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Gut microbes fatten up

Unfortunate combinations of genetics and environment are often eyed as culprits in obesity. But now researchers are considering another offender: a particular type of microbe in the gut. A study in mice has found that a tiny gut archaean, a member of a class of one-celled organisms resembling bacteria, may influence how many ingested calories turn into fat. Hundreds of types of microbes live in the gut, where they break down many types of food. One common target is polysaccharides, found in everything from corn syrup to wheat products. Gut microbes chop polysaccharides into short-chain fatty acids that account for up to 10% of a person’s daily calorie intake. Two years ago, gastroenterologist Jeffrey Gordon of Washington University in St. Louis, Missouri, and colleagues found that gut microbes can influence how many calories are transformed into fat, but they couldn’t tell exactly which organisms were responsible. Recently, Gordon began to suspect archaeans. Because archaeans consume some leftovers of bacterial digestion of polysaccharides, such as hydrogen, Gordon had a hunch they might speed up digestion, possibly causing an animal to get fatter.

Gordon and his graduate student Buck Samuel turned to three common gut microbes. Two were bacteria, Desulfovibrio piger and Bacteroides thetaiotaomicron, and the third was an archaean called Methanobrevibacter smithii. The pair created mice lacking any gut microbes and then gave them various combinations of the archaeans and the two bacteria. All the mice received the same amount of food. But animals that got the archaean M. smithii and the bacterium B. thetaiotaomicron were about 54% fatter than mice given the bacteria alone. By analyzing more carefully how the microbes interacted in the lab, researchers found that the archaeans actually changed the behavior of B. thetaiotaomicron, so that the bacteria would covet the more plentiful polysaccharides in the diet known as fructans, the pair report online this week in the Proceedings of the National Academy of Sciences. “At least in our system, this helps the host get more calories from its diet,” says Samuel.

Microbiologist Martin Blaser of New York University says the findings are convincing and are “beginning to establish a scientific basis” for a lingering theory that hasn’t gotten much attention. “Changes in microbial composition of the human body are contributing to this phenomena of obesity,” says Blaser, opening up a potentially new field of study in obesity research.

ScienceNow Magazine
July 3, 2006

Original web page at ScienceNow Magazine

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Ancient rocks ‘built by microbes’

Odd-shaped rocks in the Pilbara region of Western Australia offer compelling evidence they were built by microbes 3.43 billion years ago, scientists say. The structures, known as stromatolites, could only have taken the forms they have if bacteria had been present, a Sydney-led team tells Nature journal. The rocks’ origin is disputed, with some claiming purely chemical processes could have made them. But the Nature study suggests the biological explanation is the simplest. “For all these shapes to be formed a-biologically would have required highly unusual and unexpected chemical processes to occur simultaneously in this [one location],” said Abigail Allwood from the Australian Centre for Astrobiology. “It just becomes ridiculous to support that hypothesis; especially when the biological explanation is so readily acceptable.”

Ms Allwood and colleagues have made an extensive survey of a 10km (six miles) stretch of land not far from the town of Marble Bar. The area is now well inland but shows clear evidence of having been covered by a shallow sea in the ancient past. The researchers have detailed an array of unusual sedimentary structures – seven clear types in all. Some look like upside-down ice cream cones; others resemble egg cartons. These laminated structures have been described as stromatolites – the rock piles that in more recent settings are known to have been built by mats of microbes capturing grains and sticking them together. But the Pilbara structures, found 30 years ago in a rock formation called the Strelley Pool Chert, are controversial. Claims for individual microfossils of the original organisms within Pilbara’s stromatolites have been challenged; and some scientists prefer an entirely non-biogenic explanation for the structures’ creation. These dissenters believe the piles resulted from the chemical precipitations that occurred around undersea volcanic vents.

Allwood’s response has been to describe the complexity of shapes and explain how these forms can be linked to different environmental niches in a shallow-sea reef setting. “We have found an ecosystem-scale remnant of the early biosphere. It’s not just a couple of individual or isolated fossils or dubious structures; it is in an entire, pretty well intact, section of hundreds of thousands of stromatolites in a reef ecosystem,” Ms Allwood told the BBC News website.
“With that we now gain insight into the conditions that nurtured early life – the biological responses to different environmental processes.” The variety points to an entire ecosystem, say the scientists. The Pilbara stromatolites are not the oldest claim for life on Earth.

Some researchers argue that rocks at Isua in Greenland show the imprint of life at least 3.75 billion years ago. At that time, these rocks were also on the sea bed. Thin layers of black sediment, separated by distinct layers of volcanic ash, look like they could be composed of the debris of ocean-dwelling microbes. There are no fossil forms, but the nature of the carbon is consistent with the idea it was processed by living organisms. There are no known older remnants of the Earth’s surface than the Greenland rocks – which probably makes Isua the closest science can ever get to the first life. Researchers are keen to trace the story of the first microbes on Earth because it should provide clues in the hunt for possible life elsewhere in the Solar System.

Mars rovers should look out for stromatolite-like structures. The type of study conducted on the Pilbara stromatolites might, for example, help scientists interpret similar structures on Mars, should rovers sent to the planet ever come across them. Commenting on this dimension, Dr Ian Crawford, a planetary scientist at Birkbeck College, London, UK, said: “Searching for ancient stromatolite-like structures such as those reported by Allwood et al should certainly be high on the list of future exploration strategies. “However, given the amount of fieldwork performed by Allwood and colleagues, it must be doubtful whether purely robotic exploration of Mars would be able compellingly to identify such features in the field, and in the longer term effective Martian palaeontology may necessitate human exploration of the planet.”

BBC News
June 20, 2006

Original web page at BBC News

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Innocuous intestinal bacteria may be reservoir for resistance

“Harmless” bacteria in the digestive tracts of dairy cows, may not be so harmless after all. They may be a reservoir for antibiotic resistance genes that can be transferred to more harmful, disease-causing bacteria, according to research presented at the 106th General Meeting of the American Society for Microbiology in Orlando, Florida. “There is concern that veterinary therapeutic usage of antibiotics in animals is responsible for the emergence of drug-resistant Salmonella. For dairy farms recently surveyed in Georgia, there was no association found between antibiotic use and isolation of multi-drug resistant Salmonella. Where does the drug resistance in Salmonella originate?” says Susan Sanchez of the University of Georgia, who conducted the study with other researchers from the University of Georgia and the Universidad Complutense of Madrid.

Using DNA-based technology Sanchez and her colleagues discovered that a significant number of non-pathogenic, commensal bacteria isolated from cow manure contain the same antibiotic-resistance genes as those found in multi-drug resistant Salmonella strains found on the same farm. In addition, isolation of antibiotic-resistant Salmonella appears to be associated with whether or not commensal bacteria carry these resistance genes rather than antibiotic use on the farm. “This work suggests that mobile DNA elements like plasmids are responsible for the rapid spread of drug resistance on farms. Ecology appears to play a more important role in the emergence of drug resistance in Salmonella than therapeutic antibiotic use,” says Sanchez.

Science Daily
June 20, 2006

Original web page at Science Daily

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Bacterium that causes kidney stones and complicated urinary tract infections gives up its genetic secrets

Scientists now have inside information to use in the fight against Proteus mirabilis — a nasty bacterium that can cause kidney stones, as well as hard-to-treat urinary tract infections. Data from the first complete genome sequence for P. mirabilis, which includes at least 3,693 genes and 4.063 megabases of DNA, was presented at the 106th general meeting of the American Society of Microbiology, Orlando from May 21-25. Melanie M. Pearson, Ph.D., a research fellow in microbiology and immunology at the University of Michigan Medical School, is the first scientist to perform an in-depth analysis of the genome sequence. “Access to the full genome sequence will help scientists determine the virulence factors produced by the organism and learn how it causes disease,” Pearson says. “Part of our goal is finding potential targets for new vaccines that could protect people from infection.”

“E. coli causes urinary tract infections in otherwise healthy individuals, but P. mirabilis causes more infections in those with ‘complicated’ urinary tracts. In cases where stones form, the bacteria can become resistant to antibiotics,” says Harry L.T. Mobley, Ph.D., professor and chair of microbiology and immunology in the U-M Medical School. “It is particularly prevalent in nursing home residents with indwelling catheters.” Mobley is an expert on urease, an enzyme produced by P. mirabilis, which breaks down urea in the urinary tract, reduces the acidity of urine and leads to the formation of kidney or bladder stones. Once a stone begins to form, bacteria stick to the stone and live within its layers, where they are protected from antibiotics.

When Pearson examined the genomic sequence data for Proteus mirabilis, she discovered an explanation for the bacterium’s “stickiness.” “This bacterium has an unusually high number of genes that encode for 15 different adherence factors or fimbriae on its surface,” Pearson explains. “All these different fimbriae help the bacterium stick to bladder cells, catheters, kidney stones or each other. It’s not unusual for bacteria to have several ways of attaching to surfaces, but I’ve never heard of one with 15 different adherence factors before.” “Over the course of 20-plus years of laboratory research, we had painstakingly identified four P. mirabilis fimbriae,” says Mobley. “Suddenly, here were 11 more predicted in the genome sequence data. We couldn’t believe it.”

Pearson also discovered what she calls a “pathogenicity island” in the P. mirabilis genome made up of 24 genes that encode components of a system used to inject bacterial proteins into host cells. Until we reviewed the sequence data, we had no idea P. mirabilis had these genes,” Mobley says. “When Melanie analyzed the sequences of these 24 genes, she noticed that they have smaller amounts of two of the four nucleotides in DNA — guanine and cytosine — than are present in the overall genome. This implies that another bacterium contributed this little piece of DNA to P. mirabilis at some point during its evolution.”

In future research, Pearson will use gene microarrays to identify the Proteus mirabilis genes that are turned on, or expressed, during the infection stage. Genes involved in the infection process will be prime targets for future vaccine development, according to Pearson, although she says that years of additional research will be needed before vaccines could be commercially available.

Science Daily
June 6, 2006

Original web page at Science Daily

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Common practices at petting zoos put visitors at risk

While petting zoos pose a risk for gastrointestinal illness, most visitors aren’t aware that simple prevention measures could prevent infection. In addition, some engage in behaviors that might increase their risk of infection according to several studies being presented this week at the International Conference on Emerging Infectious Diseases. Researchers from the CDC today release the results of a case-control study of an outbreak of E. coli O157:H7 associated with two Florida petting zoos, in which they interviewed visitors who did and did not get sick to identify which behaviors were predictors of infection. Some behaviors that were most strongly associated with illness were feeding a cow or goat, touching a goat and stepping in manure or having manure on your shoes. Not surprisingly, simple handwashing after visiting the petting zoo, including lathering with soap and washing hands before eating and after visiting the petting zoo, were found to protect against infection.

“There is an increasing incidence of reported outbreaks of illness associated with petting zoos over the years. People need to be aware of these risks and take the appropriate precautions such as washing their hands after visiting,” says Fred Angulo of the Centers for Disease Control and Prevention (CDC). Unfortunately, according to two other studies being presented at the meeting this week, many visitors do not even engage in this simplest of preventive measures. Researchers from the South Carolina Department of Health and Environmental Control conducted an observational survey of visitors to a petting zoo at the 2005 South Carolina state fair. Despite the availability of numerous handwashing facilities and posted warnings regarding risk factors, approximately 28% of people observed exiting the petting zoo did not wash their hands.

In a similar survey, researchers from the Tennessee Department of Health monitored the use of hand-sanitizer stations at the exits of petting zoos in middle Tennessee. Of the 1,700 visitors, approximately 62% did not use the hand-sanitizer station after visiting the petting zoo. Both studies also noted that a sizeable percentage of petting zoo visitors were also engaging in a number of other risky behaviors. The most common risky behavior observed by the South Carolina researchers was visitors bringing food or drink items into the petting zoo with them. In the Tennessee survey one in five visitors was observed eating or drinking in the petting zoo. “Our petting zoo had a lot of signage warning of risk factors and people still brought in food and drink, failed to wash their hands and otherwise engaged in behaviors that put them at risk for infection,” says Dan Drociuk, an author on the South Carolina survey.

Angulo notes that the lack of handwashing is not entirely the fault of the petting zoo visitors. “Most petting zoo visitors do not know that there is a risk and are not informed that there is a risk. Signs do not work. People need to be told by another human being to wash their hands.” To help address the risks associated with petting zoos, the CDC has entered a partnership with the National Association of State Public Health Veterinarians to develop a compendium of measures to prevent disease associated with animals in public settings. The compendium, which includes specific recommendations for managing contact between animals and people visiting a petting zoo environment, is published annually in the CDC publication Morbidity and Mortality Weekly Report. The 2005 compendium can be found online at http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5404a1.htm. The 2006 compendium will be published later this year.

Science Daily
April 11, 2006

Original web page at Science Daily

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PDT kills drug-resistant bacteria, fungus in lab tests

Photodynamic therapy may be an effective treatment for fungal infections and certain bacterial infections of the oral cavity, including some that are resistant to antibiotics, research from the University at Buffalo’s School of Dental Medicine has shown. Researchers found that the bacteria S. mutans, as well as fungal organisms of the genus Candida, cultured from HIV patients, were highly susceptible to killing with minimal doses of PDT, both in laboratory dishes and on biofilms grown on denture material. Results of the research were presented March 10, 2006 at the International Association of Dental Research meeting in Orlando, Fla. “The results of the studies so far, while not completed, may have important implications in the treatment of oral infectious diseases currently confounding the medical and dental community,” said Thomas S. Mang, Ph.D., associate professor of oral and maxillofacial surgery and senior author on the study.

“PDT may provide an adjunct to current antibiotic treatment or an alternative where antibiotics no longer are working. This may be vital for patients undergoing cancer therapy, HIV patients who demonstrate resistance to antibiotics and the elderly with persistent oral infections.” Photodynamic therapy is based on the propensity of certain types of cells or organisms to absorb light-sensitive drugs. This selective retention allows researchers to direct a laser beam into the organism, which activates the drug and kills the organism but does not damage surrounding tissue.

PDT has been shown to be effective against certain types of cancer, particularly Kaposi’s sarcoma, cancer of the esophagus and breast cancer that has metastasized to the chest wall. The drug Photofrin® has been approved by the FDA as a sensitizer for PDT in the treatment of early and late stage endobronchial and esophageal cancers, as well as high-grade abnormal tissues associated with Barrett’s esophagus, a peptic ulcer of the lower esophagus caused by the presence of cells that normally stay in the stomach lining.

In the current research, after adding the light-sensitive drug Photofrin® to the cultured samples and biofilm, the samples were exposed to various intensities of light. Results showed that the photosensitizer accumulated in the samples within 15 minutes. Very low doses of light killed nearly all the S. mutans bacteria, reducing its concentration to less than 0.1 percent. PDT also demonstrated significant killing of three types of Candida: C. albicans, which causes thrush, and C. glabrata and C. krusei, in samples harvested from immunocompromised (HIV) patients.

Science Daily
April 11, 2006

Original web page at Science Daily

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Salmonella caught red-handed: Research provides clues to antibiotic development

Pathogens are becoming increasingly resistant to antibiotics, causing problems for therapy. Doctors need to have antibiotics available that work in new kinds of ways. The last few years of research have, however, found few such ways. One major difficulty for developers of antibiotics is choosing the proper point of attack against bacteria. There are hundreds of possible points of attack, according to genome analysis and laboratory culture experiments — but validation in in vivo infection models is largely lacking.

The Salmonella were isolated from mouse intestines. Infection biologists and proteomics researchers have now identified all the proteins involved in Salmonella metabolic paths during an infection. Dirk Bumann of Hannover Medical School led a team including Daniel Becker, Claudia Rollenhagen, Matthias Ballmaier and Thomas Meyer of the Max Planck Institute for Infection Biology. They isolated Salmonella from infected mice. Proteomics researchers Matthias Selbach and Matthias Mann from the Max Planck Institute of Biochemistry then turned to highly-sensitive mass spectrometry to look at the protein mixture — and discovered hundreds of different Salmonella metabolic path proteins. The scientists compared them with special protein databanks and identified possible points of attack for antibiotics.

Bumann and his team then examined what role these proteins play in a Salmonella infection. The scientists turned off genes responsible for the proteins to see how it affected the disease’s progress. “Knocking out” the gene was equivalent to blocking its corresponding metabolic path, thereby simulating the effect of antibiotics. The analysis demonstrated the following: in the two possible types of salmonella-related illness (diarrhoea and typhoid), the bacteria is surprisingly unaffected by the blockade of several central metabolic pathways. The reason for this is redundant enzymes, as well as the host offering a wide range of nutrients, which means Salmonella does not depend on its own biosynthetic abilities. Only a few enzymes in certain metabolic pathways are really necessarily to keep Salmonella bacteria alive. Most of these essential enzymes are missing in other important pathogens, or they are also present in the human organism, so they cannot be considered possible points of attack for new broad-spectrum antibiotics with a wide range of effectiveness. The remaining potentially useful metabolic paths are already used as the targets of current antibiotics — or have already been considered for development of an effective antibiotic. A comprehensive analysis of two infection models — typhoid and diarrhoea — shows clearly that there are far fewer than expected possible points of attack for developing urgently needed antibiotics. It is also now obvious that increasingly ineffective antibiotics ought to be replaced by similar, but not identical, active principles. This points the way for future antibiotic research.

Science Daily Health & Science
April 11, 2006

Original web page at Science Daily Health & Medicine

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Anthrax acts in surprising ways

In order for the anthrax toxin to enter a cell, its receptor-binding subunit must heptamerize, thus allowing the two enzymatic subunits to join prior to endocytosis. Laurence Abrami and colleagues at the University of Geneva and the National Institute of Allergy and Infectious Diseases recently revealed that endocytosis is regulated by counteracting posttranslational modifications in the receptor itself. Palmitoylation of the receptor’s cytoplasmic tail facilitates endocytosis of the toxin and receptor by preventing the receptor from being prematurely incorporated into lipid rafts, ubiquitinated, and degraded. “This is the first time that the relationship between palmitoylation, recruitment to lipid raft, and ubiquitination has been clarified,” says Faculty of 1000 reviewer Giampietro Schiavo, a cell biologist at the London Research Institute.

“The authors find that palmitoylation prevents the receptors’ entry into lipid rafts. This mechanism was totally unexpected. The general view was exactly the opposite: That palmitoylation would mediate targeting to lipid rafts. That makes the paper clearly interesting for a lot of people working in completely different fields, not only in anthrax or toxin trafficking. “This is an example of a toxin that is recognizing a cellular receptor of a known function and somehow enhancing its internalization. In that sense, anthrax is exploiting the endocytic route used by natural ligands. This is a paradigm that could be used by native or endogenous ligands that are trafficking through the cell.”

The Scientist
April 11, 2006

Original web page at The Scientist

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DNA from the deep

Thousands of different types of microbes inhabit every cubic centimeter of seawater. Although a few types of microbes been studied in detail, DNA studies will help scientists learn about the many species that have yet to be identified. Working with microbiologist Ed DeLong and his team at MIT, and with David Karl at the University of Hawaii, Preston recently coauthored a paper that describes the DNA of microbe communities at seven different depths in the tropical Pacific Ocean, from the surface down to 4,000 meters (about 13,000 feet). This paper was published in the January 27, 2006 issue of Science magazine.

Smaller but more numerous than marine algae, marine microbes such as bacteria and blue-green algae have huge effects on ocean chemistry and possibly even climate. Many of these organisms can’t be cultured in the laboratory, and have only recently been discovered using DNA analysis.
Probably thousands of additional species have yet to be discovered or named. Even though only a small fraction of marine microbes have been studied in detail, DeLong, Preston, and others have learned a lot by analyzing the combined DNA of all the marine microbes in a sample of seawater. The resulting data can give scientists a ‘birds-eye-view’ of entire microbial communities. DeLong first pioneered this technique about 12 years ago. In the last few years, however, technological advances have made it possible for scientists to sequence really large quantities of DNA in a matter of weeks or months. This allows biologists to study not just microbial communities as a whole, but individual groups of microbes within those communities.

For this project, Preston worked with scientists at the University of Hawaii to collect water from the open ocean about 100 kilometers (60 miles) north of the island of Oahu. This spot, the Hawaii Ocean Time Series station, was chosen because it is far from any terrestrial influences, yet its chemistry and (non-microbial) biology are relatively well studied . Because concentrations of microbes were so low in this ‘oceanic desert’ area, Preston and fellow MBARI researcher Lynne Christianson had to spend five to six hours filtering up to 600 liters (160 gallons) of seawater for each sample, in order to obtain enough microbial DNA for analysis.

One of the researchers’ overall goals was to determine how the microbes near the surface are different from those that live thousands of meters down. Not surprisingly, in samples from the sunlit waters within about 100 meters of the surface, the researchers found a lot of microbial DNA sequences that were associated with photosynthesis. This means many microbes in these waters were probably using sunlight as a source of energy. Surface samples also contained microbial DNA that was associated with movement and propulsion. This suggests that movement is important for these microbes, perhaps helping them follow chemical gradients or move from food particle to food particle. In contrast, DNA from microbes in deeper waters suggests many survive by attaching to and breaking down particles of organic material. Such particles continually sink down from the surface waters into the deep sea, providing food for many organisms in the form of ‘marine snow.’

Perhaps the most surprising finding of this study was the large amount of DNA that came from viruses, especially in near-surface waters. Since the researchers excluded free-living viruses from their initial sample, they believe that this viral DNA must have come from viruses that had infected living bacteria. Such viruses reproduce within bacterial cells, and can actually transfer DNA from one bacterium to another. This makes the already complicated process of analyzing microbial DNA even more challenging. Although the paper in Science describes some of the initial findings from DeLong’s team, other researchers will be analyzing their DNA sequences for years to come. As Preston explains, ‘One thing that other researchers can do is to compare our sequences with those from microbial communities in other regions of the ocean, in soil, in salty brines, or in fresh water environments. They may see similar metabolic pathways or find entirely new ones.’ In fact, just a few years ago DeLong and his colleagues did just this. They compared DNA from marine microbes to DNA from salt pond microbes (archaea) and discovered a new type of photosynthetic pigment, which they called proteorhodopsin. This eventually led to the discovery that marine microbes can obtain energy from the sun through photosynthesis. Similar breakthroughs may emerge from detailed analyses of Preston and DeLong’s seawater samples from the tropical Pacific.

Science Daily
March 28, 2006

Original web page at Science Daily

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Seeing single protein production

Researchers can now observe real-time production of individual proteins, according to two papers in this week’s Science and Nature. The studies report two different methods of seeing the synthesis of single protein molecules in live cells — an achievement the authors say will be especially useful for studying proteins found in low-copy numbers. “The single-molecule approach really is a powerful one” for studying how proteins are made and operate in live cells, said X. Sunney Xie of Harvard University, senior author of both papers. “This process has never been viewed directly in a live cell in real time on a single-molecule basis.”

Researchers have been able to track mRNA transcription at the single-molecule level, Xie said, but no one has done the same for protein translation. Fluroescence-tagged proteins diffuse around the cytoplasm of live cells, and the signal of one protein will not show up against the cell’s background autofluorescence, Xie said. In the Science paper, the researchers — also led by Jie Xiao and Ji Yu at Harvard — reveal how they solved this problem: They attached the fluorescent reporter to a membrane protein. This protein attaches to the cell membrane, where its fluorescent signal is kept in one place long enough for its image to be captured. The researchers placed this fusion protein under control of the lac promoter in Escherichia coli cells. A repressor normally prevents gene expression at this site, but occasionally the repressor stochastically dissociates from the DNA, Xie said, allowing brief mRNA transcription. Ribosomes produce a few fluorescent protein molecules before the mRNA degrades and the repressor re-attaches.

Each time this process produced a fusion protein molecule, the scientists saw a flicker of fluorescence inside the cell. They created time-lapse movies that allowed them to watch as the bacterial cell synthesized new proteins. You can watch an E. coli cell, and suddenly there’s a flash of yellow and a protein molecule’s just been made,” said Kevin Plaxco of the University of California, Santa Barbara, who was not involved in the research but recently saw the time-lapse movies at a conference. “It was very satisfying work.”

By statistically analyzing more than 60 movies of bacterial protein production, Xie and his colleagues determined that just one mRNA molecule is synthesized each time the lac repressor briefly detaches from the DNA. A short burst of protein production then follows, with a variable number of protein molecules produced each time. The number of protein molecules synthesized from each mRNA molecule follows an exponential decay distribution — a pattern that was first theorized in the 1980s but had never before been experimentally observed, Xie said. The pattern likely results from the average lifespan of an mRNA molecule, which also follows an exponential decay distribution, Xie said.

“The single-molecule approach gave them a lot here,” Plaxco told The Scientist. “This is a fundamentally stochastic process and by looking at it at a single molecule level, they could see that stochasticity that we all knew was there. So this was a very gratifying paper to read.” The same pattern of small bursts of protein synthesis was found with a different single-molecule technique reported in Nature by Xie and co-first authors Nir Friedman and Long Cai, both also at Harvard. In this study, the researchers used fluorescence generated by the enzyme b-galactosidase as an indirect reporter of gene expression in E. coli cells.

When it hydrolyzes a synthetic substrate, a single molecule of b-galactosidase produces many fluorescent molecules, but pumps on the bacterial cell surface expel these molecules too quickly for them to be measured. To get around this, the scientists trapped E. coli cells in microfluidic chambers to prevent the fluorescent molecules from escaping completely. They mounted these chambers on a microscope and found that they could reliably detect the fluorescence generated by the translation of just one molecule of b-galactosidase. When they let the cells grow, they found abrupt, step-like changes in fluorescence in the chambers — indicating small bursts of protein production, just as in the Science study. The researchers also used b-galactosidase to measure low-level protein expression in yeast and mouse cells, and they found that their technique worked equally well in these cells.

Cells containing different proteins tagged with b-galactosidase can be placed in chambers next to each other and analyzed simultaneously, Xie said. “Then you’ll be able to see different genes get turned on and off at the same time.” The fused fluorescent-protein approach will offer a different advantage: direct imaging of protein translation and movement. The two techniques will provide complementary windows into protein translation, Xie told The Scientist, but both “will really help the characterization of low copy-number proteins,” including many transcription factors.

“You don’t really get molecular detail” with either single-molecule approach, said Gerhard Wagner of Harvard University, who did not participate in either study, but “it will be useful, because there are some things you cannot measure with any other technique.” Even for proteins whose crystal structures are known, “we want to know how they work in real time,” Xie said, “and that’s something the single-molecule technique can do.”

The Scientist
March 28, 2006

Original web page at The Scientist

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Aspergillus ustus Infections among Transplant Recipients

Aspergillus ustus is a mold that rarely infects humans; only 15 systemic cases have been reported. We report the first outbreak of invasive infection caused by A. ustus among hematopoietic stem cell transplant (HSCT) recipients. Six patients with infections were identified; 3 infections each occurred in both 2001 and 2003. Molecular typing by using randomly amplified polymorphic DNA (RAPD) and antifungal drug susceptibility testing were performed on clinical and environmental isolates recovered from our hospital from 1999 to 2003. The highest overall attack rate in HSCT patients was 1.6%. The overall death rate was 50%, and death occurred within 8 days after diagnostic culture collection. Clinical isolates exhibited decreased susceptibility to antifungal drugs, especially azoles. RAPD and phylogenetic analysis showed genetic similarity between isolates from different patients. Based on the clustering of cases in space and time and molecular data, common-source acquisition of this unusual drug-resistant species is possible.

Invasive aspergillosis (IA) has become a devastating opportunistic fungal infection among immunocompromised hosts, with a 357% increase in death rates reported in the United States from 1980 to 1997). The most common cause of IA is Aspergillus fumigatus. However, in recent years, IA has been increasingly caused by non-fumigatus Aspergillus species. For example, at the Fred Hutchinson Cancer Research Center in Seattle, the proportion of infections caused by non-fumigatus Aspergillus species increased during the latter 1990s. Most of these infections were caused by A. flavus, A. nidulans, A. terreus, and A. niger. Aspergillus ustus is a group of filamentous hyalohyphomycetes consisting of 5 species: A. ustus, A. puniceus, A. panamensis, A. conjunctus, and A. deflectus. Members of this group are rare human pathogens; only 15 cases of systemic infection have been reported in the literature since 1970, and more than half of these occurred in the past 10 years). Infections caused by A. ustus may be of particular concern, as the organisms exhibit low susceptibility to multiple antifungal drugs, and outcomes have been uniformly poor. Recognition of invasive infections that occurred in 2 clusters of hematopoietic stem cell transplant (HSCT) recipients in our institution prompted us to perform a more thorough clinical investigation and environmental sampling to identify potential sources of acquisition.

Emerging Infectious Diseases
March 14, 2006

Original web page at Emerging Infectious Diseases

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MRSA use amoeba to spread, new research shows

The methicilline-resistant staphylococcus aureus (MRSA) ‘superbug’ evades many of the measures introduced to combat its spread by infecting a common single-celled organism found almost everywhere in hospital wards, according to new research published in the journal Environmental Microbiology. Scientists from the University of Bath have shown that MRSA infects and replicates in a species of amoeba, called Acanthamoeba polyphaga, which is ubiquitous in the environment and can be found on inanimate objects such as vases, sinks and walls. As amoeba produce cysts to help them spread, this could mean that MRSA maybe able to be ‘blown in the wind’ between different locations.

Further evidence from research on other pathogens suggests that by infecting amoeba first, MRSA may emerge more virulent and more resistant to antibiotics when it infects humans. “Infection control policies for hospitals should recognise the role played by amoeba in the survival of MRSA, and evaluate control procedures accordingly,” said Professor Mike Brown from the Department of Pharmacy and Pharmacology at the University of Bath. “Until now this source of MRSA has been totally unrecognised. This is a non-patient source of replication and given that amoeba and other protozoa are ubiquitous, including in hospitals, they are likely to contribute to the persistence of MRSA in the hospital environment”.

“Adding to the concern is that amoebal cysts have been shown to trap pathogens and could potentially be dispersed widely by air currents, especially when they are dry. “Replication of MRSA in amoeba and other protozoa raises several important concerns for hospital hygiene.” In laboratory tests, the researchers found that within 24 hours of its introduction, MRSA had infected around 50 per cent of the amoeba in the sample, with 2 per cent heavily infected throughout their cellular content. Evidence with other pathogens suggests that pathogens that emerge from amoeba are more resistant to antibiotics and more virulent.

“This makes matters even more worrying,” said Professor Brown. “It is almost as though the amoeba act like a gymnasium; helping MRSA get fitter and become more pathogenic. “In many ways this may reflect how this kind of pathogenic behaviour first evolved. A good example is the bacterium that causes legionnaires disease. Probably it was pathogenic long before humans and other animals arrived on the evolutionary scene. Even today, it has no known animal host. “The most likely reason is that Legionella and many pathogens learned their pathogenicity after sparring with single-celled organisms like amoeba for millions of years. Because our human cells are very similar to these primitive, single-celled organisms, they have acquired the skills to attack us”.

For these reasons, such primitive cells are being used to replace animals for many kinds of biological tests. “Effective control of MRSA within healthcare environments requires better understanding of their ecology,” said Professor Brown. “We now need to focus on improving our understanding of exactly how MRSA is transmitted, both in hospitals and in the wider environment, to develop control procedures that are effective in all scenarios.” Recently released figures show that infections caused by MRSA rose 5 per cent between 2003 and 2004, and mortality rates increased 15-fold between 1993 and 2002. The research paper has been published online (see link) and will appear in the June or July print issue of Environmental Microbiology which will be published mid-May or mid-June respectively.

Science Daily
March 14, 2006

Original web page at Science Daily

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Science class experiment reveals vitamin B12 secret

For decades, scientists have wondered how living organisms manufacture the essential vitamin B12. Now, using laundry whitener and dirt-dwelling bacteria—the everyday ingredients of an undergraduate science experiment—researchers may have found the major clue they need to solve the mystery. Researchers led by Graham Walker, a Howard Hughes Medical Institute (HHMI) professor and American Cancer Society research professor at the Massachusetts Institute of Technology, have discovered the first known mutant bacteria with a specific defect in a gene involved in the least-understood part of B12 synthesis. They report their findings in the early online edition of the Proceedings of the National Academy of Sciences. HHMI professors are leading research scientists who received $1 million grants from the Institute to find ways to bring the excitement of the research lab into undergraduate science classrooms.

In the ancient world, B12 was probably catalyzing reactions before cells even existed. Now, all animals need B12 to help make the building blocks of DNA, and children need enough of the vitamin to help their brain develop normally. Most people consume enough B12 through animal products or fortified foods in their diet. On the other hand, animals that do not eat other animal products acquire the nutrient from bacteria in their guts or from bacteria-infected dirt on their plant food. An estimated one-quarter of people older than 60 in this country have trouble absorbing B12. B12 deficiency can lead to nerve damage, anemia, and forgetfulness.

Walker’s team’s genetic discovery was made possible by a gimmick Walker designed to capture the attention of undergraduate biology students in the early 1980s. When he added a laundry whitener to a lab dish, the symbiotic bacteria he studied glowed in ultraviolet light, just as the additive makes clothes look brighter in the sun. The teaching trick soon became a popular tool in Walker’s lab for research that had nothing to do with vitamin B12. There, researchers have been focusing on how symbiotic bacteria form and invade the nodules in alfalfa roots that provide the plant with nitrogen and the bacteria with food. The scientists noticed that some of the bacteria on the glowing lab dishes did not light up. These stubborn dark spots revealed bacteria missing key genes needed to construct and enter the nodules in plant roots, they discovered. By analyzing various mutations, the researchers were able to track the molecular details of how the bacteria provide the plant with the nutrients it needs to grow.

Several years ago, Walker’s graduate student Gordon Campbell decided to look for symbiosis defects in bacterial mutants that, instead of being dark spots on the glowing lab dish, were even brighter than their normal counterparts. His findings enabled Campbell and his co-authors to answer a question being asked by many researchers studying B12 synthesis. “That is what is so great about basic research,” Walker said. “It finds answers to things you cannot get at in a direct way.”

Campbell isolated the brightest mutants and put them onto the roots of alfalfa seedlings. Healthy symbiotic partnerships show up on the plant roots as long pink nodules stuffed with bacteria. In contrast, seedlings sharing a dish with the most obviously defective bacteria were stunted and their roots had small white nubs with barely any bacteria inside. For one of these bright mutants, it turned out that the root of the problem was the mutant bacteria’s inability to produce B12. Adopting nomenclature traditional in their field, the researchers named the mutated gene bluB, after a similar gene found in another kind of bacteria.

“The important clue came when we noticed bluB was grouped with other genes important for making vitamin B12 in the other bacterium,” Walker said. “That’s not something we are expert in.” So the researchers contacted co-author John Roth, a professor of molecular biology at University of California, Davis, who has studied in detail the intricate series of steps required to assemble B12, the largest known natural compound that is not made out of repeating units. “Out of our conversations came the idea that bluB might be required for an unknown part of the pathway,” Walker said. “B12 is a big, complicated molecule.
Researchers have been unable to crack the problem of how to make the lower ligand,” a segment of the molecule known as DMB. It was a simple experiment, said Michiko Taga, a postdoctoral fellow and co-first author of the paper. Taga took over the research when Campbell graduated. “If the mutant was broken because it could not make DMB,” she said, “then if we added DMB back it should be okay. So we added DMB, and the bacteria went back to acting like ordinary [symbiotic] bacteria. That was the defining experiment.”

When the researchers provided DMB so that the bacteria did not have to manufacture it themselves, the bacteria’s extraordinary brilliance subsided to a more uniform fluorescence on the lab dish with the laundry whitener. And in the lab dish with the seedlings, the restored bacteria produced a bigger, healthier plant. Chemist and co-author Kavita Mistry followed up with biochemical experiments to prove that the bluB mutant could not make B12 without added DMB. “Our findings just mean bluB is necessary for the reaction,” Taga said. “We are currently doing experiments to show that it directly catalyzes the reaction.” But Roth said the discovery gives him hope for finding all the steps in the pathway for synthesizing B12. “This is the part that has resisted genetics and chemistry,” he explained. “We’ve tried it. Others have tried it. This appears to be the first enzyme dedicated to synthesizing the part.”

Other bacteria, such as the Salmonella that Roth studies, appear to substitute other molecules in place of DMB, stymieing genetic approaches. But the form of B12 that people need contains DMB. The discovery of the bluB mutant may overturn a theory that DMB spontaneously forms without enzymes to speed up the reaction, Roth said. Before the bluB mutant was identified, that theory made sense because the reactions that make B12 do not require energy, in contrast to most biosynthetic reactions. Taga and Walker are following up to figure out how the bluB mutation affects the symbiotic relationship between the bacteria and the plant.
Source: Howard Hughes Medical Institute

Science Daily
March 14, 2006

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HOOF-prints help find where outbreaks begin

Locating potential sources of brucellosis outbreaks is easier now, thanks to a new DNA fingerprinting technique developed by scientists with the Agricultural Research Service (ARS) and the Animal and Plant Health Inspection Service (APHIS). A new DNA fingerprinting technique called HOOF-Prints can identify strains of Brucella bacteria. Brucellosis induces abortions in many animals including elk, sheep, goats, cattle, pigs and bison. Finding the source of these outbreaks helps with identification and isolation of infected animals, and with telling whether the outbreaks started in wildlife, according to microbiologists Betsy Bricker at ARS’ National Animal Disease Center and Darla Ewalt of APHIS’ National Veterinary Services Laboratories, both in Ames, Iowa.

The new technique — called “HOOF-Prints,” for Hypervariable Octameric Oligonucleotide Fingerprints — allows scientists to identify strains of brucellosis through differences in their DNA sequences, and to separate these strains into subtypes. Brucellosis is an extremely infectious disease caused by Brucella bacteria that induce abortions in many animals, including sheep, goats, cattle, pigs, elk and bison. Humans who come in contact with Brucella can get undulant fever, which is marked by chronic flulike symptoms.

Though almost eradicated from the United States, brucellosis can still prove costly to livestock producers through testing and losses. Outbreaks may cause states to lose brucellosis-free status, meaning their cattle must undergo extensive testing before they can be shipped away. The new method uses polymerase chain reaction (PCR) technology, which copies large amounts of DNA molecules from small amounts of source DNA. According to Ewalt, the HOOF-Prints technique is intended to complement existing PCR and bacteriological tests used to identify Brucella species. HOOF-Prints was first applied in the field in 2002 when it was used to trace a brucellosis outbreak in Fremont County, Idaho, cattle to local elk. It could eventually be applied toward generating an international database of Brucella fingerprints that would be used to control the disease, according to Bricker.

Science Daily
February 28, 2006

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Intimate kissing quadruples risk of meningitis in teenagers

Intimate kissing with multiple partners almost quadruples a teenager’s risk of meningococcal disease, finds a study published online by the British Medical Journal.
Meningococcal disease is a life threatening condition with two incidence peaks: in early childhood and in adolescence. The incidence and fatality rate among teenagers in England and the United States rose dramatically during the 1990s, but little is known about the risk factors for this disease in adolescents. The research team examined potential risk and protective factors in 15-19 year olds who had been admitted to hospital with meningococcal disease in six regions of England from January 1999 to June 2000. Each case was compared with a matched control. Blood samples and nose and throat swabs were taken and data on potential risk factors were gathered by confidential interview.

Intimate kissing with multiple partners, a history of preceding illness, and being a student conferred higher risk of disease, whereas recent attendance at a religious event and meningococcal vaccination were associated with lower risk. Despite some study limitations, these findings imply that changing personal behaviours could reduce the risk of meningococcal disease in adolescence, say the authors. Although behaviour based health promotion messages might have a small role in reducing the risk of disease, such campaigns are unlikely to have a major impact. The development of further effective meningococcal vaccines therefore remains a key public health priority, they conclude.

Science Daily
February 28, 2006

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Dirt may be a key to how bacteria that infect humans develop a resistance to antibiotic drugs

In an article in the January 20 issue of the journal Science, McMaster University researchers say that study of bacteria found in dirt may be the key in identifying how and why antibiotic resistance happens in bacteria that infect people, predicting future clinical problems, and testing new antibiotics. Antibiotic resistance has become an increasing public health concern because the organisms that cause infections in humans and animals are becoming less receptive to the healing aspect of antibiotic drugs. The team led by professor Gerry Wright, chair of Biochemistry and Biomedical Sciences of the Michael G. DeGroote School of Medicine, found that the numerous ways soil-dwelling bacteria become resistant to antibiotics are identical to the resistance patterns seen in patients.

These soil-dwelling bacteria also play a central role in the treatment of infectious diseases. Approximately two-thirds of all known antibiotics are produced by bacteria called actinomycetes, commonly found in soils, compost, and other environmental sources. “By evolving in an environment of antibiotic production, incredibly resilient bacteria must develop diverse ways to survive or resist the toxic antimicrobial compounds produced by their neighbors,” said Wright. “Their coping tactics may be able to give us a glimpse into the future of clinical resistance to antibiotics.” “This research suggests that not only can the study of resistance in the soil help predict future clinical emergence, but it can also guide the development of therapies to counteract this resistance.”

Researchers screened 480 strains of soil bacteria isolated from diverse locations for resistance to 21 clinically relevant antibiotics. At high drug concentrations, the soil-dwelling bacteria displayed a stunning level of resistance. Not only were the bacteria resistant to an average of seven to eight antibiotics, but every strain was found to be multi-drug resistant. The bacteria showed resistance to all major classes of antibiotics, regardless of whether the compounds were naturally produced, semi-synthetic, or completely synthetic. Researchers also found that the way bacteria was resistant to vancomycin, one of the most commonly prescribed antibiotics for drug resistant staphylococcal infections, was identical to resistance found in clinics. Furthermore, the researchers’ uncovered bacteria that produced enzymes capable of breaking down or modifying or rendering inactive two recently U.S. FDA-approved antibiotics, a situation which has yet to emerge clinically for these drugs.

“The link between clinical and soil-associated resistance to vancomycin illustrates the value of studying resistance in the soil to rationally anticipate future clinical resistance,” said Wright. “It suggests that the soil serves as an under-recognized source of resistance, resistance that has the potential to reach clinics. “This work could prove to be extremely valuable to the drug development process, complementing traditional laboratory studies of clinical situations. By screening newly developed drugs for resistance in soil bacteria, not only can pharmaceutical companies gain a better understanding of what may emerge in the future as clinical problems, but sufficient warning can be given to hospital microbiology laboratories, physicians and the drug discovery sector to allow for the development of diagnostic techniques and alternative therapies. “Furthermore, studying enzymes that inactivate antibiotics can serve as a foundation for the development of new combination therapies for resistant bacterial strains. Studying antibiotic resistance from an evolutionary perspective is one way that researchers are attempting to stay one step ahead of resistant bacteria.”

Antibiotic resistant bacteria have become a major health threat and have limited our ability to treat even common infections with antibiotics,” said Dr. Bhagirath Singh, Scientific Director of the Canadian Institutes of Health Research Institute of Infection and Immunity. “Dr. Wright’s exciting discovery points to the fact that in nature, bugs in the soil survive in a very hostile environment. They do this by developing resistance to the antibiotics produced by other soil bacteria. Understanding this process opens up a new avenue for finding new therapies to prevent and treat antibiotic resistance in a clinical setting.

Science Daily
February 14, 2006

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Researchers see hope for sex disease vaccine

Scientists said on Thursday that they are a step closer to a vaccine against a bacteria that causes one of the world’s leading causes of blindness and a common sexually transmitted disease. Research into the vaccine was stalled 25 years ago, but recent advances in DNA knowledge have led to a promising candidate for a vaccine against Chlamydia trachomatis, researchers Harlan Caldwell and Deborah Crane said in interviews on Thursday. The bacteria causes the sexually transmitted disease chlamydia, which can cause pelvic inflammatory disease and infertility in women. The bacteria can also cause trachoma, an infection of the eyes that can cause blindness.

Caldwell and microbiologist Crane reported in a study released this week that antibodies to one protein may prevent infection by all 15 strains of Chlamydia trachomatis. The study was released by the Rocky Mountain Laboratories of the National Institute of Allergy and Infectious Diseases.Research at the laboratory in Hamilton, Montana, has been conducted in test tubes, but will now move on to animal testing, the scientists said. Caldwell said animal testing could be complete within two to three years and clinical trials in people within five years. “When we find test tube results that are this encouraging, it gives us a lot of optimism in moving forward,” Caldwell said. “This is in the first step, there’s no question, but the fact you can kill chlamydia in a test tube, and not only kill it, but kill all the strains of the disease, it has great promise in moving forward.”

Caldwell first began work identifying the protein in 1975, but did not have adequate technology for the research. He froze the materials and did not resume work until a few years ago, when new information about the genetic makeup of the bacteria made more research possible. Trachoma is the world’s leading cause of preventable blindness, according to the World Health Organization, and more than 150 million people, mostly in developing countries, currently need treatment. There are 90 million cases of chlamydia worldwide and studies estimate four to five million new cases in the United States each year, according to the WHO, which calls chlamydia “an enormous public health problem throughout the world.” “If this does turn out to be protective against multiple variants of Chlamydia trachomatis, then this would be a very big thing in the world of chlamydia, because potentially we could protect young women from the different strains of chlamydia, and it could be used in the third world to prevent trachoma,” Crane said. “It could have a huge impact economically and to prevent STDs.”

Reuters
February 14, 2006

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Making do with the bare minimum

Mycobacterium tuberculosis is the bacterium responsible for tuberculosis. Exploring the organism’s so-called essential genes could reveal ways to battle drug-resistant strains. Several groups have touted the information that could be gleaned from a minimal set of genetic instructions in building organisms from the ground up or stripping away all nonessential genes to create a minimal organism. More practically perhaps, all antibiotics target essential genes. Finding those ingredients that an infection can’t live without might prove useful. Researchers have been looking for the essential genome for at least a decade, using tactics such as comparative genomics to computationally identify genes that organisms have in common1 and brute force mutagenesis to whittle away the chaff. The papers featured here represent two influential attempts to achieve the same goal. In one, Eric Rubin’s lab at Harvard University used probes generated from randomly transposon-mutagenized Mycobacteria tuberculosis, spotted onto microarrays, to determine where the transposons had landed, and thus which genes could be disrupted. In the other, a large consortium from Europe and Japan systematically inactivated more than 4,000 Bacillus subtilis genes to determine which mutant organisms were viable.

Knowing the essential complement of genes, like knowing the sequence, is all part of characterizing a bacterium these days, notes Nina Salama of the Fred Hutchinson Cancer Research Center. Her own Helicobacter studies use methods similar to those of Rubin. “We have a sequence, but what does it mean?” asks Howard Ochman, who studies the molecular evolution of bacterial genes and genomes at the University of Arizona. Determining a gene’s function may be important, he says, but one also needs to assess whether a particular gene is critical to an organism’s growth. By providing an answer to this question, these papers “open all sorts of avenues to develop drugs that can inhibit microorganisms,” says Dusko Ehrlich of the National Institute for Agricultural Research (INRA) in France, who led the Bacillus effort. The lists have provided a valuable reference, says James Sacchattini, director of the TB Structural Genomics Consortium from Texas A&M University. Rubin’s work has been like “a divining rod” to the consortium, says Sacchattini, helping it to identify proteins and pathways to study as potential targets for chemotherapy. These papers examine “experimentally, what is the minimal gene set required to make a living cell,” says Ehrlich. About 80% of the approximately 250 genes found essential for B. subtilis are present in all bacteria that have a genome of “a decent size, about 2.5 to 3 megabases or above,” he says.

In contrast, Salama’s group has found surprisingly little overlap, only 11%, among the essential genomes of Helicobacter pylori and the other bacteria they examined, with 55% of the genes shared by only some species.5 “I think that reflects all these subtly different niches for which these different bacteria are adapted,” she says. “Targeted disruption is a gold standard, but it’s very time consuming.”

Other distinctions are important. Rubin tries to avoid the word ‘essential,’ and prefers instead to talk about genes required for optimal in-vitro growth. Ehrlich points out that essential genes really need to be defined by the conditions under which they were tested: “We used rich medium for our test. If we used different medium, many more genes would be required, because [the bacteria may] have to synthesize all the amino acids and vitamins.” Assays such as Rubin’s screen for optimal growth in randomly mutagenized cultures. Thus, a mutation conveying drastically slower growth would probably be scored as lethal (because the bacteria harboring it would be out-competed), and the gene would be seen as essential. “Our method is just a screen, but it’s fast and easy,” Rubin says.

“The Bacillus method is very precise – there’s no arguing with it – but it’s a huge amount of work,” he says. “Targeted disruption is kind of a gold standard, in that you’re specifically targeting each of the open reading frames,” Salama agrees. Yet both random and targeted approaches still rely on negative results: The genes considered to be essential are those that cannot be, or are not, mutagenized. “If a gene is essential, you can’t knock it out,” says Ehrlich.

Researchers employ a variety of strategies to assure that the inability to obtain a mutant is not merely an artifact of the methodology. Ehrlich’s consortium placed recalcitrant genes behind an inducible promoter, allowing them to demonstrate that the bacteria were viable when the gene was induced, and nonviable when it was not. Rubin’s group takes cosmids containing the gene, inserts them into Escherichia coli, and then mutagenizes them, showing that the gene can be inactivated. Salama adds a second copy of the gene to her bacteria, and then knocks out one of the copies. But even these methods do not assure that every open reading frame gets queried. “It’s hard to measure, but I think in general, the list of genes has held up pretty well,” says Rubin. “It’s held up to the analysis that we applied, and subsequently it has held up pretty well in other people’s experiments.”

The Scientist
January 17, 2006

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Profiles of infection

Potential perils from bioterrorism to bird flu are increasingly pushing proteomics researchers to identify molecules involved in the infection process. Often stymied in characterizing all the proteins of a single organism, investigators must now contend with the complexities inherent in characterizing two intertwined, antagonistic organisms: host and pathogen. “There’s really just not a whole lot of proteomic work published yet” on host-pathogen interactions, says Sandra L. McCutchen-Maloney, biodefense proteomics group leader at Lawrence Livermore National Laboratory in Livermore, Calif., who recently coauthored a review of the literature. Prospects for such research are improving, however, thanks to technical advances and increased funding. If presentations at meetings are any indication, significant papers should emerge within a year, predicts Philip C. Hanna, an associate professor of microbiology and immunology at the University of Michigan Medical School in Ann Arbor.

Hanna directs one of seven biodefense proteomics research centers (BPRCs) that the US National Institute of Allergy and Infectious Diseases funded in 2004 for $81 million. Joseph J. Breen, the NIAID program officer who oversees the centers, describes their goal as generating targets for diagnostics, therapeutics, and vaccines. To attain it, some BPRC investigators are trying a bold new approach – monitoring host and pathogen proteomes simultaneously. Earlier studies, in contrast, identified proteins in either host or pathogen. McCutchen-Maloney, for example, separately explored proteomes of the plague bacterium Yersinia pestis and of the human cells it infects.

Most projects to date have focused on the pathogen’s proteome, which is simpler than the host’s and easier to manipulate genetically in follow-up studies. Findings about bacteria, in particular, are “more easily interpreted” because microbes regulate protein expression much more strictly than hosts do, says Eustache Paramithiotis, head of the BPRC at Caprion Pharmaceuticals in Montreal. But a pathogen-centered approach requires that a bacterium, virus, or parasite be able to thrive on its own or be extricable from its host. Otherwise, the host’s proteome can swamp the pathogen’s.

A host-centered approach, on the other hand, benefits from this imbalance, which renders host proteins easier to identify. But the most abundant – albumin in plasma, for example – must be selectively removed, or else they can mask the rarer signaling molecules thought to be crucial to the host’s response to infection. Moreover, large discrepancies seem to occur between protein sets expressed by hosts of the same species. In an unpublished study of 12 people, McCutchen-Maloney found that about 200 plasma proteins varied enough to differentiate one subject from another. Joshua N. Adkins, who manages the BPRC at Pacific Northwest National Laboratory in Richland, Wash., is initially focusing on the bacterium Salmonella typhimurium, though he eventually plans to scrutinize the macrophages that it infects. Adkins has cultured the pathogen in LB broth, which promotes its growth, and in magnesium-minimal medium (MgM), which mimics its intracellular environment.
He has already cataloged more than 2,400 proteins, 200 of which are unique to the MgM condition. In a related project, his team is seeking to purify the intracellular vacuole that contains the bacteria and to examine the pathogen and host proteins there. Adkins reports that in early experiments, vacuole isolates have been contaminated by host-cell mitochondria, which are “about the same size and similar in structure.”

The Scientist
December 20, 2005

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Can vaccines replace the hunt?

In a 1997 study the National Academies of Science concluded that, short of a wholesale slaughter of elk and bison in the greater Yellowstone area, the only way to control the disease was to vaccinate all of the park’s bison and elk. Two brucellosis vaccines have been developed for cattle, and one is being tested for use in bison. But the results to date have not been promising, according to Tom Roffe, chief of wildlife health for the U.S. Fish and Wildlife Service. “[The vaccine] confers some immunity in cattle, but it is not great,” he said, noting that cattle in Wyoming that had been vaccinated still contracted brucellosis in 2003. “We know [the vaccine]’s not highly effective in bison.”

Furthermore, Roffe said, tracking and vaccinating 4,900 wild bison is not like giving shots to animals in pens. Given the low level of protection the vaccination affords, he said, it is not worth the expense to vaccinate the park’s herds until a better vaccine is available. Steven Olsen, a researcher at the USDA’s Animal Research Service, said promising work is underway. “There are new vaccine strains, and new technologies have been developed to make more strains,” Olsen said. “Completing the research is not simple. It is going to be years.”

In the meantime the state of Montana has started a plan to create a brucellosis-free bison herd. State rangers have captured 14 Yellowstone bison and plan to capture and quarantine 200 more. The animals go through repeated tests, a process that takes months, to determine whether they are brucellosis-free. The herd will then be bred and relocated in the wild, but not in Yellowstone, where they would again be exposed to brucellosis. The brucellosis-free bison will remain free-ranging outside the park, since they will pose no threat to livestock. Keith Aune, chief of wildlife research at the Montana Department of Fish, Wildlife and Parks, said the project is already under attack from some quarters. “There is opposition to anything you do with bison,” Aune said. “The agriculturalists fear we might be helping spread brucellosis. The environmentalists say the project is cruel to the animals. I look at it as one way to preserve the species.”

Some biologists, including Roffe, believe elk pose a much greater threat to livestock than bison. Recent outbreaks of brucellosis in Idaho and Wyoming have been traced to elk that had mingled with cattle herds. Terry Kreeger, director of veterinary services at Wyoming’s Department of Fish and Game, said there is a lot of debate over how to handle elk in Wyoming, where the animals are kept at feeding grounds during winter. “The elk who feed at the feeding grounds have a rate of infection that is ten times higher than those that do not come to the feeding grounds,” Kreeger said, noting that concentrating the animals increases the spread of brucellosis.

“But we can’t just do away with the feeding grounds, because people don’t want to see elk starving in winter either. Also the feeding grounds can actually help to direct the elk away from cattle.” There are no vaccines that work on elk, and elk have been known to pass the disease to cattle in Wyoming.

Now the state is planning to slaughter female elk that test positive for brucellosis at one of its feeding grounds this winter as part of a test program. But Wyoming doesn’t expect its elk-kill to grab headlines or draw protesters the way Montana’s bison hunt has. “The bison are icons, because they are in Yellowstone,” said Aasheim of Montana’s wildlife department. “But until there’s a solution, we are going to use hunting as a tool to manage them.”

National Geographic
December 6, 2005

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Defensins neutralize anthrax toxin

Defensins can kill Bacillus anthracis by producing a protein called alpha-defensin. This discovery might now pave the way towards the development of new therapies for the fatal lung form of anthrax.

Bacillus anthracis is the causative agent of anthrax. What makes Bacillus anthracis especially dangerous is that these bacteria can form spores. The spores are extremely resistant against environmental stress and can survive for years. Infection with Bacillus anthracis can take place either via the lung or through the skin. Interestingly, the lung form of anthrax is almost always fatal, whereas skin infections remain localized and are rarely lethal. In contrast to the lung form, the skin form of anthrax can be treated without problems and most patients recover. During the past few years, Bacillus anthracis has also been used as a weapon for bioterrorism. Anthrax spores were sent in envelopes and inhaled and resulted in the death of 5 people in the USA.

The findings of the lab of Arturo Zychlinsky now help clarifying why the skin form is harmless in contrast to the lung form. After a skin infection with Bacillus anthracis, neutrophils are recruited to the site of infection.
Neutrophils are white blood cells that can identify and kill microbes. In the skin, neutrophils take up the spores, which germinate inside the neutrophil to a vegetative (“growing”) bacterium. This vegetative bacterium is then attacked and killed within the neutrophil. The scientists succeeded in identifying the substance responsible for the killing of the bacteria. After fractionation of neutrophil components only one protein remained which is sufficient for killing Bacillus anthracis: alpha-defensin. This mechanism is not effective in the lung form of anthrax.
Here, the number of neutrophils recruited to the site of infection is known to be low, and insufficient to kill bacteria. Thus, inhaled spores can germinate and spread through the organism. The scientists in Berlin now hope that their discovery will help to develop new drugs against the lung form of anthrax. There might be the possibility that the inhalation of alphadefensin might kill vegetative bacteria in the lung and prevent dissemination.

Science Daily Health & Medicine
December 6, 2005

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Can clothes spread germs?

Researchers at the New York Hospital Medical Center of Queens sampled neckties worn by physicians, physician assistants and medical students at a teaching hospital in New York. For comparison purposes, they also sampled neckties worn by security personnel at the hospital. The doctors’ ties were much more likely to harbor potential disease-causing bacteria than the security workers’, according to study author Steven Nurkin. “This study brings into question whether wearing a necktie is in the best interest of our patients,” said Nurkin. “Being well dressed adds to an aura of professionalism and has been correlated with higher patient confidence. Senior physicians and hospital administrators often encourage staff to wear neckties in order to help promote this valuable relationship, but in so doing, they may also be facilitating the spread of infectious organisms.”

Nurkin had been studying medicine in Israel, where men wore their shirt collars open. When taking a course in a New York City hospital, he noticed neckties swing over bedding, touch patients and equipment and get coughed on. He presented his findings at a conference of the American Society of Microbiology in New Orleans in May 2004. “There was a similar study that found germs on the stethoscopes of doctors — and another on a blood pressure cuff — but the point is the germs on the membrane (tube) of the stethoscope can’t penetrate solid skin and the doctor wouldn’t put the stethoscope on an open wound,” Nathan Belkin, who is retired but still publishes research papers, told UPI’s Caregiving. However, clothing worn by both visitors and patients in hospitals are a leading source of transmission of spores of Aspergillus fungus, a common fungus long known to pose a potentially deadly threat of infection in hospital patients with damaged or impaired immune systems.

Kay Obendorf, professor of textiles and apparel at Cornell University in Ithaca, N.Y., said that by simply walking into a patient’s room one can easily dislodge the spores from clothing. “One of our researchers had a relative with leukemia — and getting better — but Aspergillus spores came in from the outside environment even though they say they have filtered air. Unless you can control exposure from the outside it can be fatal for someone with a seriously compromised immune system,” Obendorf told Caregiving. “Aspergillus can be carried from place to place off of textiles — the textile acts as a medium to transport the spores from one place to another.”

Hugging, kissing, sitting on a patient’s bed or pulling up a chair creates air turbulence and friction within and around the fabric, releasing the potentially deadly spores, according to Obendorf. However, less than 7 percent of bone marrow units in a national survey conducted by other researchers restrict such activities, Obendorf pointed out. Some studies have found Aspergillus spores are responsible for as many as 40 percent of deaths among leukemia patients, as well as many deaths among chemotherapy, organ and marrow transplant and AIDS patients, all of whom have weakened immune systems, according to Obendorf. “For a normal patient this is not a big concern, but there’s a different level of concern when dealing with someone with a bone marrow transplant,” said Obendorf, who presented the findings at the American Society for Testing and Materials.

Since clothing and bedding harbor germs, should caregivers be concerned about how they launder them? “If you’re a healthy professional couple in their 50s who work in an office, you really have nothing to worry about,” Obendorf said. “But if you have an infant or care for someone incontinent you want to separate — to avoid cross-contamination from person to person — all personal care items such as underwear, towels and bedclothes and wash them separately in hot water with a little bleach.”

Belkin is also concerned about hospital laundering of linens and other fabrics. “There is nothing less expensive than chlorine bleach, but many hospitals fear the use of bleach will prematurely wear out linens and other textiles. But when it comes to disinfecting, hot water and bleach is what you want. Cooler water or oxygenating treatment may clean and get rid of stains, but they don’t disinfect,” Belkin said.

Science Daily
December 6, 2005

Original web page at Science Daily

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Report focuses on challenges to unlocking future promise of vaccines

Vaccines have helped eradicate and tame some of history’s worst infectious diseases, but there are many more diseases out there that vaccines can help overcome. The challenges society needs to confront to unlock the future promise of vaccines against the plagues of the 21st century are the focus of a new report by the American Academy of Microbiology. “The success of vaccines in controlling disease has been profound. Many diseases that formerly raged unchecked are now under control and others have been eliminated in parts of the world. Despite this success, infectious diseases continue to be public health problems particularly in developing countries where vaccines are unavailable, unaffordable, or both,” says James Kaper of the University of Maryland School of Medicine, co-author of the report, Vaccine Development: Current Status and Future Needs.

The report is the outcome of a colloquium convened by the Academy in March 2005 to discuss vaccines, current infectious disease problems, the potential for new and better vaccines, vaccine safety, research issues surrounding vaccines, education, and training topics. Experts in vaccine research and development from academia, industry, and government deliberated and determined several recommendations for future progress in creating and applying vaccines. The report identifies over 40 infectious agents that pose significant human health problems in the United States or abroad, the most significant of which is HIV. Of the infectious agents identified, only 12 currently have effective vaccines. In addition, the report also identifies a number of infectious agents that are relatively rare today, but are poised to emerge by either natural or terrorism-related means, like avian influenza, West Nile virus, and botulism toxin.

According to the report, research and development must continue the progress of the past to address those diseases that have eluded the development of effective vaccines, and existing vaccines must be improved. The report also provides recommendations to overcome obstacles that prevent the best use of existing vaccines. “Vaccines are available for some diseases that continue to plague humans, but not for others. Even when a licensed vaccine is available for a given disease, numerous barriers can block its use, including technical, economic, cultural, and legal obstacles,” says Rino Rappuoli of Chiron SpA in Siena, Italy, another co-author of the report.

Science Daily
November 8, 2005

Original web page at Science Daily

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US army plans to bulk-buy anthrax

The US military wants to buy large quantities of anthrax, in a controversial move that is likely to raise questions over its commitment to treaties designed to limit the spread of biological weapons. A series of contracts have been uncovered that relate to the US army’s Dugway Proving Ground in Utah. They ask companies to tender for the production of bulk quantities of a non-virulent strain of anthrax, and for equipment to produce significant volumes of other biological agents. Issued earlier this year, the contracts were discovered by Edward Hammond, director of the Sunshine Project, a US-German organisation that campaigns against the use of biological and chemical weapons.

One “biological services” contract specifies: “The company must have the ability and be willing to grow Bacillus anthracis Sterne strain at 1500-litre quantities.” Other contracts are for fermentation equipment for producing 3000-litre batches of an unspecified biological agent, and sheep carcasses to test the efficiency of an incinerator for the disposal of infected livestock. Although the Sterne strain is not thought to be harmful to humans and is used for vaccination, the contracts have caused major concern. “It raises a serious question over how the US is going to demonstrate its compliance with obligations under the Biological Weapons Convention if it brings these tanks online,” says Alan Pearson, programme director for biological and chemical weapons at the Center for Arms Control and Non-Proliferation in Washington DC. “If one can grow the Sterne strain in these units, one could also grow the Ames strain, which is quite lethal.”

The US renounced biological weapons in 1969, but small quantities of lethal anthrax were still being produced at Dugway as recently as 1998. It is not known what use the biological agents will be put to. They could be used to test procedures to decontaminate vehicles or buildings, or to test an “agent defeat” warhead designed to destroy stores of chemical and biological weapons. There are even fears that they could be used to determine how effectively anthrax is dispersed when released from bombs or crop-spraying aircraft. “I can definitely see them testing biological weapons delivery systems for threat assessment,” says Hammond. Whatever use it is put to, however, the move could be seen as highly provocative by other nations, he says. “What would happen to the Biological Weapons Convention if other countries followed suit and built large biological production facilities at secretive military bases known for weapons testing?”

New Scientist
October 25, 2005

Original web page at New Scientist

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Australians win Nobel Prize for linking bug to stomach ulcers

Two Australians have won the 2005 Nobel Prize in Physiology or Medicine for establishing that bacteria cause stomach ulcers, it was announced on Monday. Working at the Royal Perth Hospital, Barry Marshall and Robin Warren established beyond all doubt in the 1980s that Helicobacter pylori causes stomach ulcers by infecting and aggravating the gut lining. Moreover, they showed that ulcers could be cured altogether by killing the bacteria with antibiotics. Hitherto, ulcers had been considered incurable. Instead, patients’ symptoms were treated with a lifetime of drugs to reduce the acidity of the gut.

The pair’s claims provoked a fierce backlash from the medical establishment, which held to the dogma that ulcers were brought on by stress and lifestyle, and could not be cured. By revealing a simple cure, the researchers also threatened to destroy huge and lucrative global markets for the existing anti-ulcer drugs, which simply eased symptoms. At conferences, the two scientists were subjected to abuse and ridicule. “There was such a prejudice against the idea that bacteria could grow in the acidity of the stomach,” says David Kelly, a senior microbiologist at the University of Sheffield, UK. The controversy is euphemistically alluded to in the Nobel citation, which credits the pair with “tenacity and a prepared mind [to challenge] prevailing dogmas”.

Warren, a pathologist from Perth, first noticed in 1982 that strange, curved bacteria frequently colonised the lower part of the stomach in biopsies from patients with ulcers, and that the bugs always lived close to sites of inflammation. Marshall, a young clinical fellow, became interested in Warren’s findings and together they initiated a crucial study of biopsies from 100 patients. From these, Marshall eventually learned how to grow the bacteria in the lab, and named the species Helicobacter pylori. They established that the organism was almost always present in patients with gastric inflammation, duodenal ulcers or gastric ulcers. Next, the pair proved that patients could be cured, but only by eradicating the bacteria with antibiotics. Notably, Marshall proved in 1985 that the bacteria caused gastric inflammation by infecting himself, then curing his condition with antibiotics.

“This extraordinary act demonstrated outstanding dedication and commitment to his research,” says Bob May, president of the UK Royal Society. Kelly believes that Marshall performed his “heroic experiment” out of sheer frustration at the failure of other doctors to accept his results. Since their discovery, it has been accepted beyond all dispute that H. pylori causes more than 90% of duodenal ulcers and 80% of gastric ulcers.

Half of all humans carry the bugs in their stomachs for life, but on average only 10 to 15% of those infected develop gastric inflammation or ulcers. In some individuals, infections can lead to stomach cancer. Although the idea that bacteria cause chronic inflammatory disease was seen as heresy back in the 1980s, there is now increasing evidence that bacteria might be to blame for other conditions, such as Crohn’s disease, rheumatoid arthritis and even the clogging of arteries that leads to coronary heart disease. Marshall, who has set up his own Helicobacter pylori Research Laboratory in Perth, affiliated with the University of Western Australia, posted a notice on his website saying: “Thank you to everyone. At the moment I am overwhelmed with phone calls and congratulations pouring in from all over the world.”

New Scientist
October 25, 2005

Original web page at New Scientist

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Bacterial conversation stoppers

While a chattering crowd of various species of bacteria is essentially a microbial tower of Babel, certain snippets of their chemical conversation are almost universally understood. Howard Hughes Medical Institute (HHMI) researchers have found that bacteria of different species can talk to each other using a common language – and also that some species can manipulate the conversation to confuse other bacteria. The interspecies crosstalk and misdirection could have important consequences for human health, said Bonnie L. Bassler, an HHMI investigator at Princeton University whose study was published in the September 29, 2005, issue of Nature. “The ability of cells to communicate with one another and the ability to interfere with the communication process could have consequences in niches containing competing species of bacteria or in niches where bacteria associate with humans,” Bassler said. “In the gut, you can imagine how the normal microflora might interfere with cell-cell communication to thwart bacterial invaders.”

Using a chemical communication process called quorum sensing, bacteria converse among themselves to count their numbers and to get the population to act in unison. A synchronized group of bacteria can mimic the power of a multi-cellular organism, ready to face challenges too daunting for an individual microbe going it alone. Swelling populations trigger their quorum-sensing apparatuses, which have different effects in different types of bacteria. One species might respond by releasing a toxin, while another might cut loose from a biofilm and move on to another environment. Each species of bacteria has a private language, but most also share a molecular vernacular that Bassler’s lab discovered about 10 years ago. A chemical signal called autoinducer-2 (AI-2), originating from the same gene in all bacteria, is released outside the cell to announce the cell’s presence. Nearby bacteria take a local census by monitoring AI-2 levels and conduct themselves as the circumstances warrant.

Researchers have speculated that AI-2 is a universal language, and the new study from Bassler’s lab is the first to show those conversations taking place – and producing consequences — between co-mingling species. Postdoctoral fellow Karina Xavier mixed E. coli, beneficial bacteria that live in the human gut, with Vibrio harveyi, a marine species that naturally glows in the dark in the presence of a crowd. In the test tube, AI-2 production by either species turned up the marine bacteria’s light and turned on the quorum-sensing genes in E. coli. That confirmed what the scientists already suspected: the linguistic versatility of AI-2. But this common language does not guarantee the correct message gets through, the researchers discovered. In earlier work, Xavier had found that E. coli both produces and consumes AI-2. In this study, she set up an experiment where multitudes of E. coli first produced then devoured enough AI-2 to dim the lights of the marine bacteria, essentially fooling the thriving oceanic gang into thinking its members were few, thereby terminating its quorum-sensing behaviors.

In a more realistic encounter, Xavier mixed E. coli with V. cholerae, the cholera-causing bacteria that mixes with E. coli in human guts. When cholera bacteria sense a quorum, they turn off their toxins and excrete an enzyme to cut themselves loose from the intestine, so they can move out of the body where they can infect another person. Here, E. coli squelched much of the quorum-sensing response of the cholera bacteria, although the effect was not as dramatic as with the marine bacteria. “The real take-home point is the interference,” Bassler said. “Consumption of the signal could be a mechanism that allows one kind of bacteria to block another kind of bacteria from counting how many neighbors they have and, in turn, properly controlling its behavior.”

“This study moves us closer to really understanding how these interactions happen in nature,” Bassler said. “Bacteria can communicate between species, and they have evolved mechanisms to interfere with the communication. Probably this is but one of many cunning strategies they have for manipulating chemical communication. You can imagine that, in niche one, the bacteria we consider good guys might be using AI-2 and winning. And unfortunately, in niche two, the bad guys might be using AI-2 and winning.”

Science Daily
October 25, 2005

Original web page at Science Daily

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Gaining ground in the race against antibiotic resistance

Antibiotic resistance has put humans in an escalating ‘arms race’ with infectious bacteria, as scientists try to develop new antibiotics faster than the bacteria can evolve new resistance strategies. But now, researchers have a new strategy that may give them a leg up in the race—reproducing in the lab the natural evolution of the bacterial enzymes that confer resistance. A team of scientists in Argentina and Mexico identified mutations that increased the efficiency of a bacterial enzyme that renders penicillin and cephalosporin antibiotics useless. The results could lead to more effective enzyme inhibitors by giving drug designers a sneak peek at the next generation of resistance. Alejandro Vila, a Howard Hughes Medical Institute international research scholar, and colleagues at the University of Rosario’s Institute of Molecular and Cellular Biology in Argentina and at the Biotechnology Institute of the National Autonomous University of Mexico reported their findings in the early online edition of the Proceedings of the National Academy of Sciences the week of September 19, 2005.

Staying one step ahead of resistance with new antibiotics and treatments for infections is a huge challenge because bacteria evolve quickly to evade them. When the scientists introduced random mutations into the gene for a bacterial resistance enzyme and grew the bacteria on increasing concentrations of antibiotics, it took only a few days of test tube evolution to increase drug resistance. Eventually, they found four mutations in the evolved enzyme that allowed the bacteria to survive on a drug dose 64 times higher than the dose that kills bacteria hosting the un-evolved enzyme. “We were mimicking what is going on in the doctor’s clinic—putting selection pressure on the enzyme by giving higher doses of antibiotic,” said Vila. “The only ones to survive will be those that have an enzyme that can work more efficiently.”

The researchers conducted their experiments using a drug called cephalexin, a member of the widely prescribed cephalosporin class of antibiotics. These drugs and the penicillins, which share a common chemical backbone called the ß-lactam ring, work by disrupting the bacterial cell wall. Bacteria have evolved enzymes called ß-lactamases, which chop the ß-lactam ring in half, inactivating the drugs. An inhibitor for one type of lactamase has already been marketed as part of a ‘package drug’ with amoxicillin to fight resistance. But the lactamase enzyme that Vila’s group studied is in a different class that is causing an emerging problem around the world. This class, the metallo-ß-lactamases, is more threatening, said Vila, because it is effective against a broader spectrum of antibiotics, such as carbapenems. However, it also represents a younger set of enzymes that are still evolving, and that enabled the scientists to observe that evolution in fast-forward.

The group used a lactamase gene from the Bacillus cereus soil bacteria and tested it in the laboratory strain E. coli. The gene is very similar to lactamase genes found in disease-causing bacteria such as Pseudomonas and Acinetobacter—common culprits in resistant, hard-to-treat hospital infections. And it is almost identical to a lactamase gene found in Bacillus anthracis, which causes anthrax. Together, the four mutations identified by the group increased the enzyme’s efficiency at inactivating cephalexin seven-fold. The mutations influenced the enzyme’s active site, where the chopping of antibiotic molecules takes place. One of the mutations has already been found in nature, in a lactamase from Pseudomonas.

In some cases, there is a tradeoff associated with antibiotic resistance: the bacteria’s success in fighting a particular antibiotic can cause it to lose efficiency in inactivating other antibiotics. But that was not the case here. “This evolved enzyme works better against cephalexin and with the same efficiency on other antibiotics, as well,” said Vila. In fact, the mutant enzyme inactivated seven other cephalosporins as efficiently as or better than the original enzyme. “So it hasn’t lost anything, and the outcome is that the bacterium has increased its range of resistance. This is a huge concern in the clinic.”

To date, there are no known inhibitors of metallo-ß-lactamases, but directed evolution could help in their design, Vila said, by giving drug makers a reliable prediction of what the next generation of enzymes will look like. “Since we were able to reproduce the natural evolution in the test tube, you could generate a more efficient lactamase to use as a target, so that your inhibitor would be one step ahead.” This would give science an edge in the resistance race, and it might help slow the vicious cycle enough to develop antibiotics impervious to lactamases.

Science Daily
October 25, 2005

Original web page at Science Daily

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Lions in South Africa pressured by bovine tuberculosis

Attacks by African lions on people and livestock have been in the news lately, but on the whole humans present a much greater threat to Africa’s lions than the lions do to humans. South Africa’s free-ranging lion population, an estimated 2,700 animals living mostly in the ecosystem surrounding Kruger National Park in the northeast corner of the country, is among those at risk. One possible threat is bovine tuberculosis, a disease probably introduced to South Africa through domestic cattle brought in by European settlers at the end of the 18th century.

The disease also afflicts animals in the Serengeti grasslands and woodlands in northern Tanzania and southern Kenya. But according to Craig Packer, professor of zoology at the University of Minnesota, TB isn’t as important an issue there. “While it seems that TB is a worse problem in Kruger than elsewhere, it is still not clear that the disease is as devastating as people originally claimed,” he said. “While we still have TB in Tanzania, it isn’t a problem that we worry much about.” Dewald Keet, the chief veterinarian at Kruger National Park, does worry. He said that bovine tuberculosis is an ever-increasing threat to Kruger lions. But because TB is increasing at a slow rate, people may have the mistaken impression that it has stabilized.

“Nothing is being done to control the disease except research,” he said. According to Keet, the prevalence of the disease in lions in the southern half of the park varies between 48 percent and 78 percent. He explained that lions first contracted the disease when eating infected buffalo carcasses, and the southern region of the park is where TB prevalence is highest in African buffalo. Lions in Kruger are also infecting each other through biting and aerosol transmission, Keet said.

About 25 lions die of TB every year in Kruger, but even more important is the effect of the disease on lion social behavior. Males are weakened by the chronic disease, and this, Keet said, leads to “faster territorial male turnover and consequent infanticide, eviction of entire prides, and a decrease in average longevity.” “Hunting lions is still legal in South Africa. According to Karyl Whitman, a graduate student in the Department of Ecology, Evolution, and Behavior at the University of Minnesota, “nearly all of the hunting is conducted on private ranches, and thus on small ‘manicured’ populations as opposed to ‘wild’ viable populations.”

National Geographic
October 25, 2005

Original web page at National Geographic

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Critically important antibacterial agents for human medicine for risk management strategies of non-human use

The World Health Organization (WHO) convened an international expert Drafting Group on Critically Important Antimicrobials for Human Health from 15 to 18 February 2005 in Canberra, Australia. The meeting was organized to follow up a FAO/WHO/OIE consultative process on Non-Human antimicrobial agents are essential drugs for human health and animal health and welfare. Resistance to antimicrobials is a global public health concern that is impacted by both human and non human usage.

Procedure The panel that met in Canberra, Australia, first developed criteria to identify Critically important antibacterial agents and then applied the criteria to each drug or class of drugs. The term “class” of drugs as used here refers to agents with similar chemical structures that exert an effect on the same target in bacteria and may be affected by the same mechanisms of resistance (for example, ketolides are considered a variation on the macrolide class and not a separate class of drugs). In developing the criteria, the panel took into account how certain antibacterial agents are used in human medicine, the seriousness of the diseases treated with those agents and the availability of alternative therapies in the treatment of such diseases. In this way, the panel was able to assess the potential impact to human health of the potential loss of utility of antibacterial agents due to bacterial resistance to them. The panel also took into consideration pathogenic and commensal bacteria (or their genes) that may transfer to people from animals, food products, or the environment. The panel did not consider how this list will ultimately be used to formulate risk management strategies for use of antimicrobials in animals. This will be the focus and task of future meetings.

World Veterinary Association
October 11, 2005

Original web page at World Health Organization

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An electronic nose that sniffs out infections could help hospitals tackle outbreaks of the antibiotic-resistant superbug MRSA

Culture tests routinely used to identify MRSA (methicillin-resistant Staphylococcus aureus) take two or three days to complete. This hampers attempts to manage outbreaks as infected patients remain untreated and at risk of infecting others. DNA-based tests are being trialled that promise to reduce test times to 2 hours, but now UK-based researchers have come up with a test using an electronic sniffer that could cut the time further, to just 15 minutes. Writing in the journal Sensors and Actuators B (vol 109, p 355), engineers at the University of Warwick and doctors at the Heart of England Hospital, Birmingham, say the electronic nose can recognise the unique cocktail of volatile organic compounds that S. aureus strains excrete.

E-noses analyse gas samples by passing the gas over an array of electrodes coated with different conducting polymers. Each electrode reacts to particular substances by changing its electrical resistance in a characteristic way. Combining the signals from all the electrodes gives a “smell-print” of the chemicals in the mixture that neural network software built into the e-nose can learn to recognise. Each e-nose is about the size of a pair of desktop PCs and costs about £60,000. The food industry uses similar machines to root out rotten ingredients.

David Morgan, a surgeon at the hospital, says the idea of sniffing out superbugs came to him one day in the operating theatre. “I was operating on neck abscesses on two different patients and noticed their infections had slightly different smells, so I wondered if a machine could work out what the bacterial infections were from the smell alone.” Morgan approached Warwick engineer Ritaban Dutta and his colleagues to develop the idea. They first trained an e-nose to recognise the smell-prints of MRSA and the related but more easily treated MSSA (methicillin susceptible S. aureus) by exposing them to nasal swabs from people carrying the infection. They then put their e-nose to the test using swabs from 150 patients whose infection status was already known from culture tests. The system correctly detected 96 per cent of those who had an S. aureus infection.

“They trained an electronic nose to recognise the smell-prints of MRSA ”The e-nose system cannot yet distinguish the methicillin-resistant superbug from the methicillin-susceptible strain. If it cannot be trained to do so, Morgan suggests the e-nose be used as a quick screening system to prioritise which patients or healthcare workers are given the 2-hour DNA-based test, which can tell the difference. The UK government’s Department of Health says that while the panel which investigates new infection controls will study the e-nose, hopes for tackling MRSA remain focused on the emerging DNA-based tests.

Source: Sensors and Actuators B (vol 109, p 355)

New Scientist
October 11, 2005

Original web page at New Scientist