intestines. When
you do so, you upset the delicate balance of your intestinal terrain. Yeasts grow unchecked into large
colonies and take over, in a condition called dysbiosis.
Yeasts are opportunistic organisms. This means that, as the intestinal bacteria die, yeasts thrive, especially
when their dietary needs are met. They can use their tendrils, or hyphae, to literally poke holes through the
lining of your intestinal wall. This results in a syndrome called leaky gut. Yeasts are not the only possible
cause of this syndrome. Some scientists have linked non-steroidal, anti-inflammatory drugs (NSAIDS) such
as naproxen and ibuprofen to the problem. Given their ability to alter intestinal terrain, antibiotics also likely
contribute to leaky gut syndrome.
In addition to possibly causing leaky gut syndrome, I believe that parasitic yeasts can also cause you to
change what you eat in that they encourage you to binge on carbohydrates including pasta, bread, sugar,
potatoes, etc. So, it should come as no surprise that weight gain counts as one of the telltale signs of
antibiotic damage and subsequent yeast overgrowth.
By altering the normal terrain of the intestines, antibiotics can also make food allergies more likely. An
array of intestinal disorders can ensue, as well. Sadly, most doctors claim ignorance concerning their
patients�?? intestinal disorders rather than admit that the drugs they themselves prescribed actually caused the
disorders to begin with.
Tons of antibiotics are fed to American livestock on a daily basis, purportedly to proof them against
bacteria. This practice not only possibly contributes to antibiotic resistance in humans �?? many experts feel
weight gain, and not disease prevention, is the real reason antibiotics are so widely used. Fat cattle sell for
more than thin cattle. That�??s all very well, but imagine what the antibiotics thereby possibly present in dairy
products could be doing to our children�??s health.
Back in the 1950s, two researchers in Albany, New York, worked to develop an antimicrobial drug from a
substance produced by a soil-based fungus. Although the nystatin they discovered is technically a
mycotoxin, it works wonders as an intestinal antifungal. This as yet revolutionary drug stops the yeast
overgrowth caused by all other antibiotics and is 100 percent safe to use. In addition, nystatin works with no
side effects, though it can cause a pseudo sickness that patients often confuse with side effects.
Also in the 1950s, scientists used mice to grade the relative toxicity of 340 antibiotics (Dr. William S.
Spector, The Handbook of Toxicity, 1957). The researchers based their rankings on the amount of a given
antibiotic required to kill half of the lab mice injected with it. I relate this story only to ask you, before 1957,
how did scientists decide what would serve as prescriptive doses for these very same antibiotics when used
in humans?
I�??ll assume that the same toxicity scale remains in place today. If it does, and if a given dose of penicillin
will kill 50 percent of mice injected, it stands to reason that a much larger dose, or perhaps repetitive doses
extended over 40 years, might prove fatal to a human. I don�??t know if larger doses are in fact administered
to people. And, the 40-year scenario has its problems. But you have to admit, it�??s certainly food for thought.
The time span between when patients take rounds of antibiotics and when they die interests me. That�??s
because I believe that few people really die of heart disease and diabetes. In actuality, antibiotics are
responsible for deaths attributed to these diseases, because these drugs are what caused people to develop
the diseases to begin with. And yet, incredibly, death certificates usually state the probable cause of death
without mentioning whether the deceased had a history of taking antibiotics.
Remember, antibiotics are dangerous mycotoxins �?? fungal metabolites. Just as importantly, medical
experts have written articles maintaining that these drugs kill people. But, other experts insist on remaining
sceptical as to the problem, even though these same experts readily recognize the link between weakened
immune systems and death.
According to the 2001 Allergy and Asthma Report, the first immunodeficiency syndrome was identified in
1952. This document tells us that since that time, �??more than 95 immune syndromes have been identified,
with new conditions coming to light every day.�?? The report goes on to say that research indicates that
�??increased antibiotic use in human infancy may be associated with increased risk of developing allergies.�??
Max Planck won the 1918 Nobel Prize in Physics. He once weighed in as to why science is slow to change
even in the presence of overwhelming evidence that it should do so.
�??A new scientific truth does not triumph by convincing its opponents and making them see the light,�??
Planck said, �??but rather because its opponents eventually die and a new generation grows up that is familiar
with the ideas from the beginning.�??
That a new generation will grow up knowing of the dangers inherent in taking antibiotics is a good thing.
That doctors will continue randomly prescribing fungal toxins should teach us the importance of knowing
medical facts before blindly accepting any prescription. Please study the antimicrobial benefits and the
immune system stimulants that nature provides. Know also that, in some instances, antibiotics may become
necessary.
If you reach the point where no alternatives exist, I recommend that you ask your doctor to prescribe
nystatin simultaneously with the antibiotic (see Dr. Holland�??s article). Also, keep in mind the post-antibiotic
importance of restoring the intestinal terrain with plain yogurt and probiotics. If you experience bloating,
belching, gas, constipation, diarrhea, GERD, or other intestinal problems, probiotics can play an important
role in restoring your intestinal terrain.
Antibiotics �?? to Take or Not to Take?
by David A. Holland, M.D.
I looked up antibiotics in Harrison�??s Textbook of Internal Medicine. The listing referred me to
�??antimicrobials.�?? This caused me to realize how much more accurately the second term describes these
substances, given the broad-spectrum nature of a lot of them.
I must confess that, as a doctor, I do prescribe �??antimicrobials.�?? Perhaps I prescribe more antifungals and
nonprescription remedies than the usual doctor, but I do prescribe antibiotics, as well. Perhaps even more
horrifying, considering Doug�??s articles condemning them, is that I�??ve taken them myself! In fact, in these
times it�??s a rare individual who goes through life without ingesting those little pills. So, three questions have
become important �?? when should you take antibiotics, when should you refrain, and what will you do
when you�??ve already taken them?
Alexander Fleming, by the grace of God, brought us a mixed blessing in 1928 with his accidental discovery
of penicillin produced by, of all things, a fungus. Medicine�??s interest treating people for exposure to fungi
dropped dramatically in succeeding years, until the microbes were only thought important insofar as their
ability to produce increasingly diverse varieties of antibiotics.
Interest in fighting bacteria proliferated like a flesh-eating Strep infection, fueling the race to discover ever
more antibiotics. Pharmaceutical salespeople invaded doctors�?? offices and hospitals, intent on convincing
physicians their antibiotic was better than the others. These salespeople supported their pitches with studies,
graphs, charts and convincing stats, while often failing to mention that their research had been funded by
their own companies. The possible conflict of interest was, and remains, enormous.
I have no quarrel with such salespeople. They�??re regular men and women like you and me, just trying to
make a living. However, when human lives are involved, funding research to prove that your own product is
better than the competition�??s is just plain wrong. The advantage is obvious, and the danger that a great deal
of objectivity could be lost is only all too real.
I believe that an impartial, third party should be assigned to perform such research, funded by a mandatory
�??ante�?? from all pharmaceutical companies involved in producing a given category of drug. Of course, that
will be the day! In case the above scenario never happens, we would do well to take with several grains of
salt the unregulated information that companies provide about their own products.
Perhaps you are wondering about the use �?? and abuse �?? of antibiotics in general. Let me give you an
example. One of the most common diagnoses given at a doctor�??s office is the upper respiratory infection
(URI). It accounts for up to 70 percent of all antibiotics dispensed (Annals of Internal Medicine. American
College of Physicians. American Society of Internal Medicine. March 20, 2001).
However, according to Dr. Carol Kauffman, most URIs are not caused by the bacteria that antibiotics are
designed to fight. Rather, Kauffman says, they are caused by fungi. So, unless a secondary, bacterial
infection presents itself �?? and even then, the rules change �?? most URIs do not require the use of
antibiotics.
Regarding ear infections, in one study, children administered antibiotics for acute otitis media suffered
double the rate of adverse effects compared to children in the study who took placebos (Clinical Evidence.
2000). The difference in outcome for those children in the study who took antibiotics compared to those
who do not was almost negligible. Some scientists counter that children who take antibiotics run lower risks
of secondary ear infections such as meningitis or mastoiditis (infection of the angular bone located behind
your ear).
Of course, the landscape is complicated by noncompliance. The portion of people who take their antibiotics
as prescribed has been estimated at anywhere between 8 to 68 percent. So it�??s difficult to say just how
effective antibiotics actually are.
Now, say my daughter were to get sick for 10 days, miserable with a high fever and screaming ear pain. Say
our doctor said her ear canal checked out as angry red. Am I going to have my daughter take the
prescription? Probably so. We cared for a young woman at the hospital where I worked who was literally at
her death bed with overwhelming Streptococcal �?? bacterial �?? pneumonia. One of her lungs was saturated
with the infection, which had also spread throughout her bloodstream.
I went on to my next rotation thinking that was the last I would hear of that patient. However, I later spoke
with her attending physician. He told me she walked out of that hospital, completely cured. So, antibiotics
save lives, but it�??s not exactly a common occurrence. Certainly, most of you out there suffering from the
common cold are not near death, so you should think twice about taking antibiotics.
The non-synthetic antibiotics are fungal by-products called mycotoxins. Penicillin is perhaps the best
example. In other words, mycotoxins kill off fungi�??s competitors, allowing fungi to grab up all of the
nutrients for themselves. Alexander Fleming himself observed this in action, and it later led him to develop
penicillin. When a mold �?? molds are fungi �?? contaminated a bacteria colony upon which Fleming was
performing an experiment, the invader cleared the area around it of all bacteria. When Fleming investigated,
It turned out that the fungus had produced a substance he would later call penicillin, killing the bacteria in
residence.
Just because they kill bacteria, you may be thinking, doesn�??t mean that some, many or especially all of the
mycotoxins used as antibiotics are necessarily harmful to human beings. A. V. Costantini in effect counters
this idea when he speaks of the work of two scientists by the name of Bernstein and Ross. Costantini says
that the men found that two or more months of treatment with penicillin and other antibiotics contributed to
what they saw as a �??significantly increased risk of non-Hodgkin�??s lymphoma in humans (Costantini, A. V.
Fungalbionics. 1998).�??
How many people, children included, have undergone dose after dose of antibiotics for recurring infections?
Doug and I believe that these relatively small doses taken over long periods of time are actually harming us
in similar, incremental fashion, later showing up as cancer, diabetes, vasculitis or other diseases.
We take antibiotics when we are sick, when our immune systems weaken. The mycotoxins pharmacies
dispense for use as antibiotics only exacerbate the problem, because the lion�??s share of these substances
have been shown to be immunosuppressants (CAST Report No. 116. November 1989.). Not only are they
capable of hamstringing our immune systems, they also destroy the friendly bacteria that guard our
intestines.
These friendly bacteria include Lactobacillus acidophilus, Bifidus and Bulgaricus, supplements for which
can be found in any health food store�??s refrigerated section. They protect us against pathogens such as
Salmonella, yeast, cholera, and the bad E. coli. They are so potent that, prior a trip abroad, to protect
yourself from traveler�??s diarrhea you�??d do better to skip the usual antibiotics and instead take acidophilus
supplements.
Unfortunately, these good flora are so vulnerable to antibiotics that, in mice, a �??single injection of
streptomycin can eradicate the protective effect of the normal flora. (Mandell. Principles and Practice of
Infectious Diseases. 2000.)�?? And, once gone, these friendly bacteria are replaced by hostile bacteria such as
Pseudomonas, Clostridium, and Klebsiella, and by Candida yeast, a powerful member of the fungi family.
So, we have the good and the bad regarding our chemical friends known as antibiotics. They can �??save the
day�?? at times, but they have ruined them at others �?? just ask any woman with a yeast infection or look at
any baby who suffers from thrush. You should know that, even should you just say �??no�?? when your doctor
moves to prescribe antibiotics for you, theoretically speaking you may still be taking them with every bite of
steak and pork you eat.
That�??s because more antibiotics per pound are used on livestock than in human medicine. How much of
those antibiotics are passed on is difficult to determine, but the mere possibility of this kind of thing is
certainly a worry.
Our goal in this book is to educate you and to help you make informed decisions. Some final, simple tips
follow:
1. An ounce of prevention.... Exercise, eat intelligently and take a few supplements. Avoid alcohol,
smoking, and recreational drugs. Get some rest once in a while. Pray.
Despite our best efforts, most of us will get sick at some point and decide to go see a doctor. If you
are a stubborn, married man, your wife will likely make the appointment for you.
2. Ask Questions. If your doctor diagnoses you with an upper respiratory infection, sore throat (in
which the strep test is negative), bronchitis, sinusitis, or ear infection, and you wonder if you really
need an antibiotic, make a point of asking her about it. A lot of physicians would be pleasantly
surprised that one of their patients would even consider trying to recuperate without antibiotics. Ask
if you can treat your condition symptomatically and come back or call in a couple of days if you are
not better.
If your questions annoy your doctor, then get another doctor. After all, you pay the bills, either
directly or out of your paycheck in the form of insurance, and you deserve adequate treatment. On
the other hand, if you feel you, in fact, do need an antibiotic and your doctor disagrees, try to work a
deal in which she will prescribe an antibiotic for you if you don�??t feel better in a couple of days. I
learned an important lesson about this kind of disagreement during college, on a visit to the
infirmary. The doctor there refused to give me an antibiotic for a URI I�??d come down with. I had to
suppress my anger at what I saw as arrogance on his part, but lo and behold, he was right. I got better
without the pills I�??d been sure I�??d needed. I think a lot of people tend to underestimate their bodies�??
healing abilities, in much the same way as I did. That�??s just one reason why doctors are oftentimes in
a better position to make the call as to whether or not to prescribe.
3. Take an objective look at yourself and your life-style. If you keep coming down with the same thing,
do some research and a little thinking. Do you drink a lot of soda? Do you smoke? Are you taking
antibiotic after antibiotic and now have a secondary yeast or fungal infection? How is your spiritual
life? Your stress level? The point is, myriad factors contribute to �??wellness.�??
As far as chronic sinus infections go, Johns Hopkins researchers are now saying most such conditions are
caused by a fungus. So, if you do have chronic sinusitis, stop taking antibiotics, get on an antifungal diet,
and ask your doctor for antifungal medications. If your doctor refuses, visit a health food store for natural,
off-the-shelf antifungals such as olive leaf extract, garlic, and Caprylic acid.
Once you improve, make sure you go back and let your doctor know how things worked out. Chances are
she is neither experienced nor comfortable with prescribing antifungal medication. Your story may convince
her to do her own research, the first step to changing her treatment philosophy.
It shouldn�??t be too difficult to convince your doctor to let you try a prescription of nystatin. As one of the
better gut antifungals, nystatin is also remarkably safe and free of side-effects.
If you�??ve decided to go ahead and take an antibiotic:
1. Get the facts. Ask your doctor how many days you must take the antibiotic and if you, in fact, do
need the latest, most powerful one on the market. Simple urinary tract infections are now treated with
only three days of antibiotics. Sinus infections, bronchitis, and ear infections in children over two
years of age can be treated with as few as five days of antibiotics, new or old, generic or name brand.
This may not be possible, however, if you have other medical conditions or if you smoke.
2. Build trust. Commit to the full course of the antibiotic unless you experience significant side effects
or an allergic reaction. You sought medical advice and agreed to the prescription. You will build
trust with your doctor if you work as a team. This trust will be very important once you see number 3
below.
3. Take an antifungal with the antibiotic. For example, you could ask your doctor for a prescription of
nystatin to take during the course of your antibiotic. Many dermatologists do this when prescribing
long-term antibiotic courses for acne. I suggest adults take two tablets twice a day �?? 1 cc of
suspension twice a day for children �?? to prevent yeast overgrowth in your intestines. Most cases of
upset stomach or diarrhea that kick in a few days of beginning a round of antibiotics can be cured
with a single dose of the drug. Diarrhea after a two-week round of antibiotics is likely caused by a
different bug altogether �?? be sure to bring that to your doctor�??s attention.
I should tell you that, in my clinical practice years, many of my patients made great strides against
acne through taking nystatin and a change in diet alone, without the antibiotics.
4. Supplement your intake. Take an antioxidant supplement, one which includes vitamin E, zinc,
selenium, vitamin C, and vitamin A, among others. According to A.V. Costantini, all antioxidants
are antifungal. (Costantini. 1998.)
5. Keep your bowels moving. If antibiotics kill off your friendly, intestinal bacteria, once you cease
taking antibiotics you�??ll run a higher risk of infection by other, more hostile bacteria. These bacteria
will be quick to find and exploit pockets of debris that could be collecting and putrefying in your
intestines if you happen to become constipated. So, be sure to keep your digestive tract as clear as
possible until you can repopulate it with friendly bacteria. Psyllium hulls fiber from your local health
food store is the best, bulk fiber to use, as long as you don�??t have a history of intestinal obstruction.
Psyllium not only relieves constipation. It also slows diarrhea by absorbing excess water.
6. Replace the good bacteria in your intestines. Supplement with an acidophilus supplement for a few
weeks following any course of antibiotics. Do not take these simultaneously with your antibiotic, or
you will simply end up with a lot of very dead, albeit still friendly bacteria in your intestines. At the
very most, take acidophilus supplements either in between antibiotic doses or after you have
completely finished your prescription.
7. Look back at why you became ill to begin with. I once suffered from strep throat after indulging in
half a box of chocolates. That should have come as no surprise. Who wouldn�??t be crippled by that
amount of garbage? More than likely, you have your own experience regarding similar binges. My
point is, diet plays at least as much a role as actual exposure to germs as to whether we get sick �??
when we are healthy and eating correctly, our bodies are amazingly resistant to infection.
One, last note: Please ignore advertisements that recommend guzzling orange juice for the vitamin C it
contains. A big dose of sugar is what you�??d actually be getting. I have heard more than a few patients note
that once they felt they were coming down with something, they immediately began downing glass after
glass of orange juice, only to get even sicker. They concluded that they must not have caught the illness in
time, which couldn�??t have been any further from the truth.
The truth is, they simply fueled the fire of their infections with lots of sugar, all because they trusted a
corporation�??s advertisement to educate them about proper healing strategies. If you want that much vitamin
C, you will be perfectly fine taking it in the 1,000 mg pill form a few times a day. As far as fluid
requirements are concerned, your body is 70 percent water �?? and that is exactly what it needs!

Protein Structure Affects How Ligands Bind

2008-04-05T13:21:00.000+05:30

The binding of a ligand to a protein is rarely as simple
as the above equations would suggest. The interaction
is greatly affected by protein structure and is often accompanied
by conformational changes. For example,
the specificity with which heme binds its various ligands
is altered when the heme is a component of myoglobin.
Carbon monoxide binds to free heme molecules more
than 20,000 times better than does O2 (that is, the Kd
or P50 for CO binding to free heme is more than 20,000
times lower than that for O2), but it binds only about
200 times better when the heme is bound in myoglobin.
The difference may be partly explained by steric hindrance.
When O2 binds to free heme, the axis of the oxygen
molecule is positioned at an angle to the FeOO bond
(Fig. 5�??5a). In contrast, when CO binds to free heme,
the Fe, C, and O atoms lie in a straight line (Fig. 5�??5b).
In both cases, the binding reflects the geometry of hybrid
orbitals in each ligand. In myoglobin, His64 (His E7),
on the O2-binding side of the heme, is too far away to
coordinate with the heme iron, but it does interact with
a ligand bound to heme. This residue, called the distal
His, does not affect the binding of O2 (Fig. 5�??5c) but
may preclude the linear binding of CO, providing one
explanation for the diminished binding of CO to heme
in myoglobin (and hemoglobin). A reduction in CO binding
is physiologically important, because CO is a lowlevel
byproduct of cellular metabolism. Other factors,
not yet well-defined, also seem to modulate the interaction
of heme with CO in these proteins.
The binding of O2 to the heme in myoglobin also depends
on molecular motions, or �??breathing,�?? in the protein
structure. The heme molecule is deeply buried in
the folded polypeptide, with no direct path for oxygen
to move from the surrounding solution to the ligandbinding
site. If the protein were rigid, O2 could not enter
or leave the heme pocket at a measurable rate. However,
rapid molecular flexing of the amino acid side
chains produces transient cavities in the protein structure,
and O2 evidently makes its way in and out by moving
through these cavities. Computer simulations of
rapid structural fluctuations in myoglobin suggest that
there are many such pathways. One major route is provided
by rotation of the side chain of the distal His
(His64), which occurs on a nanosecond (109 s) time
scale. Even subtle conformational changes can be critical
for protein activity.

PROTIEN DENAURATION AND FOLDING

2008-04-05T12:53:00.000+05:30

Protein Denaturation and Folding

All proteins begin their existence on a ribosome as a linear
sequence of amino acid residues (Chapter 27). This
polypeptide must fold during and following synthesis to
take up its native conformation. We have seen that a native
protein conformation is only marginally stable. Modest
changes in the protein�??s environment can bring about
structural changes that can affect function. We now explore
the transition that occurs between the folded and
unfolded states.
Loss of Protein Structure Results in Loss of Function
Protein structures have evolved to function in particular
cellular environments. Conditions different from those
in the cell can result in protein structural changes, large
and small. A loss of three-dimensional structure sufficient
to cause loss of function is called denaturation.
The denatured state does not necessarily equate with
complete unfolding of the protein and randomization of
conformation. Under most conditions, denatured proteins
exist in a set of partially folded states that are
poorly understood.
Most proteins can be denatured by heat, which affects
the weak interactions in a protein (primarily hydrogen
bonds) in a complex manner. If the temperature
is increased slowly, a protein�??s conformation generally
remains intact until an abrupt loss of structure (and
function) occurs over a narrow temperature range (Fig.
4�??26). The abruptness of the change suggests that unfolding
is a cooperative process: loss of structure in one
part of the protein destabilizes other parts. The effects
of heat on proteins are not readily predictable. The very
heat-stable proteins of thermophilic bacteria have
evolved to function at the temperature of hot springs
(~100 C). Yet the structures of these proteins often differ
only slightly from those of homologous proteins derived
from bacteria such as Escherichia coli. How these
small differences promote structural stability at high
temperatures is not yet understood.
Proteins can be denatured not only by heat but by
extremes of pH, by certain miscible organic solvents
such as alcohol or acetone, by certain solutes such as
urea and guanidine hydrochloride, or by detergents.
Each of these denaturing agents represents a relatively
mild treatment in the sense that no covalent bonds in
the polypeptide chain are broken. Organic solvents,
urea, and detergents act primarily by disrupting the hydrophobic
interactions that make up the stable core of
globular proteins; extremes of pH alter the net charge
on the protein, causing electrostatic repulsion and the
disruption of some hydrogen bonding. The denatured
states obtained with these various treatments need not
be equivalent.

genetics

2008-04-03T19:50:00.000+05:30

INTRODUCTION

Genetics is the area of biological study concerned with heredity and with the variations between organisms that result from it. It demands an understanding of numerous terms, such as DNA (deoxyribonucleic acid), a molecule in all cells that contains blueprints for genetic inheritance; genes, units of information about particular heritable traits, which are made from DNA; and chromosomes, DNA-containing bodies, located in the cells of most living things, that hold most of the organism's genes. The vocabulary of genetics goes far beyond these three terms, as we shall see, but these are the core concepts. Among the areas in which genetics is applied is forensic science, or the application of science to matters of law�??specifically, through "DNA fingerprinting," whereby samples of skin, blood, semen, and other materials can be used to prove or disprove a suspect's innocence. Another fascinating application of genetics is the Human Genome Project, an effort whose goals include the location and identification of every gene in the human body.

The Genetics Revolution

In the modern world genetics plays a part in more dramatic breakthroughs than any other field of biological study. These breakthroughs have an impact in a wide variety of areas, from curing diseases to growing better vegetables to catching criminals. The field of genetics is in the midst of a revolution, and at the center of this exciting (and, to some minds, terrifying) phenomenon is the realm of genetic engineering: the alteration of genetic material by direct intervention in genetic processes. In agriculture, for instance, genes are transplanted from one organism to another to produce what are known as transgenic animals or plants. This approach has been used to reduce the amount of fat in cattle raised for meat or to increase proteins in the milk produced by dairy cattle. Fruits and vegetables also have been genetically engineered so that they do not bruise easily or have a longer shelf life.

Not all of the work in genetics is genetic engineering per se; in the realm of law, for instance, the most important application of genetics is genetic fingerprinting. A genetic fingerprint is a sample of a person's DNA that is detailed enough to distinguish it from the DNA of all others. The genetic fingerprint can be used to identify whether a man is the father of a particular child (i.e., to determine paternity), and it can be applied in the solving of crimes. If biological samples can be obtained from a crime scene�??for example, skin under the fingernails of a murder victim, presumably the result of fighting against the assailant in the last few moments of life�??it is possible to determine with a high degree of accuracy whether that sample came from a particular suspect. The use of DNA in forensic science is discussed near the conclusion of this essay.

The Human Genome Project

One of the most exciting developments in genetics is the initiation of the Human Genome Project, designed to provide a complete genetic map outlining the location and function of the 40,000 or so genes that are found in human cells. (A genome is all of the genetic material in the chromosomes of a particular organism.) With the completion of this map, genetic researchers will have easy access to specific genes, to study how the human body works and to develop therapies for diseases. Gene maps for other species of animals also are being developed.

The project had its origins in the 1990s, with the efforts of the United States Department of Energy (DOE) and the National Institutes of Health (NIH). The NIH connection is probably clear enough, but the DOE's involvement at first might seem strange. What, exactly, does genetics have to do with electricity, petroleum, and other concerns of the DOE? The answer is that the DOE grew out of agencies, among them the Atomic Energy Commission (AEC), established soon after the explosion of the two atomic bombs over Japan in 1945. Even at that early date, educated nonscientists understood that the radioactive fallout produced from nuclear weaponry can act as a mutagen; therefore, Congress instructed the AEC to undertake a broad study of genetics and mutation and the possible consequences of exposure to radiation and the chemical by-products of energy production.

Eventually, scientists in the AEC and, later, the DOE recognized that the best way to undertake such a study was to analyze the entire scope of the human genome. The project formally commenced on October 1, 1990, and is scheduled for completion in the middle of the first decade of the twenty-first century. Upon completion, the Human Genome Project will provide a vast store of knowledge and no doubt will lead to the curing of many diseases.

Still, there are many who question the Human Genome Project in particular, and genetic engineering in general, on ethical grounds, fearing that it could give scientists or governments too much power, unleash a Nazi-style eugenics (selective breeding) program, or result in horrible errors, such as the creation of deadly new diseases. In fact, it is impossible to search "genetic engineering" on the World Wide Web without coming across the Web sites of literally dozens and dozens of agencies, activist groups, and individuals opposed to genetic engineering and the mapping of the human genome. For more about the Human Genome Project, genetic engineering, and their opponents, see Genetic Engineering.

Gene expression and the creation of phenotype

The genetic code

Main article: Genetic code

The genetic code: DNA, through a messenger RNA intermediate, codes for protein with a triplet code.

The dynamic structure of hemoglobin is responsible for its ability to transport oxygen within mammalian blood.

Genes generally express their functional effect through the production of proteins, which are complex molecules responsible for most functions in the cell. Proteins are chains of amino acids, and the DNA sequence of a gene (through an RNA intermediate) is used to produce a specific protein sequence. Each group of three nucleotides in the sequence, called a codon, corresponds to one of the twenty possible amino acids in protein �?? this correspondence is called the genetic code. The flow of information is unidirectional: information is transferred from nucleotide sequences into the amino acid sequence of proteins, but never from protein back into the sequence of DNA �?? a phenomenon Francis Crick called the central dogma of molecular biology.

The specific sequence of amino acids results in a unique three-dimensional structure for that protein, and the three-dimensional structures of protein are related to their function.^[34]^[35] Some are simple structural molecules, like the fibers formed by the protein collagen. Proteins can bind to other proteins and simple molecules, sometimes acting as enzymes by facilitating chemical reactions within the bound molecules (without changing the structure of the protein itself). Protein structure is dynamic; the protein hemoglobin bends into slightly different forms as it facilitates the capture, transport, and release of oxygen molecules within mammalian blood.

A single amino acid change causes hemoglobin to form fibers.

A single nucleotide difference within DNA can cause a single change in the amino acid sequence of a protein. Because protein structures are the result of their amino acid sequences, some changes can dramatically change the properties of a protein by destabilizing the structure or changing the surface of the protein in a way that changes its interaction with other proteins and molecules. For example, sickle-cell anemia is a human genetic disease that results from a single base difference within the coding region for the β-globin section of hemoglobin, causing a single amino acid change that changes hemoglobin's physical properties. Sickle-cell versions of hemoglobin stick to themselves, stacking to form fibers that distort the shape of red blood cells carrying the protein. These sickle-shaped cells no longer flow smoothly through blood vessels, having a tendency to clot or degrade, causing the medical problems associated with the disease.

Nature vs. nurture

Siamese cats have a temperature-sensitive mutation in pigment production.

Although genes contain all the information an organism uses to function, the environment plays an important role in determining the ultimate phenotype �?? a dichotomy often referred to as "nature vs. nurture". The phenotype of an organism depends on the interaction of genetics with the environment. One example of this is the case of temperature-sensitive mutations. Often, a single amino acid change within the sequence of a protein does not change its behavior and interactions with other molecules, but it does destabilize the structure. In a high temperature environment, where molecules are moving more quickly and hitting each other, this results in the protein losing its structure and failing to function. In a low temperature environment, however, the protein's structure is stable and functions normally. This sort of mutation is visible in the coat coloration of Siamese cats, where a mutation in an enzyme responsible for pigment production causes it to destabilize and lose function at high temperatures.The protein remains functional in areas of skin that are colder �?? legs, ears, tail, and face �?? and so the cat has dark fur at its extremities.

Environment also plays a dramatic role in effects of the human genetic disease phenylketonuria.The mutation that causes phenylketonuria disrupts the ability of the body to break down the amino acid phenylalanine, causing toxic build-up of an intermediate molecule that, in turn, causes severe symptoms of progressive mental retardation and seizures. If someone with the phenylketonuria mutation is kept on a strict diet that avoids this amino acid, however, they remain normal and healthy.

biotech studies

2008-03-29T14:12:00.000+05:30

INTRODUCTION

Biotechnology is an interdisciplinary science including not only biology, but also subjects like mathematics, physics, chemistry and engineering. It is a blend of various technologies applied together to living cells for production of a particular product or for improving upon it. Its use and application ranges from fields like agriculture to industry (food, pharmaceutical, chemical, bioproducts, textiles etc.), medicine, nutrition, environmental conservation, animal sciences etc. making it one of the fastest growing fields. The work is generally carried out in the laboratories, as it is a scientific research oriented field.

Nature of Work

The nature of work of biotechnologists, being interdisciplinary, requires working together of people from different fields such as biology, chemistry, biochemistry, microbiology, molecular biology, immunology, genetics, engineering, food science, agriculture etc. Some of the fields where biotechnology studies are applicable are as follows.

MEDICINE AND HEALTH CARE: Biotechnology's application in this area has helped in the development of various medicines, vaccines and diagnostics. The remarkable development work carried out by biotechnologists in this field has led to improvement in the methods of diagnosis, medicines and vaccinations for diseases which once thought were incurable are no more a cause of worry, which has been a blessing for humankind.
INDUSTRIAL RESEARCH AND DEVELOPMENT: Both the government and the private sector employ biotechnologists. They conduct research and development work, for increasing productivity, improving energy production and conservation, minimizing pollution and industrial waste etc. Biotechnologists also find opportunities at places involving activities like chemical processes, genetic engineering, textile development, cosmetic development etc..
AGRICULTURE AND ANIMAL HUSBANDRY: Indian economy is very much dependent on agriculture and biotechnologists have made major advancements in this area. Over the years, the agricultural output has been improving, owing to the improvements in the quality of seeds, insecticides and fertilizers. The latest technologies like micro propagation and tissue culture has further helped agriculturists to overcome problems like soil imbalances, genetic breeding and crop diseases. Biotechnologists are also encouraging a shift from chemically prepared fertilizers and insecticides to biochemicals and bioinsecticides.
Biotechnology's intervention in the area of animal husbandry has improved animal breeding. Numerous kinds of genetically engineered, high yielding animal breeds have come up which has increased the output of dairy products as well as the meat products. India has in fact, become the largest milk producer in the world
ENVIRONMENT: Environmental biotechnology has become another area of extensive work due to the dangers brought about by increasing levels of environmental pollution. A lot of hard work is being done to protect our environment. In this field, the job of a biotechnologist spans from checking industrial air pollution levels, treatment of industrial waste to recycling of sewage sludge..

Personality

As the work is largely related to scientific research. It becomes quite important to have a good academic background in science. Hard work and high level of intelligence with a scientific bent of mind, determination, perseverance, imagination, innovative attitude, ability to work for long hours, originality, team spirit are some important essentials for becoming a successful biotechnologist.

Professional Courses

Candidates having background in science at the intermediate level can take up:

B.Tech in Biotechnology.
P.G. courses available are
M.Sc. Biotechnology
M.Sc. (Agriculture) Biotechnology
M.V.Sc. (Animal) Biotechnology
M.Tech. Biotechnology, M.Sc./M.V.Sc. Veterinary Biotechnology
M.Sc. (Marine) Biotechnology
Medical Biotechnology
M.Tech. in Biomedical Engineering/Biotechnology.

Depending upon the aptitude and necessity, more advanced courses such

Ph.D. and Post-DoctoralResearch in Biotechnology can also be pursued.

Colleges, Institutions and Universities

Specialization

Being an interdisciplinary subject with diverse areas of study, biotechnological procedures apply themselves to a wide range of fields allowing students from different backgrounds and interests to specialize in fields of their choice. Some of the fields of specialization are

Molecular Biology
Microbiology
Biochemistry
Biophysics
Botany
Zoology
Pharmacology
Physiology
Horticulture
TissueCulture
AgriculturalEngineering
Animal Sciences
Dairy Technology,
Fisheries
Medicine,Life Sciences,
Genetics

Career Prospects

In recent times, biotechnology as a subject has grown rapidly. And as far as employment is concerned, it has become the second fastest growing sector after multi-media. Candidates with postgraduate degree in biotechnology get absorbed in corporate and government sector, both. Qualified biotechnologists are employed in leading indian business houses and MNCs including pharmaceutical companies, chemical industries, bio-processing industries, agriculture related industries and pollution control activities of the major industries etc. They can even join government and corporate run research and development organizations. On the whole making it a good career opportunity for the bright young people.

Remunerations

Remuneration very much depends upon academic qualification, institute or university from which the degree is attained and the level of work experience. In the corporate sector, fresh IIT pass outs may get anything in the range of Rs. 70,000 p.a. to Rs. 85,000 p.a. and fresh B.Sc./B. Tech. graduates from other universities may get anything in the range of Rs. 50,000 p.a. to Rs. 70,000 p.a. Those workimg in the research institutes can expect something around Rs. 60,000 p.a.