Bacterial Research

[Techne]

Post interesting research or articles associated with bacteria.

Some view Bacteria as computers making computers. Some view cells as Robust Computational Systems. Populations of bacteria appear to collectively weigh and initiate different survival strategies and Expect The Unexpected. These critters appear to be smarter than you thought being able to 'Learn' And Plan Ahead with their own language.

And now we are seeing the 'Dawning of a New Age' in Bacteria Research

ScienceDaily (July 12, 2010) — Lowly bacteria are turning out to be much more complex than previously thought.

In the July 2010 issue of the journal Molecular Microbiology, Loyola University Health System researchers describe an example of bacterial complexity, called "protein acetylation," which once was thought to be rare in bacteria.

This discovery that protein acetylation is common in bacteria has led to the "dawning of a new age" in bacterial research, senior author Alan Wolfe, PhD. and colleagues wrote.

Protein acetylation is a molecular reaction inside the cell. It modifies and thus affects the function of proteins, including the molecular machinery responsible for turning genes on or off.

Bacteria make up one of the three domains of life. The other two domains are archaea (single-cell organisms distinct from bacteria) and eukaryotes (which include plants and animals). Bacteria evolved before eukaryotes, but they are not as primitive as once thought.

"Bacteria have long been considered simple relatives of eukaryotes," Wolfe and colleagues wrote. "Obviously, this misperception must be modified."

For example, protein acetylation historically had been considered mostly a eukaryotic phenomenon. But recent research indicates that acetylation also has a broad impact on bacterial physiology.

"There is a whole process going on that we have been blind to," Wolfe said.

Wolfe's laboratory works with intestinal bacteria called Escherichia coli, commonly called E. coli. While some strains of E. coli can cause serious food poisoning, most strains are harmless or even beneficial.

E. coli and its 4,000 genes have been extensively studied for decades. Consequently, researchers now have the ability to quickly determine what happens when a gene is deleted or made more active. "We're explorers with lots of tools," Wolfe said.

Studying protein acetylation will improve scientists' basic understanding of how bacterial cells work. This in turn could lead to new drugs to, for example, kill or cripple harmful bacteria.

"We're in the very early days of this research," Wolfe said. "We're riding the front of the wave, and that's exhilarating. The graduate students in my lab are working practically around the clock, because they know how important this is."

Wolfe is a microbial geneticist and professor in the Department of Microbiology and Immunology at Loyola University Chicago Stritch School of Medicine. His co-authors are graduate students Linda Hu and Bruno Lima.

Wolfe's lab is supported by the Stritch School of Medicine Research Funding Committee and by a four-year $2 million grant from the National Institutes of Health.

Enjoy.

 

[Techne]

Wow, bacteria communicate via nanowires.... and make powergrids :wtf:.
Bacteria Grow Electrical Hair: Specialized Bacterial Filaments Shown to Conduct Electricity

ScienceDaily (Oct. 11, 2010) — Some bacteria grow electrical hair that lets them link up in big biological circuits, according to a University of Southern California biophysicist and his collaborators.

The finding suggests that microbial colonies may survive, communicate and share energy in part through electrically conducting hairs known as bacterial nanowires.

"This is the first measurement of electron transport along biological nanowires produced by bacteria," said Mohamed El-Naggar, assistant professor of physics and astronomy at the USC College of Letters, Arts and Sciences.

El-Naggar was the lead author of a study appearing online in Proceedings of the National Academy of Sciences.

Knowing how microbial communities thrive is the first step in finding ways to destroy harmful colonies, such as biofilms on teeth. Biofilms have proven highly resistant to antibiotics.

The same knowledge could help to promote useful colonies, such as those in bacterial fuel cells under development at USC and other institutions.

"The flow of electrons in various directions is intimately tied to the metabolic status of different parts of the biofilm," El-Naggar said. "Bacterial nanowires can provide the necessary links … for the survival of a microbial circuit."

A bacterial nanowire looks like a long hair sticking out of a microbe's body. Like human hair, it consists mostly of protein.

To test the conductivity of nanowires, the researchers grew cultures of Shewanella oneidensis MR-1, a microbe previously discovered by co-author Kenneth Nealson, Wrigley Professor of Geobiology at USC College.

Shewanella tend to make nanowires in times of scarcity. By manipulating growing conditions, the researchers produced bacteria with plentiful nanowires.

The bacteria then were deposited on a surface dotted with microscopic electrodes. When a nanowire fell across two electrodes, it closed the circuit, enabling a flow of measurable current. The conductivity was similar to that of a semiconductor -- modest but significant.

When the researchers cut the nanowire, the flow of current stopped.

Previous studies showed that electrons could move across a nanowire, which did not prove that nanowires conducted electrons along their length.

El-Naggar's group is the first to carry out this technically difficult but more telling experiment.

Electricity carried on nanowires may be a lifeline. Bacteria respire by losing electrons to an acceptor -- for Shewanella, a metal such as iron. (Breathing is a special case: Humans respire by giving up electrons to oxygen, one of the most powerful electron acceptors.)

Nealson said of Shewanella: "If you don't give it an electron acceptor, it dies. It dies pretty rapidly."

In some cases, a nanowire may be a microbe's only means of dumping electrons.

When an electron acceptor is scarce nearby, nanowires may help bacteria to support each other and extend their collective reach to distant sources.

The researchers noted that Shewanella attach to electron acceptors as well as to each other, forming a colony in which every member should be able to respire through a chain of nanowires.

"This would be basically a community response to transfer electrons," El-Naggar explained. "It would be a form of cooperative breathing."

El-Naggar and his team are among the pioneers in a young discipline. The term "bacterial nanowire" was coined in 2006. Fewer than 10 studies on the subject have been published, according to co-author Yuri Gorby of The J. Craig Venter Institute in San Diego, discoverer of nanowires in Shewanella.

Gorby and others became interested in nanowires when they noticed that reduction of metals appeared to be occurring around the filaments. Since reduction requires the transfer of electrons to a metal, the researchers suspected that the filaments were carrying a current.

Nanowires also have been proposed as conductive pathways in several diverse microbes.

"The current hypothesis is that bacterial nanowires are in fact widespread in the microbial world," El-Naggar said.

Some have suggested that nanowires may help bacteria to communicate as well as to respire.

Bacterial colonies are known to share information through the slow diffusion of signaling molecules. Nealson argued that electron transport over nanowires would be faster and preferable for bacteria.

"You want the telegraph, you don't want smoke signals," he said.

Bacteria's communal strategy for survival may hold lessons for higher life forms.

In an op-ed published in Wired in 2009, Gorby wrote: "Understanding the strategies for efficient energy distribution and communication in the oldest organisms on the planet may serve as useful analogies of sustainability within our own species."

In addition to El-Naggar, Gorby and Nealson, the study's authors were Thomas Yuzvinsky of USC College; Greg Wanger of The J. Craig Venter Institute; and Kar Man Leung, Gordon Southam, Jun Yang and Woon Ming Lau from the University of Western Ontario.

Funding for the research came from the Air Force Office of Scientific Research, the U.S. Department of Energy, the Legler-Benbough Foundation, the J. Craig Venter Institute, the Canadian Natural Science and Engineering Research Council, the Canada Foundation for Innovation and Surface Science Western.

Do Ocean-Bottom Bacteria Make Their Own Power Grids?

Deep on the ocean floor, colonies of bacteria appear to have connected themselves via microscopic power grids that would be the envy of any small town. Much remains unknown about the process, but if confirmed the findings could revolutionize scientists' understanding of how the world's smallest ecosystems operate.

Oxygen-breathing bacteria that live on the ocean bottom have a problem. Those sitting atop the sediment have ready access to oxygen in the water but not to the precious mineral nutrients that lie out of reach a centimeter or so below the ground. Meanwhile, those microbes that live in the sediment can access the nutrients, but they lack oxygen. How do both groups survive?

Microbial ecologist Lars Peter Nielsen of Aarhus University in Denmark figured the surface and subsurface bacteria were somehow exchanging oxygen and nutrients with one another. To find out how, he and colleagues scooped up some mud from the bottom of the 20-meter-deep ocean in Aarhus Bay and other waters near the university and plopped it into a beaker in their lab.

Then the researchers did something they knew would make the bacteria unhappy: They started removing the oxygen from the water. If the bacteria were swapping materials, as Nielsen had suspected, those living below the surface of the mud would have gradually noticed that their oxygen supply was being cut off; they would have registered chemical changes in the sediment that could be detected by sensors. But instead, Nielsen and colleagues witnessed something far more rapid. Almost as soon as the researchers began removing the oxygen, the subsurface bacteria stopped consuming hydrogen sulfide in the mud. More important, this metabolic shutdown was a sign that the buried bacteria almost instantly realized something in the environment far above them had changed. The researchers also detected very rapid pH changes in the water in the beaker.

These responses occurred too quickly for any sort of chemical exchange or molecular process such as osmosis, says Nielsen. The most plausible option, his team reports in the 25 February issue of Nature, is that the bacteria are somehow communicating electrically by transmitting electrons back and forth. How exactly they do this is unclear, but Nielsen suspects the organisms may all be connected to each other via a microscopic electric grid, possibly made from tiny grains of metal, such as iron and manganese, in the sediment.

If the wiring idea turns out to be true, it essentially would turn the bacterial community into a cross-sediment power grid—one that would span some 20 kilometers if scaled up for humans. Instead of receiving oxygen from the surface and turning it into energy—something the researchers say is not possible given the thickness of the sediment depth observed—the buried bacteria would simply receive energy in the form of electrons from the grid. In response, the subsurface bacteria could survive while buried and send nutrients back up to their comrades on the surface via chemical migration.

Still, Nielsen says, much remains unknown about how such a grid would work. "What are the wires made of?" he asks. "How do they connect to cells and one another, and how are they built?"

Geobiologist Kenneth Nealson of the University of Southern California in Los Angeles agrees that new findings "fall into the category of 'must have an explanation other than chemistry.' The excitement now lies in coming up with the mechanism responsible for electron movement."

 

[Techne]

Bacteria Can Stand-Up and 'Walk'

ScienceDaily (Oct. 8, 2010) — Many drug-resistant infections are the result of bacterial biofilms, structured aggregates of bacteria that live on surfaces and that are extremely resistant to environmental stresses. These biofilms impact human health in many ways -- cystic fibrosis, for example, is a disease in which patients die from airway bacterial biofilm infections that are invulnerable to even the most potent antibiotics.

Artist's representation of a bacterium "walking." (Credit: Image courtesy of UCLA)​

Now, UCLA researchers and their colleagues have found that during the initial stages of biofilm formation, bacteria can actually stand upright and "walk" as part of their adaptation to a surface.

"Bacteria exist in two physiological states: the free-swimming, single-celled planktonic state and the surface-mounted biofilm state, a dense, structured, community of cells governed by their own sociology," said Gerard Wong, a professor of bioengineering at the UCLA Henry Samueli School of Engineering and Applied Science and at the California NanoSystems Institute at UCLA.

"Bacteria in biofilms are phenotypically different from free-swimming bacteria even though they are genomically identical. As part of their adaptation to a surface and to the existence of a community, different genes are turned up and down for bacteria in biofilms, leading to drastically different behavior," he said.

In the study, which appears in the current issue of the journal Science, Wong and his research group describe the new surface adaptation -- the "walking" motility mechanism, which was observed in Pseudomonas aeruginosa, a biofilm-forming pathogen partly responsible for the lethal infections in cystic fibrosis.

What enables this upright walking are appendages called type IV pili, which function as the analog of legs. What's more, walking allows P. aeruginosa to move with trajectories optimized for surface exploration, so that they can forage more effectively. The upright orientation is also the first step in surface detachment for bacteria.

"We've shown that vertical orientation plays a critical role in key life-cycle events: vertically oriented bacteria can more readily detach from surfaces, allowing them to spread and disperse effectively," said Jacinta Conrad, a former postdoctoral researcher with Wong's group and an assistant professor of chemical and biomolecular engineering at the University of Houston. "Our unique contribution is to directly relate single-cell behavior to specific events in the bacterial life cycle and thereby show how single-cell motility influences biofilm morphology."

The research team was able to develop a series of search engines and computer programs that use particle-tracking algorithms to quantitatively analyze time-lapse microscopy movies of bacterial motion on surfaces.

"Previously, graduate students had to look at cells manually and then laboriously track them from one frame to the next," Wong said. "Our computational approach allows us to increase the volume of data analyzed 100,000-fold and to perform the necessary analysis in a few hours rather than a few months.

"Moreover, we make sense of this mountain of information using search engine-based approaches. This represents a big advance in the way microscopes are used."

The work was conducted in collaboration with a research group at the University of Notre Dame led by Joshua Shrout, an assistant professor in the department of civil engineering and geological sciences and at the Eck Institute for Global Health.

"P. aeruginosa infections are unfortunately the leading cause of death for individuals with cystic fibrosis," Shrout said. "In addition to these lung infections, P. aeruginosa also causes skin, eye and gastrointestinal infections. As we learn how P. aeruginosa colonizes surfaces, perhaps we can develop better methods to treat these infections."

"One of the most exciting factors of this work for me is the potential for widespread impact," Conrad said. "Biofilm formation is ubiquitous in human health and also in a variety of industrial settings. Biofouling due to biofilm formation increases the hydrodynamic drag on ships, leading to increased fuel consumption, and also contributes to increased costs in water treatment, oil recovery and food processing. Controlling biofilm formation will therefore allow us to reduce biofouling-related problems across a wide range of industries."

This research was funded by the National Institutes of Health under the American Recovery and Reinvestment Act, the National Science Foundation and the Cystic Fibrosis Foundation.

Wonder if they can dance .

 

[Geriatrix]

I wonder if they dream too?

 

[Techne]

Naw, but they sure seem to worry a lot

 

[Techne]

Researchers Unlock the Secret of Bacteria's Immune System

ScienceDaily (Nov. 4, 2010) — A team of Université Laval and Danisco researchers has just unlocked the secret of bacteria's immune system. The details of the discovery, which may eventually make it possible to prevent certain bacteria from developing resistance to antibiotics, are presented in the November 4 issue of the scientific journal Nature.

The team led by Professor Sylvain Moineau of Université Laval's Department of Biochemistry, Microbiology, and Bioinformatics showed that this mechanism, called CRISPR/Cas, works by selecting foreign DNA segments and inserting them into very specific locations in a bacterium's genome. These segments then serve as a kind of immune factor in fighting off future invasions by cleaving incoming DNA.

The researchers demonstrated this mechanism using plasmids, DNA molecules that are regularly exchanged by bacteria. The plasmid used in the experiment, which contained a gene for antibiotic resistance, was inserted into bacteria used in making yogurt, Streptococcus thermophilus. Some of the bacteria integrated the segments of DNA from the resistance gene into their genome, and subsequent attempts to reinsert the plasmid into these bacteria failed. "These bacteria had simply been immunized against acquiring the resistance gene, commented Professor Moineau. This phenomenon could explain, among other things, why some bacteria develop antibiotic resistance while others don't."

The CRISPR/Cas immune system also protects bacteria from bacteriophages, a group of viruses that specifically target bacteria. This makes Professor Moineau's discovery particularly interesting for food and biotechnology sectors that use bacterial cultures, such as the yogurt, cheese, and probiotics industries. Bacterial culture contamination by bacteriophages is a serious concern with considerable financial implications for those industries.

 

[Techne]

More interesting research:
Antibiotic Resistance Is Not Just Genetic

ScienceDaily (Jan. 5, 2011) — Genetic resistance to antibiotics is not the only trick bacteria use to resist eradication- they also have a second defence strategy known as persistence that can kick in.

Researchers reporting in the Journal of Medical Microbiology have now demonstrated for the first time that interplay occurs between the two mechanisms to aid bacterial survival. The findings could lead to novel, effective approaches to treat multi-drug resistant (MDR) infections.

'Persister' bacterial cells are temporarily hyper-resistant to all antibiotics at once. They are able to survive (normally) lethal levels of antibiotics without being genetically resistant to the drug. These cells are a significant cause of treatment failure yet the mechanism behind the persistence phenomenon is still unclear.

Scientists from Centre of Microbial and Plant Genetics, at the Katholieke Universiteit Leuven, Belgium found that the number of persister cells isolated from Pseudomonas aeruginosa infections decreases when the bacterial population shows genetic resistance to the antibiotic fosfomycin.

P. aeruginosa is an opportunistic human pathogen and a significant cause of hospital-acquired infections. It can cause fatal infections in people suffering from cystic fibrosis. The bacterium is notorious for its ability to develop resistance against commonly-used antibiotics and treatment failure is common.

Professor Jan Michiels who led the study explained that persister cells are a major contributor to treatment failure. "Persister cells are produced in low numbers, but nevertheless make it almost impossible to completely remove the bug from the patient. As a result, eradication of infections through antibiotic treatment usually takes a long time," he said. "Our work shows that antibiotic treatment may also influence the number of persisters formed."

Co-administration therapies are being developed to treat MDR infections, in which drugs targeting non-essential cellular functions are combined with antibiotics. Professor Michiels explained that targeting persistence is an attractive option. "Ideally both susceptible and persistent cells would be targeted in a single therapy, but firstly we need to understand more about the interplay between genetic resistance and persistence to avoid stimulating one or the other. Unravelling the mechanism behind bacterial persistence is really important to enable us to optimise treatments of chronic bacterial infections."

 

[Techne]

A major cause in the evolution of bacterial resistance seems to be the relocation and sharing of pre-exiting resistance via horizontal gene transfer e.g. genes found on plasmids.
Gene 'Relocation' Key to Most Evolutionary Change in Bacteria

ScienceDaily (Jan. 27, 2011) — In a new study, scientists at the University of Maryland and the Institut Pasteur show that bacteria evolve new abilities, such as antibiotic resistance, predominantly by acquiring genes from other bacteria.

The researchers new insights into the evolution of bacteria partly contradict the widely accepted theory that new biological functions in bacteria and other microbes arise primarily through the process of gene duplication within the same organism. Their just released study will be published in the open-access journal PLoS Genetics on January 27.

Microbes live and thrive in incredibly diverse and harsh conditions, from boiling or freezing water to the human immune system. This remarkable adaptability results from their ability to quickly modify their repertoire of protein functions by gaining, losing and modifying their genes. Microbes were known to modify genes to expand their repertoire of protein families in two ways: via duplication processes followed by slow functional specialization, in the same way as large multicellular organisms like us, and by acquiring different genes directly from other microbes. The latter process, known as horizontal gene transfer, is notoriously conspicuous in the spread of antibiotic resistance, turning some bacteria into drug-resistant 'superbugs' such as MRSA (methicillin-resistant Staphylococcus aureus), a serious public health concern.

The researchers examined a large database of microbial genomes, including some of the most virulent human pathogens, to discover whether duplication or horizontal gene transfer was the most common expansion method. Their study shows that gene family expansion can indeed follow both routes, but unlike in large multicellular organisms, it predominantly takes place by horizontal transfer.

First author Todd Treangen, a postdoctoral researcher in the University of Maryland Center for Bioinformatics and Computational Biology and co-author Eduardo P. C. Rocha of the Institut Pasteur conclude that because microbes invented the majority of life's biochemical diversity -- from respiration to photosynthesis --, "the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families."