We're still trying to figure out how to properly harness the power of hydrogen as a clean energy source — and now we might be able to pick up some unexpected pointers from some bizarre symbiotic bacteria found at the ocean depths.
Many mussels found around hydrothermal vents live in a symbiotic relationship with bacteria, which handle key biological functions for their host. In one instance, the bacteria serve as the powerhouse for the mussels, processing materials around them into usable energy. Intriguingly, these bacteria are actually taking in hydrogen as their power source, making them the natural equivalent of the hydrogen fuel cells we're currently working to build.
Hydrothermal vents shoot out a steady stream of inorganic chemicals such as hydrogen sulfide, ammonium, methane, iron and, crucially, hydrogen. Since the bottom of the ocean is about as far away from sunlight as it's possible to get, the energy producers that live around these vents cannot make use of photosynthesis like their counterparts on land. Instead, they have to harvest the inorganic chemicals to produce energy, in a process known as chemosynthesis.
Until now, researchers were only aware of two broad types of chemosynthetic microbes - ones that processed hydrogen sulfide for their host, and ones that processed methane. But now researchers at the Max Planck Institute have discovered a third, and it's the hydrogen-harvest bacteria of the Logatchev hydrothermal vent field deep beneath the middle of the Atlantic Ocean.
It makes sense that the bacteria at this particular vent would look to hydrogen as an energy source. Logatchev has the highest known hydrogen concentrations in its plumes of any vent, and the researchers calculate that microbes could harvest seven times as much energy using hydrogen as they could with methane, and eighteen times what they could hope to get from hydrogen sulfide.
It appears that these mussels and their symbiotic partners are far from the only organisms to make use of hydrogen as an energy source, but this is the first time that we've actually observed this particular process. Now the only real question is whether there's any chance we can throw some hydrogen and some deep-sea mussels into a car engine, and just sort of see what happens next...
http://io9.com/5831033/deep+sea-mussels-are-living-hydrogen-fuel-cells
Showing posts with label Bacteria. Show all posts
Showing posts with label Bacteria. Show all posts
Friday, September 2, 2011
Saturday, August 20, 2011
'Suicide bomber' bacteria destroys superbug
Experts in the innovative field of “synthetic biology” engineered a strain of E.coli that could detect signs of Pseudomonas aeruginosa, a leading cause of infection that can be fatal to patients with weak immune systems.
Their specially designed bacteria then produced a toxin that is lethal to the bug, before blowing themselves apart like bombs and splattering the substance over the surrounding area.
When added to a culture of P. aeruginosa in lab tests, the artificial E.coli destroyed 99 per cent of its targets and prevented the formation of biofilms - slimy communities of bacteria which are difficult to destroy - by up to 90 per cent.
The method has not been tested in trials on humans or animals, but a study in the journal Molecular Systems Biology indicated it could provide a new approach to tackling drug-resistant infections, where progress using current techniques has ground to a halt.
Researchers at Nanyang Technological University, Singapore, write: “In summary, we engineered a novel biological system, which comprises sensing, killing, and lysing devices, that enables E. coli to sense and eradicate pathogenic P. aeruginosa strains by exploiting the synthetic biology framework.”
P. aeruginosa is a bacteria which infects the lungs and digestive system, particularly in patients who are critically ill or have weakened immune systems.
The strains found in hospitals are often resistant to antibiotics, creating a pressing need for new treatments.
The E.coli strain developed by researchers from the Nanyang Technological University in Singapore uses a protein called LasR to detect chemical signals given off by P. aeruginosa cells when they communicate with each other.
P. aeruginosa naturally produces a toxin known as pyocin, but the scientists engineered the E.coli to produce the same weapon when the pathogen is detected nearby.
The E.coli bacteria then burst themselves open and cover the P. aeruginosa bacteria with pyocin, which eats away at the outer cell wall and causes the insides to spill out.
http://www.telegraph.co.uk/science/science-news/8704864/Suicide-bomber-bacteria-destroys-superbug.html
The strains found in hospitals are often resistant to antibiotics, creating a pressing need for new treatments.
The E.coli strain developed by researchers from the Nanyang Technological University in Singapore uses a protein called LasR to detect chemical signals given off by P. aeruginosa cells when they communicate with each other.
P. aeruginosa naturally produces a toxin known as pyocin, but the scientists engineered the E.coli to produce the same weapon when the pathogen is detected nearby.
The E.coli bacteria then burst themselves open and cover the P. aeruginosa bacteria with pyocin, which eats away at the outer cell wall and causes the insides to spill out.
http://www.telegraph.co.uk/science/science-news/8704864/Suicide-bomber-bacteria-destroys-superbug.html
Tuesday, July 5, 2011
The beasties we need near us, for our own sake
Courtney Humphries, contributor
In The Wild Life of Our Bodies, biologist Rob Dunn argues that our modern separation from other species causes more harm than good
THERE has been no shortage of nostalgia for the "good old days" of human prehistory, when our hunter-gatherer ancestors lived in ecological harmony with nature, roaming savannahs instead of cramped in office chairs. In The Wild Life of Our Bodies, Rob Dunn shares the view of modern human life as a paradise lost, but the loss he laments is not merely of a vague sense of being one with nature. What we have sacrificed, he argues, is a physical connection with the species that shaped our bodies - from our physique to the immune system.
As humans became urban and industrial, we also separated ourselves from other species. Pets aside, we have laboured to rid our houses and cities of creatures - not just visible predators and pests but also the microbes on our countertops and hands. Some of these steps were sensible acts of self-preservation, but others were driven by an ideology of humans as separate from nature. Dunn, a biologist at North Carolina State University as well as a science journalist, catalogues the dangers of that ideology.
To illustrate how species influence one another's evolution, he points to the pronghorn, a small antelope-like mammal in North America that runs inexplicably fast. The pronghorn's speed, Dunn says, only makes sense if you consider the large predators that once hunted it. The "pronghorn principle" also applies to the human body. We too are "haunted by ghosts" of parasites, pathogens and predators that shaped our evolution.
Dunn makes the case that the influence of these ghosts can be seen in our immune systems. He highlights early evidence suggesting that chronic inflammatory diseases of modern society, such as Crohn's disease, diabetes and asthma, could be alleviated by repopulating our bodies with the parasites we evolved with. Our bodies rely so much on gut bacteria that we even give them a safe house in the form of the appendix, Dunn points out, yet our love for antibiotics could be undermining this important relationship.
Dunn also highlights research that shows how we are shaped by the species we have eaten - and that once ate us. Our brains are still wired to avoid predators we no longer encounter: our adrenal system responds to modern daily stresses as if they were mortal threats, for example, and one theory holds that our acute vision may have evolved specifically to avoid venomous snakes. Meanwhile, as we domesticated plants and animals in our quest for survival, we too became domesticated, evolving the ability to drink cows' milk and break down the starch in grains more efficiently.
Dunn makes the case for these connections through detours and anecdotes, with lively stories of patients and scientists, and research spanning archaeology, field biology, medicine, ecology and microbiology. The elaborate fungus farms of leafcutter ant colonies, for instance, become a metaphor for understanding how we humans cultivate bacteria with our immune systems. By drawing connections between work that seems unrelated, Dunn repeatedly drives home his key point: we ignore the lessons of ecology at our peril. By trying to separate ourselves from nature, we have tricked ourselves into believing we are self-sufficient.
Looking for a better way forward, Dunn is practical. Rather than issue a blanket call for "more nature", he advocates applying the lessons of studying our own ecology. Instead of surrounding ourselves only with the plants and animals we find most appealing, we also need to be aware of creatures that help keep our instincts sharp, and species like worms and bacteria that keep our immune systems in check.
Dunn doesn't go so far as to suggest letting predators loose in Central Park, but he does argue for more diversity in the species we interact with and eat. As he writes, "What is missing from our lives is not nature, but a kind of nature that most benefits us".
http://www.newscientist.com/blogs/culturelab/2011/06/the-beasties-we-need-near-us-for-our-own-sake.html
In The Wild Life of Our Bodies, biologist Rob Dunn argues that our modern separation from other species causes more harm than good
THERE has been no shortage of nostalgia for the "good old days" of human prehistory, when our hunter-gatherer ancestors lived in ecological harmony with nature, roaming savannahs instead of cramped in office chairs. In The Wild Life of Our Bodies, Rob Dunn shares the view of modern human life as a paradise lost, but the loss he laments is not merely of a vague sense of being one with nature. What we have sacrificed, he argues, is a physical connection with the species that shaped our bodies - from our physique to the immune system.
As humans became urban and industrial, we also separated ourselves from other species. Pets aside, we have laboured to rid our houses and cities of creatures - not just visible predators and pests but also the microbes on our countertops and hands. Some of these steps were sensible acts of self-preservation, but others were driven by an ideology of humans as separate from nature. Dunn, a biologist at North Carolina State University as well as a science journalist, catalogues the dangers of that ideology.
To illustrate how species influence one another's evolution, he points to the pronghorn, a small antelope-like mammal in North America that runs inexplicably fast. The pronghorn's speed, Dunn says, only makes sense if you consider the large predators that once hunted it. The "pronghorn principle" also applies to the human body. We too are "haunted by ghosts" of parasites, pathogens and predators that shaped our evolution.
Dunn makes the case that the influence of these ghosts can be seen in our immune systems. He highlights early evidence suggesting that chronic inflammatory diseases of modern society, such as Crohn's disease, diabetes and asthma, could be alleviated by repopulating our bodies with the parasites we evolved with. Our bodies rely so much on gut bacteria that we even give them a safe house in the form of the appendix, Dunn points out, yet our love for antibiotics could be undermining this important relationship.
Dunn also highlights research that shows how we are shaped by the species we have eaten - and that once ate us. Our brains are still wired to avoid predators we no longer encounter: our adrenal system responds to modern daily stresses as if they were mortal threats, for example, and one theory holds that our acute vision may have evolved specifically to avoid venomous snakes. Meanwhile, as we domesticated plants and animals in our quest for survival, we too became domesticated, evolving the ability to drink cows' milk and break down the starch in grains more efficiently.
Dunn makes the case for these connections through detours and anecdotes, with lively stories of patients and scientists, and research spanning archaeology, field biology, medicine, ecology and microbiology. The elaborate fungus farms of leafcutter ant colonies, for instance, become a metaphor for understanding how we humans cultivate bacteria with our immune systems. By drawing connections between work that seems unrelated, Dunn repeatedly drives home his key point: we ignore the lessons of ecology at our peril. By trying to separate ourselves from nature, we have tricked ourselves into believing we are self-sufficient.
Looking for a better way forward, Dunn is practical. Rather than issue a blanket call for "more nature", he advocates applying the lessons of studying our own ecology. Instead of surrounding ourselves only with the plants and animals we find most appealing, we also need to be aware of creatures that help keep our instincts sharp, and species like worms and bacteria that keep our immune systems in check.
Dunn doesn't go so far as to suggest letting predators loose in Central Park, but he does argue for more diversity in the species we interact with and eat. As he writes, "What is missing from our lives is not nature, but a kind of nature that most benefits us".
http://www.newscientist.com/blogs/culturelab/2011/06/the-beasties-we-need-near-us-for-our-own-sake.html
Friday, December 10, 2010
'Logic Gates' Made to Program Bacteria as Computers
ScienceDaily (Dec. 8, 2010) — A team of UCSF researchers has engineered E. coli with the key molecular circuitry that will enable genetic engineers to program cells to communicate and perform computations.
The work builds into cells the same logic gates found in electronic computers and creates a method to create circuits by "rewiring" communications between cells. This system can be harnessed to turn cells into miniature computers, according to findings reported in the journal Nature.
That, in turn, will enable cells to be programmed with more intricate functions for a variety of purposes, including agriculture and the production of pharmaceuticals, materials and industrial chemicals, according to Christopher A. Voigt, PhD, a synthetic biologist and associate professor in the UCSF School of Pharmacy's Department of Pharmaceutical Chemistry who is senior author of the paper.
The most common electronic computers are digital, he explained; that is, they apply logic operations to streams of 1's and 0's to produce more complex functions, ultimately producing the software with which most people are familiar. These logic operations are the basis for cellular computation, as well.
"We think of electronic currents as doing computation, but any substrate can act like a computer, including gears, pipes of water, and cells," Voigt said. "Here, we've taken a colony of bacteria that are receiving two chemical signals from their neighbors, and have created the same logic gates that form the basis of silicon computing."
Applying this to biology will enable researchers to move beyond trying to understand how the myriad parts of cells work at the molecular level, to actually use those cells to perform targeted functions, according to Mary Anne Koda-Kimble, dean of the UCSF School of Pharmacy.
"This field will be transformative in how we harness biology for biomedical advances," said Koda-Kimble, who championed Voigt's recruitment to lead this field at UCSF in 2003. "It's an amazing and exciting relationship to watch cellular systems and synthetic biology unfold before our eyes."
The Nature paper describes how the Voigt team built simple logic gates out of genes and inserted them into separate E. coli strains. The gate controls the release and sensing of a chemical signal, which allows the gates to be connected among bacteria much the way electrical gates would be on a circuit board.
"The purpose of programming cells is not to have them overtake electronic computers," explained Voigt, whom Scientist magazine named a "scientist to watch" in 2007 and whose work is included among the Scientist's Top 10 Innovations of 2009. "Rather, it is to be able to access all of the things that biology can do in a reliable, programmable way."
The research already has formed the basis of an industry partnership with Life Technologies, in Carlsbad, Cal., in which the genetic circuits and design algorithms developed at UCSF will be integrated into a professional software package as a tool for genetic engineers, much as computer-aided design is used in architecture and the development of advanced computer chips.
The automation of these complex operations and design choices will advance basic and applied research in synthetic biology. In the future, Voigt said the goal is to be able to program cells using a formal language that is similar to the programming languages currently used to write computer code.
The lead author of the paper is Alvin Tamsir, a student in the Biochemistry & Molecular Biology, Cell Biology, Developmental Biology, and Genetics (Tetrad) Graduate Program at UCSF. Jeffrey J. Tabor, PhD, in the UCSF School of Pharmacy, is a co-author.
The work builds into cells the same logic gates found in electronic computers and creates a method to create circuits by "rewiring" communications between cells. This system can be harnessed to turn cells into miniature computers, according to findings reported in the journal Nature.
That, in turn, will enable cells to be programmed with more intricate functions for a variety of purposes, including agriculture and the production of pharmaceuticals, materials and industrial chemicals, according to Christopher A. Voigt, PhD, a synthetic biologist and associate professor in the UCSF School of Pharmacy's Department of Pharmaceutical Chemistry who is senior author of the paper.
The most common electronic computers are digital, he explained; that is, they apply logic operations to streams of 1's and 0's to produce more complex functions, ultimately producing the software with which most people are familiar. These logic operations are the basis for cellular computation, as well.
"We think of electronic currents as doing computation, but any substrate can act like a computer, including gears, pipes of water, and cells," Voigt said. "Here, we've taken a colony of bacteria that are receiving two chemical signals from their neighbors, and have created the same logic gates that form the basis of silicon computing."
Applying this to biology will enable researchers to move beyond trying to understand how the myriad parts of cells work at the molecular level, to actually use those cells to perform targeted functions, according to Mary Anne Koda-Kimble, dean of the UCSF School of Pharmacy.
"This field will be transformative in how we harness biology for biomedical advances," said Koda-Kimble, who championed Voigt's recruitment to lead this field at UCSF in 2003. "It's an amazing and exciting relationship to watch cellular systems and synthetic biology unfold before our eyes."
The Nature paper describes how the Voigt team built simple logic gates out of genes and inserted them into separate E. coli strains. The gate controls the release and sensing of a chemical signal, which allows the gates to be connected among bacteria much the way electrical gates would be on a circuit board.
"The purpose of programming cells is not to have them overtake electronic computers," explained Voigt, whom Scientist magazine named a "scientist to watch" in 2007 and whose work is included among the Scientist's Top 10 Innovations of 2009. "Rather, it is to be able to access all of the things that biology can do in a reliable, programmable way."
The research already has formed the basis of an industry partnership with Life Technologies, in Carlsbad, Cal., in which the genetic circuits and design algorithms developed at UCSF will be integrated into a professional software package as a tool for genetic engineers, much as computer-aided design is used in architecture and the development of advanced computer chips.
The automation of these complex operations and design choices will advance basic and applied research in synthetic biology. In the future, Voigt said the goal is to be able to program cells using a formal language that is similar to the programming languages currently used to write computer code.
The lead author of the paper is Alvin Tamsir, a student in the Biochemistry & Molecular Biology, Cell Biology, Developmental Biology, and Genetics (Tetrad) Graduate Program at UCSF. Jeffrey J. Tabor, PhD, in the UCSF School of Pharmacy, is a co-author.
'Logic Gates' Made to Program Bacteria as Computers
ScienceDaily (Dec. 8, 2010) — A team of UCSF researchers has engineered E. coli with the key molecular circuitry that will enable genetic engineers to program cells to communicate and perform computations.
The work builds into cells the same logic gates found in electronic computers and creates a method to create circuits by "rewiring" communications between cells. This system can be harnessed to turn cells into miniature computers, according to findings reported in the journal Nature.
That, in turn, will enable cells to be programmed with more intricate functions for a variety of purposes, including agriculture and the production of pharmaceuticals, materials and industrial chemicals, according to Christopher A. Voigt, PhD, a synthetic biologist and associate professor in the UCSF School of Pharmacy's Department of Pharmaceutical Chemistry who is senior author of the paper.
The most common electronic computers are digital, he explained; that is, they apply logic operations to streams of 1's and 0's to produce more complex functions, ultimately producing the software with which most people are familiar. These logic operations are the basis for cellular computation, as well.
"We think of electronic currents as doing computation, but any substrate can act like a computer, including gears, pipes of water, and cells," Voigt said. "Here, we've taken a colony of bacteria that are receiving two chemical signals from their neighbors, and have created the same logic gates that form the basis of silicon computing."
Applying this to biology will enable researchers to move beyond trying to understand how the myriad parts of cells work at the molecular level, to actually use those cells to perform targeted functions, according to Mary Anne Koda-Kimble, dean of the UCSF School of Pharmacy.
"This field will be transformative in how we harness biology for biomedical advances," said Koda-Kimble, who championed Voigt's recruitment to lead this field at UCSF in 2003. "It's an amazing and exciting relationship to watch cellular systems and synthetic biology unfold before our eyes."
The Nature paper describes how the Voigt team built simple logic gates out of genes and inserted them into separate E. coli strains. The gate controls the release and sensing of a chemical signal, which allows the gates to be connected among bacteria much the way electrical gates would be on a circuit board.
"The purpose of programming cells is not to have them overtake electronic computers," explained Voigt, whom Scientist magazine named a "scientist to watch" in 2007 and whose work is included among the Scientist's Top 10 Innovations of 2009. "Rather, it is to be able to access all of the things that biology can do in a reliable, programmable way."
The research already has formed the basis of an industry partnership with Life Technologies, in Carlsbad, Cal., in which the genetic circuits and design algorithms developed at UCSF will be integrated into a professional software package as a tool for genetic engineers, much as computer-aided design is used in architecture and the development of advanced computer chips.
The automation of these complex operations and design choices will advance basic and applied research in synthetic biology. In the future, Voigt said the goal is to be able to program cells using a formal language that is similar to the programming languages currently used to write computer code.
The lead author of the paper is Alvin Tamsir, a student in the Biochemistry & Molecular Biology, Cell Biology, Developmental Biology, and Genetics (Tetrad) Graduate Program at UCSF. Jeffrey J. Tabor, PhD, in the UCSF School of Pharmacy, is a co-author.
The work builds into cells the same logic gates found in electronic computers and creates a method to create circuits by "rewiring" communications between cells. This system can be harnessed to turn cells into miniature computers, according to findings reported in the journal Nature.
That, in turn, will enable cells to be programmed with more intricate functions for a variety of purposes, including agriculture and the production of pharmaceuticals, materials and industrial chemicals, according to Christopher A. Voigt, PhD, a synthetic biologist and associate professor in the UCSF School of Pharmacy's Department of Pharmaceutical Chemistry who is senior author of the paper.
The most common electronic computers are digital, he explained; that is, they apply logic operations to streams of 1's and 0's to produce more complex functions, ultimately producing the software with which most people are familiar. These logic operations are the basis for cellular computation, as well.
"We think of electronic currents as doing computation, but any substrate can act like a computer, including gears, pipes of water, and cells," Voigt said. "Here, we've taken a colony of bacteria that are receiving two chemical signals from their neighbors, and have created the same logic gates that form the basis of silicon computing."
Applying this to biology will enable researchers to move beyond trying to understand how the myriad parts of cells work at the molecular level, to actually use those cells to perform targeted functions, according to Mary Anne Koda-Kimble, dean of the UCSF School of Pharmacy.
"This field will be transformative in how we harness biology for biomedical advances," said Koda-Kimble, who championed Voigt's recruitment to lead this field at UCSF in 2003. "It's an amazing and exciting relationship to watch cellular systems and synthetic biology unfold before our eyes."
The Nature paper describes how the Voigt team built simple logic gates out of genes and inserted them into separate E. coli strains. The gate controls the release and sensing of a chemical signal, which allows the gates to be connected among bacteria much the way electrical gates would be on a circuit board.
"The purpose of programming cells is not to have them overtake electronic computers," explained Voigt, whom Scientist magazine named a "scientist to watch" in 2007 and whose work is included among the Scientist's Top 10 Innovations of 2009. "Rather, it is to be able to access all of the things that biology can do in a reliable, programmable way."
The research already has formed the basis of an industry partnership with Life Technologies, in Carlsbad, Cal., in which the genetic circuits and design algorithms developed at UCSF will be integrated into a professional software package as a tool for genetic engineers, much as computer-aided design is used in architecture and the development of advanced computer chips.
The automation of these complex operations and design choices will advance basic and applied research in synthetic biology. In the future, Voigt said the goal is to be able to program cells using a formal language that is similar to the programming languages currently used to write computer code.
The lead author of the paper is Alvin Tamsir, a student in the Biochemistry & Molecular Biology, Cell Biology, Developmental Biology, and Genetics (Tetrad) Graduate Program at UCSF. Jeffrey J. Tabor, PhD, in the UCSF School of Pharmacy, is a co-author.
Wednesday, November 10, 2010
Bacteria can lead to evolution of new species
A new study has suggested that bacteria that live on the fruitfly Drosophila melanogaster can affect their host's choice of mate by altering the fly's pheromones.
This in turn could lead to the evolution of new fly species — suggesting that bacteria can indirectly change the species of their hosts, reports Nature.
Eugene Rosenberg, a microbiologist at Tel-Aviv University, suspected that a change in diet acts on symbiotic bacteria living on the flies, rather than directly on the flies themselves.
The find is consistent with ''hologenome'' theory – which suggests that natural selection, which drives evolution, acts on a host and its symbiotic partners as a single unit rather than on each species in isolation.
The fruitflies developed a mating preference just a single generation after they were introduced to a new diet.
"There's a hint from analytical data that they are altering the sexual pheromones, but this really has to be looked at more closely," said Rosenberg.
Rosenberg says the next step is to investigate whether this mechanism is occurring in natural fruitfly populations, and to pin down how the bacteria are passed from one generation to the next.
The findings are published this week in Proceedings of the National Academy of Sciences.
This in turn could lead to the evolution of new fly species — suggesting that bacteria can indirectly change the species of their hosts, reports Nature.
Eugene Rosenberg, a microbiologist at Tel-Aviv University, suspected that a change in diet acts on symbiotic bacteria living on the flies, rather than directly on the flies themselves.
The find is consistent with ''hologenome'' theory – which suggests that natural selection, which drives evolution, acts on a host and its symbiotic partners as a single unit rather than on each species in isolation.
The fruitflies developed a mating preference just a single generation after they were introduced to a new diet.
"There's a hint from analytical data that they are altering the sexual pheromones, but this really has to be looked at more closely," said Rosenberg.
Rosenberg says the next step is to investigate whether this mechanism is occurring in natural fruitfly populations, and to pin down how the bacteria are passed from one generation to the next.
The findings are published this week in Proceedings of the National Academy of Sciences.
Bacteria can lead to evolution of new species
A new study has suggested that bacteria that live on the fruitfly Drosophila melanogaster can affect their host's choice of mate by altering the fly's pheromones.
This in turn could lead to the evolution of new fly species — suggesting that bacteria can indirectly change the species of their hosts, reports Nature.
Eugene Rosenberg, a microbiologist at Tel-Aviv University, suspected that a change in diet acts on symbiotic bacteria living on the flies, rather than directly on the flies themselves.
The find is consistent with ''hologenome'' theory – which suggests that natural selection, which drives evolution, acts on a host and its symbiotic partners as a single unit rather than on each species in isolation.
The fruitflies developed a mating preference just a single generation after they were introduced to a new diet.
"There's a hint from analytical data that they are altering the sexual pheromones, but this really has to be looked at more closely," said Rosenberg.
Rosenberg says the next step is to investigate whether this mechanism is occurring in natural fruitfly populations, and to pin down how the bacteria are passed from one generation to the next.
The findings are published this week in Proceedings of the National Academy of Sciences.
This in turn could lead to the evolution of new fly species — suggesting that bacteria can indirectly change the species of their hosts, reports Nature.
Eugene Rosenberg, a microbiologist at Tel-Aviv University, suspected that a change in diet acts on symbiotic bacteria living on the flies, rather than directly on the flies themselves.
The find is consistent with ''hologenome'' theory – which suggests that natural selection, which drives evolution, acts on a host and its symbiotic partners as a single unit rather than on each species in isolation.
The fruitflies developed a mating preference just a single generation after they were introduced to a new diet.
"There's a hint from analytical data that they are altering the sexual pheromones, but this really has to be looked at more closely," said Rosenberg.
Rosenberg says the next step is to investigate whether this mechanism is occurring in natural fruitfly populations, and to pin down how the bacteria are passed from one generation to the next.
The findings are published this week in Proceedings of the National Academy of Sciences.
Friday, May 28, 2010
Bacteria Living in 'Cloud Cities' May Control Rain and Snow Patterns
Some bacteria can influence the weather. Up high in the sky where clouds form, water droplets condense and ice crystal grow around tiny particles. Typically these particles are dust, pollen, or even soot from a wildfire.
But recently scientists have begun to realize that some of these little particles are alive -- they are bacteria evolved to create ice or water droplets around themselves. Some of them live in clouds , and here and there they may be numerous enough to change rain and snowfall patterns.
Might make you think twice about trying to catch snow flakes or raindrops with your tongue.
One of these weather gifted bacteria is called Pseudomonas syringae. Known to live on agricultural crops, this bacteria does more than provide any old surface for the ice crystal to grow.
Thanks to a special protein, the bugs promote freezing at higher temperatures than usual, an attack mechanism that damages plants so the microbes can feed.
But David Sands, a scientist from Montana State University, and other researchers believe the bacteria are part of a little known weather system.
The magical ability of this protein is well known. Ski resorts use cannons to shoot this protein into the air to promote snow formation.
The fact that these bacteria employ the protein is the intriguing part (and, oh yeah, they can LIVE IN CLOUDS!) and could open up doors for more than the snow-building industry.
The most nagging question for scientists, however, is determining just how widespread this and other species of bacteria are, and how much they influence precipitation patterns. From Tuesday's New York Times article about the discovery, cloud physicist Roy Rasmussen of the National Center for Atmospheric Research said:
“The question is, do these guys get into the atmosphere in large enough concentrations to have an effect? My gut feeling is this may be important for specific places and specific times, but it’s not global.”
If bacteria really do play an important role in modifying weather patterns, it could help explain how poor land use practices like overgrazing and logging contribute to droughts. Rid an environment of plants and the microbes have nothing to eat. Strip away enough vegetation and there aren't enough bugs around to seed clouds -- and the rains disappear.
The flip side of the coin is that certain crops could be planted to encourage bacteria growth, and thus bring rain to a dry region.
"Wheat or barley might differ a thousandfold” in terms of bacteria amount, Sands said, “depending on the variety.”
But before scientists attempt to engineer weather patterns -- which could open up its own can of worms -- they must understand the full extent of these bugs' miraculous ability to work as natural rainmakers.
(Submitted by Chad Arment)
But recently scientists have begun to realize that some of these little particles are alive -- they are bacteria evolved to create ice or water droplets around themselves. Some of them live in clouds , and here and there they may be numerous enough to change rain and snowfall patterns.
Might make you think twice about trying to catch snow flakes or raindrops with your tongue.
One of these weather gifted bacteria is called Pseudomonas syringae. Known to live on agricultural crops, this bacteria does more than provide any old surface for the ice crystal to grow.
Thanks to a special protein, the bugs promote freezing at higher temperatures than usual, an attack mechanism that damages plants so the microbes can feed.
But David Sands, a scientist from Montana State University, and other researchers believe the bacteria are part of a little known weather system.
The magical ability of this protein is well known. Ski resorts use cannons to shoot this protein into the air to promote snow formation.
The fact that these bacteria employ the protein is the intriguing part (and, oh yeah, they can LIVE IN CLOUDS!) and could open up doors for more than the snow-building industry.
The most nagging question for scientists, however, is determining just how widespread this and other species of bacteria are, and how much they influence precipitation patterns. From Tuesday's New York Times article about the discovery, cloud physicist Roy Rasmussen of the National Center for Atmospheric Research said:
“The question is, do these guys get into the atmosphere in large enough concentrations to have an effect? My gut feeling is this may be important for specific places and specific times, but it’s not global.”
If bacteria really do play an important role in modifying weather patterns, it could help explain how poor land use practices like overgrazing and logging contribute to droughts. Rid an environment of plants and the microbes have nothing to eat. Strip away enough vegetation and there aren't enough bugs around to seed clouds -- and the rains disappear.
The flip side of the coin is that certain crops could be planted to encourage bacteria growth, and thus bring rain to a dry region.
"Wheat or barley might differ a thousandfold” in terms of bacteria amount, Sands said, “depending on the variety.”
But before scientists attempt to engineer weather patterns -- which could open up its own can of worms -- they must understand the full extent of these bugs' miraculous ability to work as natural rainmakers.
(Submitted by Chad Arment)
Thursday, June 18, 2009
Scientists Show Bacteria Can 'Learn' And Plan Ahead
ScienceDaily (June 18, 2009) — Bacteria can anticipate a future event and prepare for it, according to new research at the Weizmann Institute of Science. In a paper that appeared June 17 in Nature, Prof. Yitzhak Pilpel, doctoral student Amir Mitchell and research associate Dr. Orna Dahan of the Institute's Molecular Genetics Department, together with Prof. Martin Kupiec and Gal Romano of Tel Aviv University, examined microorganisms living in environments that change in predictable ways.
Their findings show that these microorganisms' genetic networks are hard-wired to 'foresee' what comes next in the sequence of events and begin responding to the new state of affairs before its onset.
E. coli bacteria, for instance, which normally cruise harmlessly down the digestive tract, encounter a number of different environments on their way. In particular, they find that one type of sugar – lactose – is invariably followed by a second sugar – maltose – soon afterward. Pilpel and his team of the Molecular Genetics Department, checked the bacterium's genetic response to lactose, and found that, in addition to the genes that enable it to digest lactose, the gene network for utilizing maltose was partially activated. When they switched the order of the sugars, giving the bacteria maltose first, there was no corresponding activation of lactose genes, implying that bacteria have naturally 'learned' to get ready for a serving of maltose after a lactose appetizer.
Another microorganism that experiences consistent changes is wine yeast. As fermentation progresses, sugar and acidity levels change, alcohol levels rise, and the yeast's environment heats up. Although the system was somewhat more complicated that that of E. coli, the scientists found that when the wine yeast feel the heat, they begin activating genes for dealing with the stresses of the next stage. Further analysis showed that this anticipation and early response is an evolutionary adaptation that increases the organism's chances of survival.
Ivan Pavlov first demonstrated this type of adaptive anticipation, known as a conditioned response, in dogs in the 1890s. He trained the dogs to salivate in response to a stimulus by repeatedly ringing a bell before giving them food. In the microorganisms, says Pilpel, 'evolution over many generations replaces conditioned learning, but the end result is similar.' 'In both evolution and learning,' says Mitchell, 'the organism adapts its responses to environmental cues, improving its ability to survive.' Romano: 'This is not a generalized stress response, but one that is precisely geared to an anticipated event.'
To see whether the microorganisms were truly exhibiting a conditioned response, Pilpel and Mitchell devised a further test for the E. coli based on another of Pavlov's experiments. When Pavlov stopped giving the dogs food after ringing the bell, the conditioned response faded until they eventually ceased salivating at its sound. The scientists did something similar, using bacteria grown by Dr. Erez Dekel, in the lab of Prof. Uri Alon of the Molecular Cell Biology Department, in an environment containing the first sugar, lactose, but not following it up with maltose. After several months, the bacteria had evolved to stop activating their maltose genes at the taste of lactose, only turning them on when maltose was actually available.
'This showed us that there is a cost to advanced preparation, but that the benefits to the organism outweigh the costs in the right circumstances,' says Pilpel. What are those circumstances? Based on the experimental evidence, the research team created a sort of cost/benefit model to predict the types of situations in which an organism could increase its chances of survival by evolving to anticipate future events. They are already planning a number of new tests for their model, as well as different avenues of experimentation based on the insights they have gained.
Pilpel and his team believe that genetic conditioned response may be a widespread means of evolutionary adaptation that enhances survival in many organisms – one that may also take place in the cells of higher organisms, including humans. These findings could have practical implications, as well. Genetically engineered microorganisms for fermenting plant materials to produce biofuels, for example, might work more efficiently if they gained the genetic ability to prepare themselves for the next step in the process.
Prof. Yitzhak Pilpel's research is supported by the Ben May Charitable Trust and Madame Huguette Nazez, Paris, France.
http://www.sciencedaily.com/releases/2009/06/090617131400.htm
Their findings show that these microorganisms' genetic networks are hard-wired to 'foresee' what comes next in the sequence of events and begin responding to the new state of affairs before its onset.
E. coli bacteria, for instance, which normally cruise harmlessly down the digestive tract, encounter a number of different environments on their way. In particular, they find that one type of sugar – lactose – is invariably followed by a second sugar – maltose – soon afterward. Pilpel and his team of the Molecular Genetics Department, checked the bacterium's genetic response to lactose, and found that, in addition to the genes that enable it to digest lactose, the gene network for utilizing maltose was partially activated. When they switched the order of the sugars, giving the bacteria maltose first, there was no corresponding activation of lactose genes, implying that bacteria have naturally 'learned' to get ready for a serving of maltose after a lactose appetizer.
Another microorganism that experiences consistent changes is wine yeast. As fermentation progresses, sugar and acidity levels change, alcohol levels rise, and the yeast's environment heats up. Although the system was somewhat more complicated that that of E. coli, the scientists found that when the wine yeast feel the heat, they begin activating genes for dealing with the stresses of the next stage. Further analysis showed that this anticipation and early response is an evolutionary adaptation that increases the organism's chances of survival.
Ivan Pavlov first demonstrated this type of adaptive anticipation, known as a conditioned response, in dogs in the 1890s. He trained the dogs to salivate in response to a stimulus by repeatedly ringing a bell before giving them food. In the microorganisms, says Pilpel, 'evolution over many generations replaces conditioned learning, but the end result is similar.' 'In both evolution and learning,' says Mitchell, 'the organism adapts its responses to environmental cues, improving its ability to survive.' Romano: 'This is not a generalized stress response, but one that is precisely geared to an anticipated event.'
To see whether the microorganisms were truly exhibiting a conditioned response, Pilpel and Mitchell devised a further test for the E. coli based on another of Pavlov's experiments. When Pavlov stopped giving the dogs food after ringing the bell, the conditioned response faded until they eventually ceased salivating at its sound. The scientists did something similar, using bacteria grown by Dr. Erez Dekel, in the lab of Prof. Uri Alon of the Molecular Cell Biology Department, in an environment containing the first sugar, lactose, but not following it up with maltose. After several months, the bacteria had evolved to stop activating their maltose genes at the taste of lactose, only turning them on when maltose was actually available.
'This showed us that there is a cost to advanced preparation, but that the benefits to the organism outweigh the costs in the right circumstances,' says Pilpel. What are those circumstances? Based on the experimental evidence, the research team created a sort of cost/benefit model to predict the types of situations in which an organism could increase its chances of survival by evolving to anticipate future events. They are already planning a number of new tests for their model, as well as different avenues of experimentation based on the insights they have gained.
Pilpel and his team believe that genetic conditioned response may be a widespread means of evolutionary adaptation that enhances survival in many organisms – one that may also take place in the cells of higher organisms, including humans. These findings could have practical implications, as well. Genetically engineered microorganisms for fermenting plant materials to produce biofuels, for example, might work more efficiently if they gained the genetic ability to prepare themselves for the next step in the process.
Prof. Yitzhak Pilpel's research is supported by the Ben May Charitable Trust and Madame Huguette Nazez, Paris, France.
http://www.sciencedaily.com/releases/2009/06/090617131400.htm
Microbiologists find magnetic bacteria in Lonar lake
Microbiologists in Maharashtra have found 'magnetic bacteria' in the ancient Lonar lake formed due to meteorite impact, a finding that might open a vista for searching extra-terrestrial life.The magnetotactic bacteria, which are object of interest of scientists from various fields world over, were isolated from the lake in Maharashtra's Buldana district which is the only impact crater formed in basaltic rock.
The bacteria are unique as they swim along geomagnetic field lines because they contain tiny magnetic crystals called magnetosomes, said Mahesh Chavadar, a microbiologist at the Yashwantrao Chavan College of Science in Karad.The fact that the bacteria was found in the lake has thrown open doors for research on life outside universe.
"This seems to hint at a certain correlation between these bacteria and meteorites, and that could have tremendous implications on the search for extra-terrestrial life. We need to explore if life outside the earth existed in this form," Chavadar said reporting his findings in a recent issue of 'Current Science'.
The bacteria was first discovered in 1975 and only a few cultures of the micro-organisms are available in laboratories across the world.Chavadar said scientists have found that magnetic nano-crystals in Martian meteorite ALH84001 were similar to bacterial magnetosomes. The meteorite dating back to 4.5 billion years was found in Antarctica in 1984.In light of the ecological importance of magnetic bacteria in bio-geochemical cycles, their study in hitherto unexplored environments can be significant.The magnetotactic bacteria have the ability to orient and migrate or swim along geomagnetic field lines, a behaviour referred to as magnetoaxis.This property is based on specific intracellular structures -- the magnetosomes -- which are tiny magnetic crystals composed of iron minerals.The presence of magnetosomes in the bacteria was confirmed by measuring their iron content which was found to be much greater than the nonmagnetic cultures."Intracellular iron accumulation studies on these bacteria showed up to 11.5 times more iron than non-magnetic bacteria," Chavadar said.
Monday, June 15, 2009
'Alien' lifeform wakened from 120,000 year Arctic slumber
[Why am I reminded of the Doctor Who story "The Seeds of Doom"? - Ed]
Meddling boffins refuse to heed sci-fi common sense
By Lewis Page • Get more from this author
Posted in Biology, 15th June 2009 09:52 GMT
American scientists, showing the reckless disregard for the warnings implicit in quality science fiction that is so regrettably common in the boffinry community, have revived an ancient lifeform which has been slumbering beneath the Arctic ice pack for 120,000 years. To add insult to injury, the scientists believe that their laboratory revenant may be related to indestructible super-aliens yet to be discovered on extraterrestrial iceworlds.
The creature in question is named Herminiimonas glaciei, and was revived from its aeons-long sleep by Dr Jennifer Loveland-Curtze and her colleagues from Pennsylvania State University. The purplish-brown, blobby entity was "coaxed back to life with great patience", according to Penn Uni.
The thinking is that if life can survive millennia of terrible cold beneath a glacier here on Earth, it might do so on other planets - perhaps here in the solar system, under the Martian or possible lunar icecaps.
"These extremely cold environments are the best analogues of possible extraterrestrial habitats", says Loveland-Curtze.
"The exceptionally low temperatures can preserve cells and nucleic acids for even millions of years... studying these bacteria can provide insights into how cells can survive and even grow under extremely harsh conditions, such as temperatures down to -56˚C, little oxygen, low nutrients, high pressure and limited space."
Loveland-Curtze believes that study of H Glacei in the lab can be done safely, as it is a micro-organism, rather than a huge, ravening blobomination type of affair. In fact, it's uncommonly small and puny even for a bacterium - 10 to 50 times smaller even than the well-known E Coli, and correspondingly more capable of worming its way in where it isn't wanted.
Loveland-Curtze assures us that H Glacei isn't a deadly pathogen like E Coli, however. Though she does sound a note of caution:
"It can pass through a 0.2 micron filter, which is the filter pore size commonly used in sterilization of fluids in laboratories and hospitals," she warns.
"If there are other ultra-small bacteria that are pathogens, then they could be present in solutions presumed to be sterile. In a clear solution very tiny cells might grow but not create the density sufficient to make the solution cloudy".
In summary, then, we're looking at an ancient lifeform - albeit tiny - recently wakened by meddling scientists from its hundred-thousand-year sleep beneath the polar icecap. It's capable of surviving, perhaps, in the most hostile alien interplanetary environments known to man. It can evade mankind's toughest lab sterilisation precautions.
Meanwhile humanity may be nearing its first attempt at a manned mission to Mars.
Coincidence? Or have the glacial supermicrobes, having long ago seeded Earth, merely been waiting for a vector species to arise and carry them onward to Mars for the next stage in their campaign of interplanetary conquest?
http://www.theregister.co.uk/2009/06/15/slumbering_arctic_alien/
Friday, April 17, 2009
Wanted: Tough Guys For Mars Mission
So, who or what has been selected to perform this toughest of tough challenges? Steven Seagal perhaps? Chuck Norris? Pah! For this mission, only the best of the best of the best is good enough. After a gruelling selection process, the winners were some bacteria, spores, crustaceans, insects, seeds and, erm, something called a woolly bear.
OK, so they won't out perfrom old Chuck but they do have other skills going for them. Bacteria, for example, are known to be able to survive just about anywhere and even a mosquito can survives a few days in the vacuum of space, which makes them perfect for understanding how life deals with long-term space travel. [During a recent Russian experiment, a mosquito was popped into an unprotected tin can and attached to the side of the International Space Station. The mosquito was subjected to temperatures ranging from 60 degrees C (140 degrees F) in sunlight to a chilly -150 degrees C (-238 degrees F) in the shade. The African mosquito, though short-lived, has the ability to enter suspended animation during times of drought by converting the water molecules in its body into sugars. This allows the mosquito to survive until the next period of rainfall or, as it turns out, 18 months in the vacuum of space.]
Should humans ever make it to Mars, it will be essential to understand not only how they are affected by the rigours of nine months in space but also how the food they will want to grow is affected - it's no use making it all the way there only to find the wheat you took along has mutated into a useless yield-free piece of grass.
Obviously, no one is going to let even the Russians throw terrestrial life around the Red Planet willy-nilly - that would violate the Outer Space Treaty of 1967, which prohibits deliberate forward contamination of this kind - so they will be going to Mars's closest moon, Phobos, instead.
Set to be carried on board Russia's Phobos-Grunt space craft, the US part of the experiment consists of a small capsule filled with ten different species including tardigrades (water bears), seeds and bacteria. Not to be outdone, the Russians are sending a small zoo including crustaceans, mosquito larvae and fungi. The experiment will also test the panspermia hypothesis, a theory that suggests that life travels from planet to planet onboard chunks of planetary material.
Phobos-Grunt is designed to land on the Martian moon, take soil samples and then return back to Earth to enable scientists to test the effects the journey has had on the zoo when it gets back.
Although the final selection has been made, it might be worth suggesting Mr Seagal go along anyway - and if you have to ask why, then you clearly haven't seen the movie On Deadly Ground.
Metro, 17 April 2009, pp18-19.
Tuesday, March 10, 2009
Aphids borrowed bacterial genes to play host
Most aphids host mutualistic bacteria, Buchnera aphidicola, which live inside specialized cells called bacteriocytes. Buchnera are vital to the aphids well being as they provide essential amino acids that are scarce in its diet. Now research published in the open access journal BMC Biology suggests that the aphids' ability to host Buchnera depends on genes they acquired from yet another species of bacteria via lateral gene transfer (LGT).
Atsushi Nakabachi from Japan's RIKEN institute with his colleagues had previously uncovered two clusters of mRNA sequences from the bacteriocyte of the pea aphid Acyrthosiphon pisum that were encoded in the aphid genome, but similar to bacterial genes. Naruo Nikoh from The Open University of Japan and Nakabachi determined these sequences in full for more detailed analysis, and used real-time quantitative RT-PCR experiments to investigate the genes' expression levels in the aphid bacteriocytes.
The evidence points to LGT from bacteria to aphids. Genetic family trees show that one of the genes came from a bacterium closely related to Wolbachia, a common inherited symbiotic microbe, which infects a high proportion of insects. The aphid strain used for the study is free from Wolbachia and other closely related bacteria, but the transferred gene could be a remnant of an infection in the distant past. The evidence suggests that the aphids use these acquired genes to host Buchnera, which has lost many genes that appear to be essential for bacterial life. The association between aphids and Buchnera is over 100 million years old, and has evolved so that today neither the bacteria nor the host can reproduce without the other.
"The cases presented here are of special interest in that these transferred bacterial genes not only retain their functionality, but are highly expressed in the bacteriocyte that is differentiated so as to harbour Buchnera, which lack such genes," says Nakabachi.
LGT (also referred to as horizontal gene transfer) occurs when genetic material from one organism finds its way into another organism other than its offspring. Genetic engineering uses LGT deliberately, but there is increasing evidence that LGT has taken place in many organisms (usually between unicellular organisms) naturally. This has caused a major shift in how biologists view genetic family trees.
http://www.eurekalert.org/pub_releases/2009-03/bc-abb030609.php
Atsushi Nakabachi from Japan's RIKEN institute with his colleagues had previously uncovered two clusters of mRNA sequences from the bacteriocyte of the pea aphid Acyrthosiphon pisum that were encoded in the aphid genome, but similar to bacterial genes. Naruo Nikoh from The Open University of Japan and Nakabachi determined these sequences in full for more detailed analysis, and used real-time quantitative RT-PCR experiments to investigate the genes' expression levels in the aphid bacteriocytes.
The evidence points to LGT from bacteria to aphids. Genetic family trees show that one of the genes came from a bacterium closely related to Wolbachia, a common inherited symbiotic microbe, which infects a high proportion of insects. The aphid strain used for the study is free from Wolbachia and other closely related bacteria, but the transferred gene could be a remnant of an infection in the distant past. The evidence suggests that the aphids use these acquired genes to host Buchnera, which has lost many genes that appear to be essential for bacterial life. The association between aphids and Buchnera is over 100 million years old, and has evolved so that today neither the bacteria nor the host can reproduce without the other.
"The cases presented here are of special interest in that these transferred bacterial genes not only retain their functionality, but are highly expressed in the bacteriocyte that is differentiated so as to harbour Buchnera, which lack such genes," says Nakabachi.
LGT (also referred to as horizontal gene transfer) occurs when genetic material from one organism finds its way into another organism other than its offspring. Genetic engineering uses LGT deliberately, but there is increasing evidence that LGT has taken place in many organisms (usually between unicellular organisms) naturally. This has caused a major shift in how biologists view genetic family trees.
http://www.eurekalert.org/pub_releases/2009-03/bc-abb030609.php
Thursday, February 19, 2009
Online collaboration identifies bacteria
Contact: Charlotte Webber
charlotte.webber@biomedcentral.com
44-207-631-9980
BioMed Central
A new website has been launched which allows scientists everywhere to collaborate on the identification of bacterial strains. This new resource, described in the open access journal BMC Biology, provides a portal for electronic bacterial taxonomy.
The multilocus sequence analysis website, www.eMLSA.net, was developed by an international team of researchers coordinated by Professor Brian G Spratt of Imperial College London. He said, "Bacteria are currently assigned to species by cumbersome procedures and every unknown bacterial isolate has to be compared to many others to find out what species it is. Our website functions as a kind of taxonomic wikipedia, allowing many hands to make short work of the entire process".
Species identification is achieved by sequencing the bacterial genome at seven key loci, uncovering similar combinations of sequences associated with particular bacterial species. Spratt and his colleagues hope that once other researchers have used the site for identification, they will add their strains to the website. He said, "The beauty of the approach is that the database grows in size and utility as taxonomists add their isolates and associated molecular data to the database. Taxonomy therefore becomes electronic - with isolates assigned to species over the internet."
The authors point out that the assignment of strains to known species and the identification and acceptance of new species cannot be completely automated, as it requires the experience, knowledge and judgment of taxonomists. They say, "We hope that those interested in a particular taxonomic group can share their experience and knowledge to provide a consensual approach to deciding whether new sequence clusters should be assigned as new species."
eMLSA.net is an actively curated open-access website.
###
1. Assigning strains to bacterial species via the internet
Cynthia J Bishop, David M Aanensen, Gregory E Jordan, Mogens Kilian, William P Hanage and Brian G Spratt
BMC Biology 2009, 7:3 doi:10.1186/1741-7007-7-3
Article available at journal website: http://www.biomedcentral.com/1741-7007/7/3
Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy.
2. BMC Biology - the flagship biology journal of the BMC series - publishes research and methodology articles of special importance and broad interest in any area of biology and biomedical sciences. BMC Biology (ISSN 1741-7007) is covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE, Zoological Record, Thomson Reuters (ISI) and Google Scholar.
3. BioMed Central (www.biomedcentral.com) is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector.
charlotte.webber@biomedcentral.com
44-207-631-9980
BioMed Central
A new website has been launched which allows scientists everywhere to collaborate on the identification of bacterial strains. This new resource, described in the open access journal BMC Biology, provides a portal for electronic bacterial taxonomy.
The multilocus sequence analysis website, www.eMLSA.net, was developed by an international team of researchers coordinated by Professor Brian G Spratt of Imperial College London. He said, "Bacteria are currently assigned to species by cumbersome procedures and every unknown bacterial isolate has to be compared to many others to find out what species it is. Our website functions as a kind of taxonomic wikipedia, allowing many hands to make short work of the entire process".
Species identification is achieved by sequencing the bacterial genome at seven key loci, uncovering similar combinations of sequences associated with particular bacterial species. Spratt and his colleagues hope that once other researchers have used the site for identification, they will add their strains to the website. He said, "The beauty of the approach is that the database grows in size and utility as taxonomists add their isolates and associated molecular data to the database. Taxonomy therefore becomes electronic - with isolates assigned to species over the internet."
The authors point out that the assignment of strains to known species and the identification and acceptance of new species cannot be completely automated, as it requires the experience, knowledge and judgment of taxonomists. They say, "We hope that those interested in a particular taxonomic group can share their experience and knowledge to provide a consensual approach to deciding whether new sequence clusters should be assigned as new species."
eMLSA.net is an actively curated open-access website.
###
1. Assigning strains to bacterial species via the internet
Cynthia J Bishop, David M Aanensen, Gregory E Jordan, Mogens Kilian, William P Hanage and Brian G Spratt
BMC Biology 2009, 7:3 doi:10.1186/1741-7007-7-3
Article available at journal website: http://www.biomedcentral.com/1741-7007/7/3
Please name the journal in any story you write. If you are writing for the web, please link to the article. All articles are available free of charge, according to BioMed Central's open access policy.
2. BMC Biology - the flagship biology journal of the BMC series - publishes research and methodology articles of special importance and broad interest in any area of biology and biomedical sciences. BMC Biology (ISSN 1741-7007) is covered by PubMed, MEDLINE, BIOSIS, CAS, Scopus, EMBASE, Zoological Record, Thomson Reuters (ISI) and Google Scholar.
3. BioMed Central (www.biomedcentral.com) is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector.
Wednesday, February 18, 2009
Engineered Bacterium Churns Out Two New Key Antibiotics
MADISON - In recent years, scientists have isolated two potent natural antibiotics - platensimycin and platencin - that are highly effective against bacterial infection, including those caused by the most dreaded drug-resistant microbes.
Now, those two promising agents are a key step closer to augmenting a depleted antibiotic pipeline with the discovery of a genetic pressure point that can send a bacterium that makes both antibiotics into overdrive.
In a report in the online editions of the journal Antimicrobial Agents and Chemotherapy, a team led by University of Wisconsin-Madison professor of pharmaceutical sciences and chemistry Ben Shen shows that a South African soil microbe can be engineered by manipulating a single gene to make large amounts of both antibiotics.
"There is no doubt about the importance of these compounds," says Shen, who conducted the work with colleagues Michael J. Smanski, Ryan M. Peterson and Scott R. Rajski. "They are active on all the drug-resistant bacterial pathogens."
The compounds are among the first discovered in the past 40 years that represent a new class of antibiotics and that exhibit a new mode of action. They work by targeting an enzyme used to make the fatty acids critical for building the cell membranes on the surface of pathogenic bacteria. The need for new antibiotics is significant and growing as pathogenic bacteria are evolving resistance to currently available antibiotics, with some infections becoming almost impossible to treat.
The new Wisconsin discovery is notable because it provides a blueprint for the manufacture of large amounts of antibiotic, a key step in the commercial development of any drug. The team showed that a liter of the engineered bacterium Streptomyces platensis can churn out as much as 300 milligrams of antibiotic, more than 100 times the amount produced by wild strains of the bacterium.
"That's a lot of material," says Shen. "We didn't even optimize production."
The ability to produce large amounts of the new antibiotics, which to date have only been tested in animals, should help speed the development of the new antibiotics, as they are difficult to produce by conventional means.
The compounds, Shen explains, work well in animals when administered by continuous infusion, but their efficacy is diminished when administered by more conventional means. That phenomenon, Shen notes, is attributed to properties associated with how the agents are processed by an animal. It may be possible, however, to improve those properties by chemical modification of the natural antibiotics, a process that can now be accelerated in the lab as researchers will have greater access to the new agents through the engineered bacterium developed by the Wisconsin team.
The new work by Shen and his colleagues also lays a foundation to develop analogs, compounds that have improved properties as a result of tinkering with the biosynthesis pathways used by the engineered bacterium to make the antibiotics.
The conversion of ordinary Streptomyces platensis into a lean, mean antibiotic-producing machine required the manipulation of only a single regulatory gene, according to the new study. By deleting the gene from the bacterium that produces the compounds, the Wisconsin team was able to find strains of the bacterium that overproduced the antibiotics.
The new study was funded by UW-Madison and the National Institutes of Health.
Terry Devitt, 608-262-8282, trdevitt@wisc.edu
Now, those two promising agents are a key step closer to augmenting a depleted antibiotic pipeline with the discovery of a genetic pressure point that can send a bacterium that makes both antibiotics into overdrive.
In a report in the online editions of the journal Antimicrobial Agents and Chemotherapy, a team led by University of Wisconsin-Madison professor of pharmaceutical sciences and chemistry Ben Shen shows that a South African soil microbe can be engineered by manipulating a single gene to make large amounts of both antibiotics.
"There is no doubt about the importance of these compounds," says Shen, who conducted the work with colleagues Michael J. Smanski, Ryan M. Peterson and Scott R. Rajski. "They are active on all the drug-resistant bacterial pathogens."
The compounds are among the first discovered in the past 40 years that represent a new class of antibiotics and that exhibit a new mode of action. They work by targeting an enzyme used to make the fatty acids critical for building the cell membranes on the surface of pathogenic bacteria. The need for new antibiotics is significant and growing as pathogenic bacteria are evolving resistance to currently available antibiotics, with some infections becoming almost impossible to treat.
The new Wisconsin discovery is notable because it provides a blueprint for the manufacture of large amounts of antibiotic, a key step in the commercial development of any drug. The team showed that a liter of the engineered bacterium Streptomyces platensis can churn out as much as 300 milligrams of antibiotic, more than 100 times the amount produced by wild strains of the bacterium.
"That's a lot of material," says Shen. "We didn't even optimize production."
The ability to produce large amounts of the new antibiotics, which to date have only been tested in animals, should help speed the development of the new antibiotics, as they are difficult to produce by conventional means.
The compounds, Shen explains, work well in animals when administered by continuous infusion, but their efficacy is diminished when administered by more conventional means. That phenomenon, Shen notes, is attributed to properties associated with how the agents are processed by an animal. It may be possible, however, to improve those properties by chemical modification of the natural antibiotics, a process that can now be accelerated in the lab as researchers will have greater access to the new agents through the engineered bacterium developed by the Wisconsin team.
The new work by Shen and his colleagues also lays a foundation to develop analogs, compounds that have improved properties as a result of tinkering with the biosynthesis pathways used by the engineered bacterium to make the antibiotics.
The conversion of ordinary Streptomyces platensis into a lean, mean antibiotic-producing machine required the manipulation of only a single regulatory gene, according to the new study. By deleting the gene from the bacterium that produces the compounds, the Wisconsin team was able to find strains of the bacterium that overproduced the antibiotics.
The new study was funded by UW-Madison and the National Institutes of Health.
Terry Devitt, 608-262-8282, trdevitt@wisc.edu
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