Do microbes swim faster or slower in elastic fluids? Research answers long-standing question

ScienceDaily (May 18, 2011) — A biomechanical experiment conducted at the University of Pennsylvania School of Engineering and Applied Science has answered a long-standing theoretical question: Will microorganisms swim faster or slower in elastic fluids? For a prevalent type of swimming, undulation, the answer is "slower."

Paulo Arratia, assistant professor of mechanical engineering and applied mechanics, along with student Xiaoning Shen, conducted the experiment. Their findings were published in the journal Physical Review Letters.

Many animals, microorganisms and cells move by undulation, and they often do so through elastic fluids. From worms aerating wet soil to sperm racing toward an egg, swimming dynamics in elastic fluids is relevant to a number of facets of everyday life; however, decades of research in this area have been almost entirely theoretical or done with computer models. Only a few investigations involved live organisms.

"There have been qualitative observations of sperm cells, for example, where you put sperm in water and watch their tails, then put them in an elastic fluid and see how they swim differently," Arratia said. "But this difference has never been characterized, never put into numbers to quantify exactly how much elasticity affects the way they swim, is it faster or slower and why."

The main obstacle for quantitatively testing these theories with live organisms is developing an elastic fluid in which they can survive, behave normally and in which they can be effectively observed under a microscope.

Arratia and Shen experimented on the nematode C. elegans, building a swimming course for the millimeter-long worms. The researchers filmed them through a microscope while the creatures swam the course in many different liquids with different elasticity but the same viscosity.

Though the two liquid traits, elasticity and viscosity, sound like they are two sides of the same coin, they are actually independent of each other. Viscosity is a liquid's resistance to flowing; elasticity describes its tendency to resume its original shape after it has been deformed. All fluids have some level of viscosity, but certain liquids like saliva or mucus, under certain conditions, can act like a rubber band.

Increased viscosity would slow a swimming organism, but how one would fare with increased elasticity was an open question.

"The theorists had a lot of different predictions," Arratia said. "Some people said elasticity would make things go faster. Others said it would make things go slower. It was all over the map.

"We were the first ones to show that, with this animal, elasticity actually brings the speed and swimming efficiency down."

The reason the nematodes swam slower has to do with how viscosity and elasticity can influence each other.

"In order to make our fluids elastic, we put polymers in them," Arratia said. "DNA, for example, is a polymer. What we use is very similar to DNA, in that if you leave it alone it is coiled. But if you apply a force to it, the DNA or our polymer, will start to unravel.

"With each swimming stroke, the nematode stretches the polymer. And every time the polymers are stretched, the viscosity goes up. And as the viscosity goes up, it's more resistance to move through."

Beyond giving theorists and models a real-world benchmark to work from, Arratia and Shen's experiment opens the door for more live-organism experiments. There are still many un-answered questions relating to swimming dynamics and elasticity.

"We can increase the elasticity and see if there is a mode in which speed goes up again. Once the fluid is strongly elastic, or closer to a solid, we want to see what happens," Arratia said. "Is there a point where it switches from swimming to crawling?"

Arratia and Shen's research was supported by the National Science Foundation.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Pennsylvania.

Journal Reference:

X. Shen, P. Arratia. Undulatory Swimming in Viscoelastic Fluids. Physical Review Letters, 2011; 106 (20) DOI: 10.1103/PhysRevLett.106.208101

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Science & the Public: Microbes may sky jump to new hosts

Terrestrial microorganisms may have adapted to use clouds as a way station.

Scientists have been probing the role of microbes in cloud formation and precipitation, something discussed in a May 24 session at the American Society for Microbiology meeting, in New Orleans. But this bioprecipitation may not be an accident of chemistry so much as an evolutionary adaptation by certain bacteria and other nonsentient beings, argues Brent Christner of Louisiana State University in Baton Rouge.

He’s referring to the ability of certain one-celled organisms to foster the nucleation of ice crystals.

Even an airborne dust mote can serve as the surface on which water vapor condenses and freezes. But he notes that the most efficient ice nucleators — micro-particles that can catalyze freezing at the highest temperatures — are living organisms. Some bacteria, like Pseudomonas syringae, for instance, can serve as nuclei for ice formation at temperatures as warm as -2 degrees Celsius, more than 10 degrees warmer than the ice-forming limit for dust motes.

Christner now thinks it’s probably no accident that “the most active ice nucleators are biological.” As part of a survival strategy, he contends, many microbes may have evolved “to essentially piggyback on the hydrological cycle.”

The plant pathogen P. syringae “can probably be found on any plant in your back yard,” Christner says. But if winds fling this germ high enough into the air, it can be entrained by currents for up to a week or more. During that time, the fragile microbe faces a risk of deadly desiccation or irradiation by damaging solar ultraviolet rays. Safety, from its perspective, is a moist leaf back on the ground.

This bacterium can return to Earth, he says, by fostering the nucleation of moisture that will eventually rain out as liquid or frozen precipitation. (And don't worry about their getting cold along the way. Christner and other biologists have isolated live germs from precipitation — including the heart of a fallen hailstone). 

The LSU scientist's postulation of bioprecipitation as a survival tactic is certainly tantilizing. I can even picture the graphic novel story line he might offer students: wind-kidnapped microbes that turn on the synthesis of ice-nucleating proteins in hopes of skydiving back home.

Found in: Agriculture, Chemistry, Earth Science, Ecology, Environment and Life

View the original article here

Do microbes swim faster or slower in elastic fluids? Research answers long-standing question

ScienceDaily (May 18, 2011) — A biomechanical experiment conducted at the University of Pennsylvania School of Engineering and Applied Science has answered a long-standing theoretical question: Will microorganisms swim faster or slower in elastic fluids? For a prevalent type of swimming, undulation, the answer is "slower."

Paulo Arratia, assistant professor of mechanical engineering and applied mechanics, along with student Xiaoning Shen, conducted the experiment. Their findings were published in the journal Physical Review Letters.

Many animals, microorganisms and cells move by undulation, and they often do so through elastic fluids. From worms aerating wet soil to sperm racing toward an egg, swimming dynamics in elastic fluids is relevant to a number of facets of everyday life; however, decades of research in this area have been almost entirely theoretical or done with computer models. Only a few investigations involved live organisms.

"There have been qualitative observations of sperm cells, for example, where you put sperm in water and watch their tails, then put them in an elastic fluid and see how they swim differently," Arratia said. "But this difference has never been characterized, never put into numbers to quantify exactly how much elasticity affects the way they swim, is it faster or slower and why."

The main obstacle for quantitatively testing these theories with live organisms is developing an elastic fluid in which they can survive, behave normally and in which they can be effectively observed under a microscope.

Arratia and Shen experimented on the nematode C. elegans, building a swimming course for the millimeter-long worms. The researchers filmed them through a microscope while the creatures swam the course in many different liquids with different elasticity but the same viscosity.

Though the two liquid traits, elasticity and viscosity, sound like they are two sides of the same coin, they are actually independent of each other. Viscosity is a liquid's resistance to flowing; elasticity describes its tendency to resume its original shape after it has been deformed. All fluids have some level of viscosity, but certain liquids like saliva or mucus, under certain conditions, can act like a rubber band.

Increased viscosity would slow a swimming organism, but how one would fare with increased elasticity was an open question.

"The theorists had a lot of different predictions," Arratia said. "Some people said elasticity would make things go faster. Others said it would make things go slower. It was all over the map.

"We were the first ones to show that, with this animal, elasticity actually brings the speed and swimming efficiency down."

The reason the nematodes swam slower has to do with how viscosity and elasticity can influence each other.

"In order to make our fluids elastic, we put polymers in them," Arratia said. "DNA, for example, is a polymer. What we use is very similar to DNA, in that if you leave it alone it is coiled. But if you apply a force to it, the DNA or our polymer, will start to unravel.

"With each swimming stroke, the nematode stretches the polymer. And every time the polymers are stretched, the viscosity goes up. And as the viscosity goes up, it's more resistance to move through."

Beyond giving theorists and models a real-world benchmark to work from, Arratia and Shen's experiment opens the door for more live-organism experiments. There are still many un-answered questions relating to swimming dynamics and elasticity.

"We can increase the elasticity and see if there is a mode in which speed goes up again. Once the fluid is strongly elastic, or closer to a solid, we want to see what happens," Arratia said. "Is there a point where it switches from swimming to crawling?"

Arratia and Shen's research was supported by the National Science Foundation.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of Pennsylvania.

Journal Reference:

X. Shen, P. Arratia. Undulatory Swimming in Viscoelastic Fluids. Physical Review Letters, 2011; 106 (20) DOI: 10.1103/PhysRevLett.106.208101

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using microbes to generate electricity?

ScienceDaily (May 23, 2011) — Using bacteria to generate energy is a significant step closer following a breakthrough discovery by scientists at the University of East Anglia (UEA).

Published May 23 by the scientific journal Proceedings of the National Academy of Sciences (PNAS), the research demonstrates for the first time the exact molecular structure of the proteins which enable bacterial cells to transfer electrical charge.

The discovery means scientists can now start developing ways to 'tether' bacteria directly to electrodes -- creating efficient microbial fuel cells or 'bio-batteries'. The advance could also hasten the development of microbe-based agents that can clean up oil or uranium pollution, and fuel cells powered by human or animal waste.

"This is an exciting advance in our understanding of how some bacterial species move electrons from the inside to the outside of a cell," said Dr Tom Clarke of UEA's School of Biological Sciences.

"Identifying the precise molecular structure of the key proteins involved in this process is a crucial step towards tapping into microbes as a viable future source of electricity."

Funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the US Department of Energy, the project is led by Dr Clarke, Prof David Richardson and Prof Julea Butt of UEA, in collaboration with colleagues at the Pacific Northwest National Laboratory in the US.

In earlier research published by PNAS in 2009, the team demonstrated the mechanism by which bacteria survive in oxygen-free environments by constructing electrical wires that extend through the cell wall and make contact with a mineral -- a process called iron respiration or 'breathing rocks'.

In this latest research, the scientists used a technique called x-ray crystallography to reveal the molecular structure of the proteins attached to the surface of a Shewanella oneidensis cell through which electrons are transferred.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of East Anglia.

Journal Reference:

Thomas A. Clarke, Marcus J. Edwards, Andrew J. Gates, Andrea Hall, Gaye F. White, Justin Bradley, Catherine L. Reardon, Liang Shi, Alexander S. Beliaev, Matthew J. Marshall, Zheming Wang, Nicholas J. Watmough, James K. Fredrickson, John M. Zachara, Julea N. Butt and David J. Richardson. Structure of a bacterial cell surface decaheme electron conduit. PNAS, May 23, 2011 DOI: 10.1073/pnas.1017200108

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Using microbes to generate electricity?

ScienceDaily (May 23, 2011) — Using bacteria to generate energy is a significant step closer following a breakthrough discovery by scientists at the University of East Anglia (UEA).

Published May 23 by the scientific journal Proceedings of the National Academy of Sciences (PNAS), the research demonstrates for the first time the exact molecular structure of the proteins which enable bacterial cells to transfer electrical charge.

The discovery means scientists can now start developing ways to 'tether' bacteria directly to electrodes -- creating efficient microbial fuel cells or 'bio-batteries'. The advance could also hasten the development of microbe-based agents that can clean up oil or uranium pollution, and fuel cells powered by human or animal waste.

"This is an exciting advance in our understanding of how some bacterial species move electrons from the inside to the outside of a cell," said Dr Tom Clarke of UEA's School of Biological Sciences.

"Identifying the precise molecular structure of the key proteins involved in this process is a crucial step towards tapping into microbes as a viable future source of electricity."

Funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the US Department of Energy, the project is led by Dr Clarke, Prof David Richardson and Prof Julea Butt of UEA, in collaboration with colleagues at the Pacific Northwest National Laboratory in the US.

In earlier research published by PNAS in 2009, the team demonstrated the mechanism by which bacteria survive in oxygen-free environments by constructing electrical wires that extend through the cell wall and make contact with a mineral -- a process called iron respiration or 'breathing rocks'.

In this latest research, the scientists used a technique called x-ray crystallography to reveal the molecular structure of the proteins attached to the surface of a Shewanella oneidensis cell through which electrons are transferred.

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by University of East Anglia.

Journal Reference:

Thomas A. Clarke, Marcus J. Edwards, Andrew J. Gates, Andrea Hall, Gaye F. White, Justin Bradley, Catherine L. Reardon, Liang Shi, Alexander S. Beliaev, Matthew J. Marshall, Zheming Wang, Nicholas J. Watmough, James K. Fredrickson, John M. Zachara, Julea N. Butt and David J. Richardson. Structure of a bacterial cell surface decaheme electron conduit. PNAS, May 23, 2011 DOI: 10.1073/pnas.1017200108

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Buried microbes coax energy from rock

In experiments, microorganisms stimulate minerals to produce hydrogen, a key fuel for growthWeb edition : Tuesday, February 8th, 2011

Here’s yet another reason to marvel at microbes: Buried deep within Earth at temperatures and pressures that would kill most living beings, bacteria and other tiny organisms not only survive but apparently even coax the rocks around them to produce food.

Researchers have found that the mere presence of microbes triggers minerals to release hydrogen gas, which the organisms then munch. “It looks like the bacteria themselves have an integral role in liberating this energy,” says R. John Parkes, a geomicrobiologist at Cardiff University in Wales.

His team’s findings appear in the March issue of Geology.

The work helps explain how microbes can survive up to kilometers deep in a subterranean world far from any sunlight to fuel photosynthesis. Such “deep biospheres” may even exist on other planets, Parkes says, with organisms tucked safely away from frigid temperatures and lethal radiation at the surface.

On Earth, some two-thirds of all bacteria, along with another group of single-celled organisms known as archaea, are thought to lurk underground. Scientists have long wondered where these critters get their energy.

Earlier work showed that the microbes fed, in part, on decayed organic matter that settled to the seafloor and formed thick sediments there — a sort of microbial smorgasbord. Parkes and his colleagues decided to look instead at inorganic minerals that can wash offshore and also end up in those sediments.

The researchers ground up a variety of minerals, such as quartz, and put them in a sludgy sediment. In some mixtures they added a dash of microbes to start things off. The scientists then heated the mixtures to various temperatures up to 100 degrees Celsius — what might be found 3 to 4 kilometers deep — and waited to see what happened over several months.

Mixtures that contained microorganisms began giving off hydrogen gas as temperatures climbed to 70° C and above, the team found. Mixtures that had been sterilized so that nothing was living in them didn’t produce much hydrogen at all. Somehow, Parkes says, the microbes help stimulate chemical reactions within the minerals that make hydrogen.

"The results are curious, but not compelling," says Steven D'Hondt, an oceanographer and geobiologist at the University of Rhode Island in Narragansett. For instance, he says, scientists would have to run the same experiments without any organic matter in the mixtures in order to be sure that the hydrogen was coming from the minerals and not from the organic matter.

Earthquake zones and other places with lots of geological activity often produce hydrogen and other gases, Parkes says, maybe because freshly split rocks and minerals provide a surface that catalyzes chemical reactions, such as the breaking apart of water molecules to produce oxygen and hydrogen. “But people had not linked that to a direct energy source for deep-sediment bacteria, and neither had they shown that the bacteria themselves could actually catalyze this process,” he says. “The fascinating thing is that we have a mechanism of obtaining energy organically in the subsurface which has not really been considered before.”

Bo Barker Jørgensen, a microbiologist at the Max Planck Institute for Marine Microbiology in Bremen, Germany, says that most buried microbes probably live at shallow depths, not the 3- to 4-kilometer depths simulated in the new study. (The deepest confirmed microorganisms come from 1.6 kilometers in sediments, and 3.5 kilometers in solid rock.) But Jørgensen adds that the new work shows how various groups of subterranean microorganisms thrive at different temperature levels.

Surface-minded researchers might do well to start thinking a bit more deeply.
Found in: Earth, Earth Science and Life

View the original article here