Archive for the ‘Microbiology’ Category

Mystery solved: How bleach kills germs

Saturday, November 15th, 2008

Molecular, Cellular, and Developmental Biology Associate Professor Ursula Jakob Reuters – Molecular, Cellular, and Developmental Biology Associate Professor Ursula Jakob (L) and Jeannette Winter, …

CHICAGO (Reuters) – Bleach has been killing germs for more than 200 years but U.S. scientists have just figured out how the cleaner does its dirty work.

It seems that hypochlorous acid, the active ingredient in bleach, attacks proteins in bacteria, causing them to clump up much like an egg that has been boiled, a team at the University of Michigan reported in the journal Cell on Thursday.

The discovery, which may better explain how humans fight off infections, came quite by accident.

“As so often happens in science, we did not set out to address this question,” Ursula Jakob, who led the team, said in a statement.

The researchers had been studying a bacterial protein called heat shock protein 33, which is a kind of molecular chaperon that becomes active when cells are in distress, for example from the high temperature of a fever.

In this case, the source of the distress was hypochlorous acid or hypochlorite.

Jakob’s team figured out that bleach and high temperatures have very similar effects on proteins.

When they exposed the bacteria to bleach, the heat shock protein became active in an attempt to protect other proteins in the bacteria from losing their chemical structure, forming clumps that would eventually die off.

“Many of the proteins that hypochlorite attacks are essential for bacterial growth, so inactivating those proteins likely kills the bacteria,” Marianne Ilbert, a postdoctoral fellow in Jakob’s lab, said in a statement.

The researchers said the human immune system produces hypochlorous acid in response to infection but the substance does not kill only the bacterial invaders. It kills human cells too, which may explain how tissue is destroyed in chronic inflammation.

Hypochlorous acid is an important part of host defense,” Jakob said. “It’s not just something we use on our countertops.”

The Most Important Disease of a Most Important Fruit

Saturday, July 19th, 2008
Randy Ploetz
Tropical Research and Education Center,
University of Florida, IFAS, Homestead

Origins and importance of banana as a food crop
Banana is one of the most fascinating and important of all crops. It is a large monocotyledenous herb that originated in Southeast Asia. Virtually all of the cultivars that are grown are thought to have been selected as naturally occurring hybrids in this region by the earliest of farmers. In fact, Norman Simmonds proposed that banana was one of the first crops to be domesticated by man. In writing of the beginnings of agriculture in Southeast Asia, he concluded, “It seems a reasonable assumption that the bananas evolved along with the earliest settled agriculture of that area and may therefore be some tens of thousands of years old.”

Despite the current, clear understanding of its ancestry, the edible bananas’ origins are often confused in the literature. Almost all of the 300 or more cultivars that are known arose from two seeded, diploid species, Musa acuminata Colla and M. balbisiana Colla; they are diploid, triploid and tetraploid hybrids among subspecies of M. acuminata, and between M. acuminata and M. balbisiana.

Conventionally, the haploid contributions of the respective species to the cultivars are noted with an A and B. For example, the Cavendish cultivars that are the mainstays of the export trades are pure triploid acuminata and, thus, AAA. The Linnaean species M. paradisiaca (the AAB plantains) and M. sapientum (the sweet dessert bananas, of which Silk AAB is the type cultivar) are invalid and no longer used.

 

Women selling fruit of Dwarf Cavendish AAA  and Pisang awak ABB  in a market in Karonga, Malawi, East Africa. The lower photograph shows preparation of male buds of Pisang awak for cooking in a market in Sungai Kolok, Thailand. For many of the world’s poorest people, banana is a nutritious and important staple food. Click images for enlargement.

Banana is now one of the most popular of all fruits. Although it is viewed as only a dessert or an addition to breakfast cereal in most developed countries, it is actually a very important agricultural product. After rice, wheat and milk, it is the fourth most valuable food. In export, it ranks fourth among all agricultural commodities and is the most significant of all fruits, with world trade totaling $2.5 billion annually. Yet, only 10% of the annual global output of 86 million tons enters international commerce. Much of the remaining harvest is consumed by poor subsistence farmers in tropical Africa, America and Asia. For most of the latter producers, banana and plantain (which is a type of banana) are staple foods that represent major dietary sources of carbohydrates, fiber, vitamins A, B6 and C, and potassium, phosphorus and calcium.

This photograph shows seed-packed fruit of Musa balbisiana, one of the ancestors of the edible bananas. Since the edible cultivars are parthenocarpic and often female or male sterile, seeds are rarely found in their fruit. The latter factors, however, have made it difficult to improve this crop by breeding.

Impact of banana diseases
Diseases are among the most important factors in banana production worldwide. They are the reasons for which all of the world’s breeding programs were created and remain a primary focus of all current programs. Recently, diseases also became principal targets of biotechnological efforts to improve this crop and www-cgi.cnn.com/TECH/science/9807/24/t_t/banana.science/index.html ).

A leaf spot disease is the most important of these problems. Black Sigatoka, which is also known as black leaf streak, causes significant reductions in leaf area, yield losses of 50% or more, and premature ripening, a serious defect in exported fruit. It is more damaging and difficult to control than the related yellow Sigatoka disease, and has a wider host range that includes the plantains and dessert and ABB cooking bananas that are usually not affected by yellow Sigatoka.

Figure5sm.jpg (22695 bytes)

A close-up of the adaxial surface of a banana leaf that is affected by black Sigatoka. Under high rainfall and humidity, these lesions will coalesce and kill the entire leaf. Click image for enlargement.

Damage caused by black Sigatoka in a planting of Dwarf Cavendish AAA in Malawi, East Africa. Note the scarcity of healthy leaf tissue on plants that carry fruit. Yields from such plants are usually a half or less than that from healthy plants.
Click image for enlargement.

Figure6sm.jpg (57557 bytes)

In export plantations, Black Sigatoka is controlled with frequent applications of fungicides and cultural practices, such as the removal of affected leaves, and adequate spacing of plants and efficient drainage within plantation. In total, these are very expensive practices. For example, fungicide application includes the use of airplanes or helicopters, permanent landing strips and facilities for mixing and loading the fungicides, and the high recurring expense of the spray materials themselves. In total, it has been estimated that the costs of control are ultimately responsible for 15-20% of the final retail price of these fruit in the importing countries. Their great expense makes them essentially unavailable to small-holder farmers who grow this crop, it is these producers who are affected most by this important disease.

Figure7sm.jpg (60203 bytes)

Aerial application of fungicides to control black Sigatoka in Honduras. In the final analysis, the costs associated with these control measures are directly responsible for 15-20% of the purchase price of exported fruit in the importing countries. (Photo courtesy of R.H. Stover)
Click image for enlargement.

Distribution, etiology and epidemiology of black Sigatoka
Black Sigatoka was first recognized in the Sigatoka Valley of Fiji in 1963, but was probably widespread in Southeast Asia and the South Pacific by that time. In the Western Hemisphere, it first appeared in 1972 in Honduras and now occurs on the mainland from central Mexico south to Bolivia and northwestern Brazil, and in the Caribbean basin in Cuba, Jamaica, the Dominican Republic and southern Florida. In Africa, the disease was first recorded in Zambia in 1973 and has since spread throughout the sub-Saharan portions of that continent. In most areas, black Sigatoka has now replaced yellow Sigatoka to become the predominant leaf spot disease of banana.

Black Sigatoka is caused by the ascomycete, Mycosphaerella fijiensis Morelet [anamorph: Paracercospora fijiensis (Morelet) Deighton] (a variant of the pathogen, M. fijiensis var. difformis, that was previously reported in tropical America, is no longer recognized). The pathogen produces conidia and ascospores, both of which are infective. They are formed under high moisture conditions, and are disseminated by wind, and in the case of conidia, also by rain and irrigation water. Due to their greater abundance and small size, ascospores are more important than conidia in spreading the disease within plants and plantations. In contrast, infected planting material and leaves, which are used often in the developing world as packing materials, are usually responsible for the long-distance spread of the disease. The recent outbreak of black Sigatoka in South Florida almost certainly resulted from the importation of infected germplasm by local growers (see Plant Disease note D-1998-1217-03N).

Figure9sm.jpg (30787 bytes)

“Damn, how did this get here?” Dr. Jonathan Crane, Extension Tropical Fruit Crops Specialist for the University of Florida in Homestead, examines a leaf of the banana cultivar Rajapuri AAB that is affected by black Sigatoka. The importation of infected propagation material, which is a common and effective means for moving this disease long distances, was probably responsible for the recent outbreak of black Sigatoka in South Florida. Click image for enlargement.

Control
Chemical control of first yellow, and then black, Sigatoka has evolved considerably over the last 65 years. Bordeaux mixture, first used in the mid-1930s, has been replaced by several succeeding generations of protectant and, later, systemic fungicides. Presently, a sterol biosynthesis inhibitor, tridemorph, several different sterol demethylation inhibitors, most importantly propiconazole, and the methoxyacrylate, azoxystrobin, are the most commonly used systemics.

Since there is a tendency for resistance or tolerance to develop in M. fijiensis towards the systemic fungicides, they are usually applied in combination or alternation with broad-spectrum, protectant fungicides, such as the dithiocarbamates and chlorothalonil. With the exception of chlorothalonil, these fungicides are usually mixed with petroleum-based spray oils. The oils themselves are fungistatic and retard the development of the pathogen in the infected leaf. When they are mixed in water emulsions with fungicides, the resulting “cocktails” provide superior disease control.

The export plantations in the Philippines and Central and South America that produce fruit for the developed world are vast monocultures of Cavendish cultivars, usually of Grand Nain but also of Williams and Valery. In order to treat these large areas with fungicides, helicopters or fixed wing aircraft are used. Application schedules in the plantations are routinely determined with disease-forecast systems that incorporate data on disease severity within the plantation and environmental factors that are known to affect infection and disease development. These epidemiological tools enabled producers in Central America to substantially reduce the number of fungicide applications that were needed for control. However, increased tolerance in the pathogen to the DMI fungicides has made it necessary to increase applications in several countries in the region to previous frequencies of 25 - 40 per year.

Aerial view of an export plantation of the Cavendish cultivar Grand Nain in the Sula Valley of Honduras. Such vast monocultures allow fruit to be produced efficiently, but require that fungicides for black Sigatoka control be applied by aircraft. Click image for enlargement.

Figure11sm.jpg (16530 bytes)

The annual cost of fungicide applications in export plantations is about $1,000 per hectare. Although the international trades can add this expense to the price they charge for fruit, this is not an option for subsistence farmers. Thus, the latter producers must use different strategies to manage black Sigatoka. These include the removal of older leaves to reduce inoculum levels in a plantation, interplanting with other nonsusceptible crops, and planting in partial shade which results in less severe disease development.

The potential for bred bananas
Given the high expense of fungicides, their unavailability for subsistence farmers, and the recurring problem with fungicide resistance in the export plantations, it is clear that genetic resistance to black Sigatoka would be most useful. If resistant, agronomically acceptable cultivars were available, they would provide the best solution to this problem in export and subsistence situations alike.

Unfortunately, resistance to black Sigatoka among pre-existing banana genotypes is poor. The Cavendish cultivars that are used for export are so susceptible that nothing short of intensive fungicide application will control the disease in most areas. Resistant cultivars that could be used in subsistence situations are available, but they are usually less productive or desirable than those that are susceptible. This situation has begun to change as a result of new, resistant hybrids that are being developed by the banana breeding programs (http://www.promusa.org ).

The first program to make significant progress in improving this crop was that of the Fundación Hondureña de Investigación Agrícola (FHIA http://www.honduras.com/fhia/espamenu.htm) in La Lima, Honduras. It was begun by the United
Fruit Company (now Chiquita Brands http://www.chiquita.com) in 1959, but was donated to this private agricultural research foundation in 1984. FHIA has developed numerous dessert, plantain and cooking hybrids, several of which have been tested in the International Musa Testing Programme of the International Network for the Improvement of Banana and Plantain (http://bananas.bioversityinternational.org/). Results from these and other trials indicate that the FHIA clones are generally very vigorous and produce high yields under a wide range of environmental and edaphic conditions. Importantly, they resist pathogenically and geographically diverse populations of M. fijiensis, as well as two other major problems, Panama disease, (fusarium wilt) and nematodes.
Unfortunately, since they do not yet meet the high standards of the export trades, they have only been adopted for local consumption in East Africa, tropical America and the Caribbean.

In the future, products of the breeding programs will play increasingly important roles in subsistence agriculture. Whether new hybrids are used eventually to replace the Cavendish cultivars that are used by the export trades, however, remains to be seen. The very substantial infrastructure that characterizes export production is focussed on producing only these cultivars. Converting these operations to the production and handling of another type of banana would be an expensive proposition. Moreover, the currently available hybrids do not meet the very high standards for fruit quality and post-harvest shelflife that are demanded by the trades. Yet, as fungicides continue to lose their effectiveness against black Sigatoka, and as the practice of fungicidal disease control becomes more expensive and less appealing to consumers in the importing countries, the trades may eventually be forced into making the difficult transition away from the Cavendish clones.

References
Carlier, J., X. Mourichon,  D. Gonzâlez de León, M.F. Zapater, and M.H Lebrun. 1994. DNA restriction fragment length polymorphisms in Mycosphaerella species that cause banana leaf spot diseases. Phytopathology 84:751-756.

Carreel, F., S. Fauré, D. Gonzâlez de León, P.J.L. Lagoda, X. Perrier, F. Bakry, H. Tezenas du Montcel, C. Lanaud,  and J.P. Horry. 1994. Évaluation de la diversité génétique chez les bananiers diploïdes (Musa spp.). Genet. Sel. Evol. 26:125s-136s.

Fullerton, R.A., and  R.H. Stover (eds.). 1990. Sigatoka Leaf Spot Diseases of Banana: Proceedings of an International Workshop held at San José, Costa Rica, 28 March – 1 April, 1989. INIBAP. Montpellier, France. 374 pp.

Gauhl, F. 1994. Epidemiology and Ecology of Black Sigatoka (Mycosphaerella fijiensis Morlet) on Plantain and Banana (Musa spp.) in Costa Rica, Central America. Ph.D. dissertation, Universität Göttingen, 1989. (translated to English from German by INIBAP, Montpellier, France). 120 pp.

International Network for the Improvement of Banana and Plantain. 1994. Annual Report, 1993. Montpellier, France. 73 pp.

Kress, W.J. 1990. The phylogeny and classification of the Zingiberales. Annals of the Missouri Botanical Garden 77:698-721.

Mourichon, X., J. Carlier, and Fouré. 1997. Sigatoka leaf spot diseases. Musa Disease Fact Sheet No. 8. INIBAP, Montpellier, France. 4 pp.

Ortiz, R. 1995. Musa genetics. In: Gowen, S. (ed.) Bananas and Plantains. Chapman & Hall. London. pp. 84-109

Ploetz, R.C., and X. Mourichon. 1999. First report of black Sigatoka in Florida. (Disease Note) Plant Disease 83:300.

Rhodes, P.L. 1964. A new banana disease in Fiji. Commonwealth Phytopathological News 10:38-41.

Simmonds, N.W. and K. Shepherd. 1955. Taxonomy and origins of cultivated bananas. Journal of the Linneaen Society of Botany (London) 55:302-312.

Simmonds, N.W. 1966. Bananas. 2nd edition. Longmans. London. 512 pp.

Stover, R.H. 1980. Sigatoka leaf spot diseases of bananas and plantains. Plant Disease 64:750-756.

Scientists find bugs that eat waste and excrete petrol

Tuesday, June 17th, 2008

Microbes Clean Up Mercury: Bacteria could detoxify Native American artifacts

Saturday, June 7th, 2008
Web edition: www.sciencenews.org

 

BOSTON — In a sequel to the smallpox-contaminated blankets hand out, museums inadvertently began another round of toxic giving to Native Americans in the 1990s — returning headdresses and other artifacts that were laced with mercury. Now scientists are looking to a microbe that converts mercury into a form that evaporates, with hopes of cleaning up the artifacts before giving back more of them to their rightful tribes.

“Do we give them something covered in mercury just to have given them their things back? No — it is not OK,” says Munira Albuthi, a microbiologist at the University of Colorado Denver who did the research to see if such a microbial method is possible. “Mercury is a potent neurotoxin.”

The neurotoxic effects of headgear laced with mercury had been recognized anecdotally for years. At Alice’s tea party, the Mad Hatter wasn’t angry — he was crazy from wearing and working with hats, which used to be cured with mercury.

The 1990 Native American Graves Protection and Repatriation Act required federal agencies and institutions to return Native American cultural items and remains to their respective peoples. But when museums began giving back ceremonial head gear and other artifacts, many of the recipients ended up ill. The specimens were laced with mercury, a component of the pesticides that museums had used for years for preservation.

Once the problem of the poisoned artifacts was recognized, scientists had to figure out a culturally sensitive means of getting rid of the toxin.

“A lot of tribes see these artifacts as live spirits — these are relatives to a lot of people,” says Albuthi, who presented the work in Boston at the 108th meeting of the American Society for Microbiology. “So we needed to use something you would be OK with using on yourself.”

Albuthi began working with Cupriavidus metallidurans, a microbe that flourishes on metal and is not dangerous to humans. It has a set of proteins that turns mercury into a form that evaporates into the air. After contaminating paper, a watery broth and auger plates with the neurotoxin, she used a pipette to put the bacterium onto the items. Seven days later, 40 percent of the mercury had been removed from the broth, 50 percent was removed from the auger plates and 60 percent was removed from the paper. Because paper is porous and organic, it is most like the specimens that museums are dealing with, she notes.

Albuthi also investigated whether different temperatures or humidities enhanced the microbes’ mercury-morphing powers. She found that the microbes worked best at room temperature and 60 percent humidity, with about 80 percent of the mercury evaporated from the items.

The experiments used mercury concentrations of 10 parts per million, which are much higher than the quantities on most museum specimens, says Albuthi. “So maybe we’ll be able to get 100 percent, if there isn’t as much to begin with,” she says.

“This is a very interesting and particularly challenging project. They were very constrained in terms of what they could treat things with,” comments Gregory Hecht, a microbiologist at Rowan University in Glassboro, N. J. “And microbes are probably the best way to get around the issue.”

Smart Microbes - Bacteria Anticipate Changing Environments

Thursday, May 8th, 2008
Science News
Web edition: www.sciencenews.org
It doesn’t take brains to have some smarts. New research shows that even bacteria can evolve to predict upcoming events based on clues, like a dog salivating at the sound of the dinner bell.

“It’s really the first evidence that single-celled organisms — bacteria — also have this ability for associative learning,” says Saeed Tavazoie, a molecular biologist at Princeton University who led the research on E. coli bacteria.

The discovery reveals a kind of predictive intelligence in how microbes interpret sensory cues from their environments. Understanding how this predictive ability affects bacteria’s behavior could help scientists control microbes better, benefitting industry and the treatment of infectious diseases.

When E. coli enters a person’s body, its environment immediately becomes warmer. Later, as the microbe moves into the person’s gut, oxygen becomes scarce. Tavazoie and his colleagues found that warm temperatures alone triggered the microbes to switch to a less efficient, low-oxygen mode. The bacteria anticipated the coming lack of oxygen and were preparing for it, the researchers reported online May 8 in Science.

This proactive behavior challenges the view that microbes can only react after-the-fact to changes that occur in their environments.

“Sometimes people fall into this trap of sort of thinking that neurons are the only game in town for learning adaptive behavior,” comments Dave Ackley, an artificial life researcher at the University of New Mexico in Albuquerque.

Bacteria obviously have no brains or nervous systems. Instead, the microbes learn through evolutionary changes in their complex networks of interacting genes and proteins. Over hundreds of generations, the “intelligence” needed to predict a coming event based on present clues becomes encoded in these networks.

An individual bacterium can’t learn this way; later generations gain this embedded intelligence over evolutionary time. “Of course microbes can’t tell the future, but they can make educated guesses about the future based on how natural selection and past experiences have shaped their gene regulatory networks,” comments Richard Losick, a microbial geneticist at Harvard University.

Tavazoie’s team also showed that, over many generations, the bacteria can “unlearn” the link between rising temperatures and dropping oxygen. When the scientists grew the microbes in controlled conditions that divorced the rise in temperature from a change in oxygen levels, the microbes stopped anticipating lower oxygen levels after a few hundred generations.

“This new way of thinking about bacteria behavior is important not just in the industrial setting where we want them to do things, make things, but also for infectious diseases where we want to control their growth,” Tavazoie says. Outside of a person, many infectious bacteria become semi-dormant, conserving energy because environmental cues indicate that rough times are ahead. Understanding how the microbes’ gene networks process these environmental signals could lead to ways to trick the bacteria into remaining in a slow-growth mode inside of people as well.

“There’s some hope that we could engineer some changes in environment for them, by the way we design our flu vaccines for example, to sort of fake them out,” Ackley says.

Slowing the microbes down instead of killing them with antibiotics could prevent the spread of antibiotic-resistant strains of diseases, Tavazoie says.