Friday, May 30, 2008

Microbes becoming visible to the (almost) naked eye

Microorganisms, which form a significant part of the Earth’s biomass, have long attracted the interest of researchers the world over. Their mysterious nature has proved difficult to examine because they cannot grow in labs. However, thanks to the skills of researchers at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, this is about to change. Their creation of a new computational method to analyse environmental DNA samples will lead to an understanding of the microbial composition of their different habitats.

Researchers put microbes under the microscope Metagenomics, otherwise known as environmental DNA sequencing, has been instrumental in supporting researchers’ quests to study microorganisms. Researchers can now sequence the DNA found in environmental samples instead of having to analyse the genome of a specific organism. Sizeable amounts of sequence fragments are collected. These fragments, said the researchers, contain genetic information of many species forming communities that colonise a specific habitat.


“We have developed a new and very precise method to classify the microbial communities that are present in a given sample,” said Peer Bork, join co-ordinator of the Structural and Computational Biology Unit at EMBL. “We first identify informative DNA sequences in a sample and then map them onto the tree of life, a phylogeny of organisms with sequenced genomes, to find out which microbes are present and where yet unknown species fit into taxonomy and evolution.”

EMBL alumnus Christian von Mering explained that the team’s new method adds to the “current classification attempts based on individual RNA molecules and also has additional unique features.” Dr von Mering said the method helps researchers to better understand the development of microbes in their habitats.

Drs Bork and von Mering classified microbial communities that exist in four diverse environments: farm soil, acidic underground mine water, ocean surface and whale bones from the deep sea. Based on the findings, some microorganisms develop slowly, others faster. The underlying factor is their habitat. Soil organisms, for example, are slow to evolve, whereas ocean surface microbes change quickly.

Part of the research involved determining whether habitat preferences of microorganisms have remained the same throughout evolution. While some microbes have adapted to different lifestyles, said Dr Bork, the majority of them did not for long periods of time. He explained that it is often difficult for microbes to adapt to new environments or even vie against the established communities within them. Consequently, microbes cannot live everywhere, quashing earlier thoughts that they do.

The research data and novel computational methods used will offer more insight into biodiversity on Earth. Dr Bork and his team also worked with Phil Hugenholtz and Susannah Green Tringe of the California-based Genome Institute.


Thursday, May 29, 2008

'Keyboards dirtier than toilet seats'

keyboard with microbes

Electronic-human interfaces such as keyboards, ATM machines, and airport kiosks present special contamination problems. Microbial counts on computer keyboards can be more than 60 times higher than on toilet seats, averaging 3,300 bacteria per square inch. Public surfaces such as those of ATM machines present even greater possibilities for the product damaging microorganisms.

Office computer keyboards could be filthier than toilet seats and cause serious diseases, according to a British microbiologist.

Tests were conducted on 33 office keyboards and compared with swabs from a toilet seat and a door handle in a public toilet. It was found that the keyboards contained dangerous levels of killer bacteria such as E.coli and S.aureus. E.coli causes diarrhoea, stomach cramps and fever, while S.aureus causes skin infections such as pimples, boils and abscesses.

Two keyboards had dangerous levels of coliform bacteria that are found in faeces and cause gastroenteritis. One keyboard was five times dirtier than the toilet seat and home to 150 times the acceptable limit of bacteria. "(It) was increasing the risk of its user becoming ill," said the micro- biologist, James Francis.

"The common causes of contamination are the user's poor personal hygiene, particularly failing to wash hands properly after eating, sneezing or coughing or using the toilet," says Dr SK Sarin of GB Pant Hospital.

Bacteria are also found on shared surfaces such as desks. "The best protection is washing hands with soap and water, especially before eating, and avoid touching the face and mouth," says Dr Shiv Lal, director, National Institute of Communicable Diseases.

Source : MSN

Wednesday, May 28, 2008


Antioxidants are molecules which can safely interact with free radicals and terminate the chain reaction before vital molecules are damaged. Although there are several enzyme systems within the body that scavenge free radicals, the principle micronutrient (vitamin) antioxidants are vitamin E, beta-carotene, and vitamin C. Additionally, selenium, a trace metal that is required for proper function of one of the body's antioxidant enzyme systems, is sometimes included in this category. The body cannot manufacture these micronutrients so they must be supplied in the diet.

VITAMIN E : d-alpha tocopherol. A fat soluble vitamin present in nuts, seeds, vegetable and fish oils, whole grains (esp. wheat germ), fortified cereals, and apricots. Current recommended daily allowance (RDA) is 15 IU per day for men and 12 IU per day for women. It prevents the oxidation of fatty acids and protects every living cell in the body as their outer membrane is mainly composed of lipids. Other benefits of this vitamin include prevention of cataracts and coronary artery disease and helping immune function.
VITAMIN C : Ascorbic acid is a water soluble vitamin present in citrus fruits and juices, green peppers, cabbage, spinach, broccoli, kale, cantaloupe, kiwi, and strawberries. The RDA is 60 mg per day. Intake above 2000 mg may be associated with adverse side effects in some individuals.Vitamin C has powerful antioxidant properties and prevents oxidation of Vitamins A and E. In addition it is involved in cell and tissue repair, particularly helping to maintain the integrity of the vascular system by strengthening cellular walls of blood vessels. Vitamin C also boosts Immune function as it increases the production of interferons, these are natural immune stimulating chemicals that have an antiviral action.

Beta-carotene is a precursor to VITAMIN A (retinol) and is present in liver, egg yolk, milk, butter, spinach, carrots, squash, broccoli, yams, tomato, cantaloupe, peaches, and grains.Vitamin A is essential for a healthy immune system, normal cell reproduction, growth and repair of tissues. It is also necessary for maintaining the mucous membranes of the respiratory, digestive and urinary tract and for healthy skin. The skin is the body's first line of defence against invading microorganisms and other toxins.
TUMERIC ROOT: Curcumin, the active constituent of Tumeric is a strong antioxidant and is also an effective detoxifying agent as it protects the liver from many toxins. In addition it has antiviral and anti-inflammatory actions and helps to lower cholesterol.

BILBERRY: Anthocyanosides are the group of active compounds found in Bilberry, they are extremely powerful antioxidants having activities many times greater than Vitamins C and E. Also, unlike these Vitamins, Anthocyanosides give protection in both the watery and fatty parts of the body. Bilberry supports and strengthens collagen structure and is known to increase capillary blood flow, with overall benefits for the eyes and the cardiovascular system.

GRAPE SEED EXTRACT: Many botanical species contain active compounds called Oligomeric Proanthocyanidins (OPC's). Grape Seed Extract provides a concentrated source of OPC's, which are unique flavonols with excellent bioavailability and extremely powerful antioxidant activity, clinical studies indicate that they are fifty times more potent then Vitamin E and a hundred times more effective then Vitamin C. OPC's also repair and strengthen connective tissue, including that of the blood vessels and the cardiovascular system. They also have anti-inflammatory, anti-ageing and anti-carcinogenic action.

BOSWELLIA RESIN: Boswellic Acids have powerful anti-inflammatory and analgesic properties. This nutrient would benefit those who suffer from inflammatory conditions such as arthritis, which can be mediated by excessive levels of free radicals in the body.

SELENIUM: Selenium enhances the utilisation of Vitamin E and both nutrients work synergistically as antioxidants. Selenium is required for the formation of the enzyme Glutathione Peroxidase. This antioxidant enzyme protects body cells against oxidative damage by hydrogen peroxide, a type of free radical in the body which is converted to water. Selenium also plays an important role in protecting and maintaining the healthy function of vital body organs such as the heart, Liver, pancreas, thyroid glands and lungs and also promotes immune response to antibodies.

Preventing cancer and heart disease -- do antioxidants help?
Epidemiologic observations show lower cancer rates in people whose diets are rich in fruits and vegetables. This has lead to the theory that these diets contain substances, possibly antioxidants, which protect against the development of cancer.

Antioxidants are also thought to have a role in slowing the aging process and preventing heart disease and strokes, but the data is still inconclusive. Therefore from a public health perspective it is premature to make recommendations regarding antioxidant supplements and disease prevention. New data from ongoing studies will be available in the next few years and will shed more light on this constantly evolving area. Perhaps the best advice, which comes from several authorities in cancer prevention, is to eat 5 servings of fruit or vegetables per day.

Monday, May 26, 2008

Cause of disease in Human being

One of the research area of my interest which I would like to share.I have developed many of in-vitro assay for 'scavenging' of free radicals. Enzymes and substrates react to form a byproduct. The formation of these by products results in release of free radicals which leads to various kinds of diseases like cancer, heart attack, arthritis and many more. Let us know what are free radicals, how they are produced and three magical enzymes. Watch today's post labeled 'Free Radicals'.

Free Radicals

Highly reactive chemicals that often contain oxygen and are produced when molecules are split to give products that have unpaired electrons. This process is called oxidation.

Free radicals can damage important cellular molecules such as DNA or lipids or other parts of the cell. They are constantly attacking body proteins, carbohydrates, fats and DNA, causing potentially serious damage unless checked.

How Are Oxygen Free Radicals Produced in the Body?
Free radicals can originate in body cells in various ways. External radiation, including ultraviolet light, X-rays and gamma rays from radioactive material, is a potent source. Such radiation acts by breaking linkages between atoms, leaving the radicals with their unpaired electrons to wreak their damage. Free radicals occur in the course of various disease processes. In a heart attack, for instance, when the supply of oxygen and glucose to the heart muscle is cut off, the real damage to the muscle is caused by the vast numbers of free radicals that are produced.

Chemical poisoning of many kinds promotes free radicals, as does excessive oxygen intake from inhaling pure oxygen. The body's necessity to break down a wide range of drugs to safer substances (detoxification) also involves free radical production. The poisonousness (toxicity) of many chemicals and drugs is actually due either to their conversion to free radicals or to their effect in forming free radicals.

Inflammation—one of the commonest kinds of bodily disorder—is associated with free radical production, but the free radicals are probably the cause of the inflammation rather than the effect. However, the body actually uses free radicals to kill bacteria within the scavenging cells of the immune system—the phagocytes—and when excessive numbers of these are present in an inflamed area the free radical load almost certainly adds to the tissue damage, making everything worse. This is probably what happens in rheumatoid arthritis, for instance.

Three Magical Enzymes
The breakthrough that caused medical scientists really to begin to look seriously at free radicals was the astonishing discovery that the body actually produces large quantities of a substance (an enzyme) whose only function is to break down the dangerous superoxide free radical. This enzyme is SuperOxide Dismutase (commonly called SOD by the scientists). There is no reason to be rude about this marvelous enzyme, for we really need it. This enzyme converts dangerous superoxide free radicals to the less dangerous hydrogen peroxide. This is still fairly powerful stuff, capable of turning us all blonde, and is quite damaging to tissues. Happily, the body produces another enzyme, called Catalase, which immediately breaks down the hydrogen peroxide to water and oxygen, and all is well. There is a third natural antioxidant enzyme called, Glutathione peroxidase which also reduces hydrogen peroxide to water.

Each of these enzymes is made in cells under the instructions of a length of genetic code in DNA. Every cell in our bodies contains the instructions for making these three enzymes.

Friday, May 23, 2008

Anti-virulence Factor In Salmonella

Researchers at the University of British Columbia have discovered an anti-virulence factor in Salmonella, knowledge that could be used to design improved Salmonella vaccines. Virulence factors allow a pathogen to thrive in the host and cause disease. An anti-virulence factor controls the degree of infectiveness.

Salmonella are bacteria that infect a variety of vertebrae hosts. Salmonellosis, infection from Salmonella, can lead to gastroenteritis or typhoid fever -- a severe life-threatening systemic disease.

The finding, published in Public Library of Science, suggests that there is a distinct pathway in Salmonella that acts as an anti-virulence factor during salmonellosis. This pathway is also involved in fine-tuning the host-pathogen balance during salmonellosis.

The research demonstrates that the pathway is activated prior to ingestion and entry into the intestine and then shut off once Salmonella penetrates the intestine.

“When the anti-virulence factor is knocked out Salmonella becomes up to 10 times more virulent,” says Brett Finlay, Peter Wall Prof. of Microbiology and Biochemistry at UBC and senior investigator at the Michael Smith Laboratories. “The research also demonstrates that Salmonella has the ability to control its virulence even before it enters the host.”

“The pathway is designed to initially control the level of virulence and not kill the host immediately,” says Finlay. “Tapering the level of infectiveness allows Salmonella to establish itself in the host and then become more virulent.”

“This research will allow us to design improved salmonella vaccines,” says Finlay. “We will be able to better tailor the vaccine strain with the appropriate level of virulence.”Adapted from materials provided by University of British Columbia.
Souces: ScienceDaily

Bacteria Resistant Films Created

Bacteria-resistant Films Created: Microbe Adhesion Depends On Surface Stiffness.
Having found that whether bacteria stick to surfaces depends partly on how stiff those surfaces are, MIT engineers have created ultrathin films made of polymers that could be applied to medical devices and other surfaces to control microbe accumulation.

The inexpensive, easy-to-produce films could provide a valuable layer of protection for the health care industry by helping to reduce the spread of hospital-acquired infections, which take the lives of 100,000 people and cost the United States an estimated $4.5 billion annually.

The researchers, who describe their work in an upcoming issue of the journal Biomacromolecules, found they could control the extent of bacterial adhesion to surfaces by manipulating the mechanical stiffness of polymer films called polyelectrolyte multilayers. Thus, the films could be designed to prevent accumulation of hazardous bacteria or promote growth of desirable bacteria.
Van Vliet and her colleagues found the same trend in experiments with three strains of bacteria: Staphylococcus epidermidis, commonly found on skin, and two types of Escherichia coli.

Stiffness has usually been overlooked in studies of how bacteria adhere to surfaces in favor of other traits such as surface charge, roughness, and attraction to or repulsion from water. The new work shows that stiffness should also be taken into account, said Van Vliet.

Various methods include coating surfaces with antimicrobial chemicals or embedding metal nanoparticles into the surface, which disrupt the bacterial cell walls.

"For those bacteria that readily form biofilms, we have no delusions that we can prevent bacterial films from starting to form. However, if we can limit how much growth occurs, these existing methods can become much more effective," Rubner said.

Jenny Lichter, suggests that the films could also be used on medical devices that go inside the body, such as stents and other cardiac implants.

"Once a foreign object enters into the body, if you can limit the number of bacteria going in with it, this may increase the chances that the immune system can defend against that infection," said Thompson.

Another possible application for the films is to promote growth of so-called "good bugs" by tuning the mechanical stiffness of the material on which these bacteria are cultured. These films could stimulate growth of bacteria needed for scientific study, medical testing, or industrial uses such as making ethanol.

The researchers built their films, which are about 50 nanometers (billionths of a meter) thick, with layers of polyelectrolytes (a class of charged polymer). Alternating layers are added at different pH (acidity) levels, which determines how stiff the material is when hydrated at near-neutral pH, such as water. Polymer films assembled at higher pH (up to 6) are stiffer because the polymer chains crosslink readily and the polymers do not swell too much; those added at lower, more acidic pH (down to 2.5) are more compliant.

Van Vliet says the team's results could be explained by the relationship between surfaces and tiny projections from the bacterial cell walls, known as pili. Stiffer surfaces may reinforce stronger, more stable bonds with the bacterial pili. The researchers are now working on figuring out this mechanism.

Wednesday, May 21, 2008

'Microbes from Venus could be reaching earth every 540 days'

Planet Venus, written off for any sign of life, has microbes in its atmosphere which may well be reaching earth every 580 days, a Sri Lankan scientist has claimed.

Delivering the keynote address at the Annual General Meeting of the Association of Professional Sri Lankans in Britain at Baylis House in Slough, he said: "Every 580 days when the Sun, Venus and Earth are in a line, microbes from Venus can be transferred to Earth.

"The planets Venus, Earth, Mars are surely interconnected biologically and life on earth represents a connected chain of being that extends to the remotest corners of the cosmos," he said.

The second rocky planet from the sun, for a long time the bright "morning star" Venus has been talked about as a sister planet of earth and the habitat of not microbial but evolved intelligent life, some time ago.

In 1686, a French "man of letters" Bernard de Fontenelle wrote that the inhabitants of Venus resembled the Moors of Granada; a small black people, burned by the sun, full of wit and fire, always in love, writing verse, fond of music..."

But after 1960s scientists came to know the surface of the planet with lead melting heat did not resemble earth at all and was always covered with a thick layer of clouds of sulphuric acid droplets.

In the late 1970s and early 1980s, the idea that life is a truly cosmic phenomenon was championed by the late Sir Fred Hoyle and Chandra Wickramasinghe.

Life is harboured in comets (there are about 100 billion comets around our planetary system) and the injection of comet-borne bacteria introduced life to Earth and to every other habitable planet, according to Wickramasinghe's theory.

He said comets brought to earth not only life but all the life-sustaining water in earth's oceans.
The Oort Cloud, at the farthest reaches of the solar system from where the spectacular comets originate indicate it consists of organic matter, he said.

Microbial life could not only travel from the farthest reaches of the universe but also from planet to planet, he said.

At the conjunction of planets, when earth, venus and sun come to one line he said one to 10 grams of bacteria is transferred from venus to earth.

This kind of transfers could be of matter consisting of primitive life but also of evolved life.
Souces:The Hindu