Archive for the ‘Biotechnology’ 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.”

Fish Tale Has A DNA Hook - Students Find Bad Labels

Friday, August 22nd, 2008

From the New York Times - August 22, 2008

Many New York sushi restaurants and seafood markets are playing a game of bait and switch, say two high school students turned high-tech sleuths.

In a tale of teenagers, sushi and science, Kate Stoeckle and Louisa Strauss, who graduated this year from the Trinity School in Manhattan, took on a freelance science project in which they checked 60 samples of seafood using a simplified genetic fingerprinting technique to see whether the fish New Yorkers buy is what they think they are getting.

They found that one-fourth of the fish samples with identifiable DNA were mislabeled. A piece of sushi sold as the luxury treat white tuna turned out to be Mozambique tilapia, a much cheaper fish that is often raised by farming. Roe supposedly from flying fish was actually from smelt. Seven of nine samples that were called red snapper were mislabeled, and they turned out to be anything from Atlantic cod to Acadian redfish, an endangered species.

What may be most impressive about the experiment is the ease with which the students accomplished it. Although the testing technique is at the forefront of research, the fact that anyone can take advantage of it by sending samples off to a laboratory meant the kind of investigative tools once restricted to Ph.D.’s and crime labs can move into the hands of curious diners and amateur scientists everywhere.

The project began, appropriately, over dinner about a year ago. Ms. Stoeckle’s father, Mark, is a scientist and early proponent of the use of DNA bar coding, a technique that greatly simplifies the process of identifying species. Instead of sequencing the entire genome, bar coders — who have been developing their field only since 2003 — examine a single gene. Dr. Stoeckle’s specialty is birds, and he admits that he tends to talk shop at the dinner table.

One evening at a sushi restaurant, Ms. Stoeckle recalled asking her father, “Could you bar code sushi?”

Dr. Stoeckle replied, “Yeah, I think you could — and if you did that, I think you’d be the first ones.”

Ms. Stoeckle, who is now 19, was intrigued. She enlisted Ms. Strauss, who is now 18.

Their field technique was simple, Ms. Stoeckle said. “We ate a lot of sushi.”

Or, as Dr. Stoeckle put it, “It involved shopping and eating, in which they were already fluent.”

They hit 4 restaurants and 10 grocery stores in Manhattan. Once the samples were home, whether in doggie bags or shopping bags, they cut away a small piece and preserved it in alcohol. They sent those off to the University of Guelph in Ontario, where the Barcode of Life Database project began. A graduate student there, Eugene Wong, works on the Fish Barcode of Life (dubbed, inevitably, Fish-BOL) and agreed to do the genetic analysis. He compared the teenagers’ samples with the global library of 30,562 bar codes representing nearly 5,500 fish species. (Commercial labs will also perform the analysis for a fee.)

Three hundred dollars’ worth of meals later, the young researchers had their data back from Guelph: 2 of the 4 restaurants and 6 of the 10 grocery stores had sold mislabeled fish.

Dr. Stoeckle said he was excited to see a technology used in a new way. “The smaller and cheaper you make something,” he said, “the more uses it has.” He compared bar coding to another high-tech wonder turned everyday gadget, GPS.

Eventually, he predicted, the process will become more automatic, cheaper and smaller so that a handheld device could perform a quick analysis and connect to the database remotely. What his daughter did, he said, is like dropping film off at the supermarket for developing. The next generation could be more like a digital camera that displays the results on the spot.

The results of Ms. Strauss and Ms. Stoeckle’s research are being published in Pacific Fishing magazine, a publication for commercial fishermen. The sample size is too small to serve as an indictment of all New York fishmongers and restaurateurs, but the results are unlikely to be a mere statistical fluke.

The experiment does serve as a general caveat emptor for fish lovers, particularly because the students, their parents and their academic mentor all declined to give the names of the vendors, citing fear of lawsuits. Besides, they noted, mislabeling could occur at any stage of the process.

Dr. Stoeckle was willing to divulge the name of one fish market whose products were accurately labeled in the test: Leonards’ Seafood and Prime Meats on Third Avenue. John Leonard, the owner, said he was not surprised to find that his products passed the bar code test. “We go down and pick the fish out ourselves,” he said. “We know what we’re doing.” As for the technology, Mr. Leonard said, “it’s good for the public,” since “it would probably keep restaurateurs and owners of markets more on their toes.”

Ms. Stoeckle said the underlying message of the research was simple: “If you’re paying for white tuna and you’re eating tilapia, I think you’d want to know that.”

Although the students did not present the project for a grade at school, they made sure to mention it on their college applications. Both will enroll at Johns Hopkins University this fall.

Neither, however, expects to major in the sciences. “I’ve always been into art history,” Ms. Strauss said, “which is really different from this.” Ms. Stoeckle, who is the granddaughter of the entertainer and arts patron Kitty Carlisle Hart, is thinking about studying writing or psychology. But that, they said, is the point. “If we found it interesting — which we did — I think lots of people like us can do it, too,” Ms. Stoeckle said.

Peter B. Marko, a professor at Clemson University who used a more detailed genetic technique in a 2004 paper to show that red snapper was commonly mislabeled, called their project “quite remarkable,” though he added that genetic analysis had been simplified to the point that high school students could now perform the task without sending samples off.

Mr. Marko prefers to work with whole genomes — “more information is better,” he explained — which can be sequenced now with lightning speed. He plans to perform a broad genetic comparison of fishes that were separated millions of years ago by the rise of the Isthmus of Panama. “The technology is allowing us to ask questions that really would not have been possible in the past.”

The students worked under the tutelage of Jesse H. Ausubel of Rockefeller University, a champion of the DNA bar coding technique. As for Ms. Strauss and Ms. Stoeckle, Dr. Ausubel said they “have contributed to global science” by adding to the database, built on a model similar to that of Wikipedia, in which people around the world can contribute.

In a way, Dr. Ausubel said, their experiment is a return to an earlier era of scientific inquiry. “Three hundred years ago, science was less professionalized,” he said, and contributions were made by interested amateurs. “Perhaps the wheel is turning again where more people can participate


Genome of simplest animal reveals ancient lineage, confounding array of complex capabilities

Friday, August 22nd, 2008
As Aesop said, appearances are deceiving—even in life’s tiniest critters. From first detection in the 1880s, clinging to the sides of an aquarium, to its recent characterization by the U.S. Department of Energy Joint Genome Institute (DOE JGI), a simple and primitive animal, Trichoplax adhaerens, appears to harbor a far more complex suite of capabilities than meets the eye. The findings, reported in the August 21 online edition of the journal Nature, establish a group of organisms as a branching point of animal evolution and identify sets of genes, or a “parts list,” employed by organisms that have evolved along particular branches.
With each sequenced genome, another dataset is made available to advance the quest of evolutionary biologists seeking to reconstruct the tree of life. The analysis of the 98 million base pair genome of Trichoplax (literally “hairy-plate”) illuminates its ancestral relationship to other animals. Trichoplax is the sole member of the placozoan (”tablet,” or “flat” animal) phylum, whose relationship to other animals, such as bilaterians (humans, flies, worms, snails, et al) and cnidarians (jellyfish, sea anemones, corals, et al), and sponges is contentious.

“Our whole genome analysis supports placing the placozoans after the sponge lineage branched from other animals,” said Daniel Rokhsar, the publication’s senior author, DOE JGI’s head of Computational Genomics Program, and Professor of Genetics, Genomics and Development at the University of California, Berkeley.

“Trichoplax has had just as much time to evolve as humans, but because of its morphological simplicity, it is tempting to think of it as a surrogate for an early animal,” said Mansi Srivastava, the study’s first author, a graduate student under the direction of Rokhsar, at the Center for Integrative Genomics, U.C. Berkeley.

Earlier mitochondrial DNA studies suggested that this “mother of all metazoans,” Trichoplax, was the earliest branch, before sponges diverged, but this remains debatable—even among collaborators.

“The latest and most complex analysis again suggests that placozoans populated the oceans long before sponges evolved,” said Bernd Schierwater, director of the Institute of Animal Ecology & Cell Biology and head of the Center for Biodiversity at TiHo Hannover, Germany. Schierwater, a study co-author, joined Stephen Dellaporta and Leo Buss of Yale University in proposing the Trichoplax sequencing project in 2004 to DOE JGI’s Community Sequencing Program [].

“The outcome of the Trichoplax adhaerens genome sequencing is so exciting that we are now culturing another 13 placozoan species in order to identify the most basal placozoan lineage and genome,” said Schierwater.

“Trichoplax is an ancient lineage—a good representation of the ancestral genome that is shedding light of the kinds of genes, the structures of genes, and even how these genes were arranged on the genome in the common ancestor 600 million years ago,” said Srivastava. “It has retained a lot of primitive features relative to other living animals.”

Originally collected from the Red Sea, and cultured over the last 40 years in the laboratory, Trichoplax is a two-millimeter flat disk containing fluid sandwiched between two cell layers. It lacks organs and only has four or five cell types. Yet, despite its apparent simplicity, its genome encodes a panoply of signaling genes and transcription factors usually associated with more complex animals.

Trichoplax has no neurons, but has many genes that are associated with neural function in more complex animals. “It lacks a nervous system, but it still is able to respond to environmental stimuli. “It has genes, such as ion channels and receptors, that we associate with neuronal functions, but no neurons have ever been reported,” explained Rokhsar.

Of the 11,514 genes identified in the six chromosomes of Trichoplax, 80 percent are shared with cnidarians and bilaterians. Trichoplax also shares over 80 percent of its introns—the regions within genes that are not translated into proteins—with humans. Even the arrangement of genes is conserved between the Trichoplax and human genomes. This stands in contrast to other model systems such as fruit flies and soil nematodes that have experienced a paring down of non-coding regions and a loss of the ancestral genome organizations.

With its pancake shape, gutless feeding, and genomic primitiveness, the rich array of metabolic capabilities begs additional consideration. While it has been observed to motor around via cilia, eat by mounting its prey, and reproduce by fission (pulling itself into pieces)—it may in fact have a secret sex life.

“Some of our new placozoan species show frequent sexual reproduction while others never show any signs of sex,” said Schierwater. “The genome data allow us to search for the genes responsible for sex and life cycle complexity.”

“It’s remarkable that we have the whole genome sequence but we still know so little about this animal in the wild,” said Rokhsar. “Hopefully the genome sequence will stimulate more studies of this enigmatic creature.”

Source: DOE/Joint Genome Institute

Shark-Inspired Boat Surface

Sunday, August 10th, 2008

Materials Engineers Turn to Ferocious Fish for Nonstick Ship Coating

May 1, 2005 — Researchers are using shark skin as a model for creating new coatings that prevent adhesion of algae and barnacles to boats. The new coating is modeled after sharks’ placoid scales, which have a rectangular base embedded in the skin with tiny spines or bristles that poke up from the surface that prevent things from attaching to the shark’s skin.

GAINESVILLE, Fla.–In the boating industry, a huge problem exists that can be summed up in three words — algae, barnacles and slime. Until now, the only way to prevent these organisms from growing was toxic paint. But researchers are studying a more natural approach that’s inspired by the ocean’s fiercest predator.

In movies, they’re the enemy, but in the world of science, sharks are allies.

Materials engineer Tony Brennan, of University of Florida in Gainesville, uses shark skin as a model for creating new surfaces. “The shark scales have a roughness that approximates the roughness that we had predicted would be a good roughness to stop adhesion,” he says.

Brennan designed the surfaces to prevent algae and barnacles from growing on boats. He says, “We started making surfaces that are mimicking the shark’s skin.”

A computer program helped researchers create the pattern and structure…

“Whatever we can draw, we can make into a surface,” says UF graduate student, Jim Schumacher.

And just like shark skin, spores can’t fit in the ridges and don’t want to balance on top of the surface Brennan and his team designed in the lab. “That’s a tremendous benefit to energy consumption, dollars and maintenance,” Brennan says.

Getting rid of those barnacles and other organisms would mean less cleaning and not having to drag around the extra weight would lower fuel costs.

“If it’s effective, it would tremendously affect the industry,” Emerson says.

When the surface hits the market in the next year, it could impact private boaters and Navy vessels, too. Researchers are also studying the shark-coated surface for medical applications.

World’s Smallest Snake Discovered

Sunday, August 3rd, 2008
World’s smallest snake discovered

By Jennifer Carpenter
Science reporter, BBC News

The world’s smallest snake, averaging just 10cm (4 inches) and as thin as a spaghetti noodle, has been discovered on the Caribbean island of Barbados.

The snake, found beneath a rock in a tiny fragment of threatened forest, is thought to be at the very limit of how small a snake can evolve to be.

Females produce only a single, massive egg - and the young hatch at half of their adult body weight.

This new discovery is described in the journal of Zootaxa.

The snake - named Leptotyphlops carlae - is the smallest of the 3,100 known snake species and was uncovered by Dr Blair Hedges, a biologist from Penn State University, US.

“I was thrilled when I turned over that rock and found it,” Dr Hedges told BBC News.

“After finding the first one, we turned hundreds of other stones to find another one.”

In total, Dr Hedges and his herpetologist wife found only two females.

Defining species

Dr Hedges thinks that the snake eats termites and is endemic to this one Caribbean island. He said that, in fact, three very old specimens of this species were already in collections - one in London’s Natural History Museum and two in a museum in Martinique.

However, these specimens had been misidentified.

Dr Hedges explained the difficulty in defining a new species when the organism is so small.

“Differences in small animals are much more subtle and so are frequently over-looked,” he said.

Modern genetic fingerprinting is often the only way to tell species apart.

“The great thing is that DNA is as different between two small snakes as it is between two large snakes, allowing us to see the differences that we can’t see by eye,” explained Dr Hedges.

Researchers believe that the snake - a type of thread snake - is so rare that it has survived un-noticed until now.

But with 95% of the island of Barbados now treeless, and the few fragments of forest seriously threatened, this new species of snake might become extinct only months after it was discovered.

Smallest of the small

In contrast to other species of snake - some of which can lay up to 100 eggs in a single clutch - the world’s smallest snake only produces a single egg.

“This is unusual for snakes but seems to be a feature of small animals,” Dr Hedges told BBC News.

By having a single egg at a time, the snake’s young are one-half the length of the adult. That would be like humans giving birth to a 60-pound (27kg) baby

Dr Hedges added that the snake’s size might limit the size of its clutch.

“If a tiny snake were to have more than one offspring, each egg would have to share the same space occupied by the one egg and so the two hatchlings would be half the normal size.”

The hatchlings might then be too small to find anything small enough to eat.

This has led the researchers to believe that the Barbadian snake is as small as a snake can evolve to be.


The smallest animals have young that are proportionately enormous relative to the size of the adults producing the offspring   As in the case of Leptotyphlops carlae , the hatchlings of the smallest snakes are one-half the length of an adult  The hatchlings of the biggest snakes on the other hand are only one-tenth the length of the adult producing the offspring  Tiny snakes produce only one massive egg - relative to the size of the mother. This is evolution at work, says Dr Hedges  The pressure of natural selection means the size of hatchlings cannot be smaller than a critical limit if they are to survive.

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 ).

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.

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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.

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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.

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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).

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“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.

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.

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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 ( ).

The first program to make significant progress in improving this crop was that of the Fundación Hondureña de Investigación Agrícola (FHIA in La Lima, Honduras. It was begun by the United
Fruit Company (now Chiquita Brands 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 ( 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.

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

Detangling DNA

Saturday, June 7th, 2008
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Deep inside our cells, the DNA that encodes the mysteries of our individuality twines into tidy little spiral staircases neatly side by side — or so we might imagine.

Consider, though, that if you scale up the nucleus of a cell to the size of a basketball, each molecule of DNA inside it would resemble fishing line more than four miles long. And now consider what happens to your iPod headphones when you cram them into a pocket: Invariably, it seems, they tangle. And they’re only a foot long!

Now you have a picture of the gargantuan task your cells face in managing the snarls that form in DNA. Storing the DNA isn’t a problem because the cell can pack each strand systematically into a tidy, tight ball. And for some tasks, the cell can just unwind the ball a bit, keeping the unruly strands in check. But when the cell needs to snip the DNA and rearrange its genetic sequence, the strands almost unavoidably kink into a tangled mess.

Researchers have found that DNA can form incredibly complex knots, sometimes with dozens of crossings. But now a pair of mathematicians has shown that DNA can only form certain kinds of knots, not any knot at all. The discovery may help biologists understand site-specific recombination, the way that cells perform surgery on their DNA.

Although we tend to think of our genetic sequence as being fixed at conception, cells occasionally need to shuffle specific bits of their DNA around. Cells might reverse a small stretch of a sequence or move a section from one strand to another. Brewer’s yeast, for example, uses recombination just before cell division to prepare its DNA to divide rapidly. Viruses use recombination to insert their own DNA into the host cell, tricking the cell into producing thousands of copies of the virus. And recombination is our tool when we create genetically engineered cells.

But the process almost always causes some nasty knots. To alter the genetic sequence, specialized enzymes grab two pieces of DNA, snip them apart, bring the ends together, reshuffle the genetic sequence between them and rejoin the ends. Because the DNA is so tightly packed together, this process often ends with strands wound around themselves or one another, forming a knot or link. Another type of enzyme cleans up the mess afterward, snipping strands, passing them through others and reattaching them until the knot is unwound.

Biologists still don’t understand very well how recombination works. “What you really want is to see an enzyme attaching to the DNA and watch it dragging it around,” says Dorothy Buck, a mathematical biologist at Imperial College London. “You want a YouTube video of the whole process, but you can’t get it.” Current technology in microbiology only allows for still images. And even getting still images of knotted DNA is very tricky.

Biologists have managed to learn some things about how recombination works, though. Buck and her collaborator Erica Flapan of Pomona College in Claremont, Calif., found three rules governing the behavior of the enzymes that perform the recombination. The precise path the enzymes take and the way they perform their surgery determines the knot that is formed. Buck and Flapan realized that their rules meant that site-specific recombination could twist the DNA only into particular knots and links, and they applied knot theory to figure out which ones they were. Only a small proportion of the very complicated knots could occur in DNA, they found.


Narrowing down the possible knots could in turn shed light back on the activities of the enzymes. Ultimately, this could help researchers use site-specific recombination to repair the faulty DNA that causes genetic diseases.

Microbes Clean Up Mercury: Bacteria could detoxify Native American artifacts

Saturday, June 7th, 2008
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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.”

One Gene, Many Shapes

Tuesday, May 13th, 2008
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A genetic dimmer switch fine-tunes leaf variation in tomato plants

A single gene may act like a genetic dimmer switch, fine-tuning leaf variation between tomato plants. The gene reveals another way evolution can increase natural variation, and hints at the genetic basis of species distinction.

Plant biologist Neelima Sinha and her colleagues looked at two tomato plants from the Galapagos Islands. The leaves of the tomato plant Solanum galapagense look like snowflakes — branching and forking into a series of smaller leaflets. A close relative Solanum cheesemaniae boasts more demure leaves that branch only once.

The team found that the intricate leaf pattern of S. galapagense is caused by a single deletion from its genetic code, says Sinha of the University of California, Davis. The snipped gene spurs S. galapagense to produce more of a protein needed for new leaf formation, the team reports in the May Current Biology.

The study links taxonomy, which scientists use to categorize different species, to genetic differences, says David Spooner, a plant biologist at the University of Wisconsin–Madison who was not involved in the research. He notes that the work characterized the genetic basis for the main taxonomic species distinction — leaf variation — between S. galapagense and S. cheesemaniae.

“This is a wonderful study,” Spooner says. “It gets to the question, how much genetic change does it take to make a species?”


Sinha and her colleagues found that the plant gene acts like a molecular dimmer switch, fine-tuning the amount leaves branch. While that in itself is not unexpected, what’s exciting is the way it does so. The variation in S. galapagense’s blueprint is in a promoter region — a kind of genetic foreman in the DNA that encourages more protein production downstream. Instead of changing the chemical makeup of the end product, the genetic tweak simply pumps up its output.

Scientists used to think that evolution only proceeded gradually and that any visible change in an organism’s physical appearance would involve complex genetic changes. But the new work is one of a growing number of recent studies that reveals how tiny changes to the DNA code can cause dramatic shifts in physical appearance.

It also reveals another way evolution increases natural variation. Since plants that grow in shade tend to have more leaf surface area to collect the dimmer sunlight, this single change in leaf pattern might have enabled S. galapagense to thrive in a shadier inland habitat than its strictly coastal cousin. “In the Galapagos these two tomatoes have very distinct environments,” Sinha says. “They’re adapted to different shade and water habitats.”