Studies Begin to Shape New Image of DNA

The figure illustrates the molecular shape of a region of nucleosomal DNA when wrapped around the histone core, with the narrow minor groove in dark grey. The red mesh shows a surface with negative electrostatic potential. The shape of narrow minor groove regions induces an enhanced negative electrostatic potential, which is read by histone arginines. Such interactions between the protein and DNA contribute to the stabilization of the nucleosome core particle.

Most of us carry a mental picture of DNA in its iconic form – the famous double helix unveiled by Francis Crick and James Watson. But researchers are beginning to develop a new picture of DNA that shows the molecule’s more dynamic side, which is capable of morphing into a large number of complex shapes. This shape-shifting ability permits proteins to attach and read the right region of DNA so genes can be turned on or off at the proper time.
The findings show that proteins are adept at reading nuances in the shape of the double helix. Those variations in shape transmit information about where proteins need to bind to make sure the right genes are activated or silenced during development.
“The ideal double helix should not be viewed as a rigid entity but rather seen as a first approximation to a large set of more complex shapes that are recognized by proteins so as to bind to DNA in a sequence-specific fashion,” said Howard Hughes Medical Institute investigator Barry Honig at Columbia University.
Honig and his colleagues have discovered a new mechanism by which proteins recognize specific regions of DNA. Their research is reported in the October 29, 2009, issue of the journal Nature.
Even for seasoned biologists, the endless stream of A, T, G and C nucleotides in the genetic code can look like a string of letters in a long book that makes no sense. It can be easy to get lost. But proteins that bind to DNA to turn genes on or off have an innate intelligence -- they know how to read the book. One of their “secrets” is to follow a set of instructions that are hidden inside the DNA sequence.
Scientists have long known that specialized DNA-binding proteins, such as transcription factors that activate and repress genes, look for their docking sites on DNA by scanning the genome for a specific nucleotide sequence that says “bind here.” When proteins recognize that sequence, they bind to DNA and begin to do their jobs. But over the last 20 years, researchers have accumulated evidence that the physical shape of DNA can also influence where and when proteins attach to DNA.
The new studies published in Nature by Honig and his colleagues, Remo Rohs, Sean West, Alona Sosinsky, Peng Liu and Richard Mann, extend those results and describe a new recognition strategy that proteins use to identify and bind to DNA. The coiled, complementary strands of DNA form 'major' and 'minor' grooves, to which proteins can bind. The recognition strategy identified by Honig’s team depends on proteins’ ability to read DNA shape – specifically, the width of the minor grooves.
The work originated with an earlier study of how a particular transcription factor, known as a Hox protein, achieves DNA binding specificity. Hox proteins are important for determining the overall body plan in all animals and need to bind to their DNA targets with great specificity, so that they can control the activity of only the appropriate genes. Previous work from a number of labs had revealed common features that all Hox proteins share when they bind to DNA, but scientists did not know how individual Hox proteins distinguish between different binding sites.
In 2007, Honig and collaborators in the labs of geneticist Richard Mann and x-ray crystallographer Aneel Aggarwal compared the structures of two different DNA sequences bound to a Hox protein. One DNA sequence was highly selective for a particular Hox protein, while the other was able to bind multiple Hox proteins. They found that the selective DNA target had a narrower minor groove than is typical for double-helical DNA. In contrast, the less selective DNA sequence had a different, less narrow, minor groove shape.
“The question for us was, why is that important?” Honig says. “What we showed is that the electrostatic potential of the DNA – which is used to attract positive charges – is stronger when a groove is narrow.” Intriguingly, the width and shape of the grooves are affected by single-letter changes in the DNA sequence. In other words, the sequence of DNA determines its precise shape, which then provides a target for the proper protein to bind.
“It is quite surprising actually,” Honig says. “If you now realize that those nucleotides determine which proteins bind the DNA, and they do it in part through their effect on shape, you begin to understand how sensitive and subtle the DNA structure really is, and how this in turn affects how it's being read.”
With proof of this new type of DNA recognition strategy in hand, the team next set out to see whether their concept was generalizable – whether it would apply to proteins outside of the Hox family.
They probed a database of molecular structure information about DNA-protein complexes, looking at how the DNA’s sequence and structure matched up with each of the protein’s amino acid building blocks. They found that narrow minor grooves tended to attract parts of the protein that contained the amino acid arginine, which is positively charged. They saw that there are many arginine binding sites in DNA that have narrower minor grooves and that these have more negative electrostatic potentials that attract positively charged regions of proteins.
“The proteins are actually reading the shape of the DNA through its effect on electrostatic potential,” Honig says. “Sequence determines shape, which determines the affinity for arginines --a mechanism made possible because DNA does not form a perfect double helix.”
Honig’s group plans to examine RNA, the intermediate molecule produced when DNA’s information is translated into protein. He and his colleagues will be looking for similar relationships between sequence, shape and electrostatic potential. They also hope to use the relationship between DNA sequence and shape to predict which sequences of the DNA are bound by transcription factors and which proteins recognize these regulatory regions. Honig says he and other researchers are now thinking about DNA in new ways: A separate research group recently compared the shapes of DNA in different species and concluded that these molecular nuances are shaped by evolution. “Taken together with our studies, the results offer a new way to think about DNA,” Honig says.

Researchers Discover RNA Repair System in Bacteria
(Oct. 22, 2009) In new papers appearing this month in Science and the Proceedings of the National Academy of Sciences, University of Illinois biochemistry professor Raven H. Huang and his colleagues describe the first RNA repair system to be discovered in bacteria. This is only the second RNA repair system discovered to date (with two proteins from T4 phage, a virus that attacks bacteria, as the first).

The novelty of the newly discovered bacterial RNA repair system is that, before the damaged RNA is sealed, a methyl group is added to the two-prime hydroxyl group at the cleavage site of the damaged RNA, making it impossible to cleave the site again. Thus, the repaired RNA is "better than new."
This discovery has implications for protecting cells against ribotoxins, a class of toxins that kills cells by cleaving essential RNAs involved in protein translation. Because the enzyme responsible for methylation in the newly discovered RNA repair system is the Hen1 homolog in bacteria, the finding has also implications for the understanding of RNA interference and gene expression in plants, animals, and other eukaryotes. The eukaryotic Hen1 is one of three enzymes (along with Dicer and Argonaute) essential for the generation of small noncoding RNAs of 19-30 nucleotides in RNA interference.
While the Science paper describes the mechanism of the entire RNA repair process, the article in PNAS focuses on the chemistry of the methylation reaction, specifically the crystal structure of the methyltransferase domain of bacterial Hen1. Because the eukaryotic Hen1 carries out the same chemical reaction, the study should further understanding of RNA interference in eukaryotic organisms.
"Hen1 is one of three essential enzymes in generating small noncoding RNAs for RNA interference in eukaryotes," Huang said. "We found out that Hen1 homologs exist in bacteria, but bacteria have no RNA interference. Therefore, we were very curious to find out what bacterial Hen1 is used for."
"Our studies demonstrated that bacterial Hen1 carries out the same chemical reaction as its counterpart in eukaryotes, which was not surprising," he said. "What surprised us was that, instead of involvement in RNA interference, the bacterial Hen1 is part of a RNA repair and modification system. And Hen1 is responsible for producing the repaired RNA that is 'better than new.'"

An Introduction to "RNA-Repair" can be aviled at the following link:

http://www3.umdnj.edu/mobioweb/moss/pdfs/BellacosaMoss.pdf

BACTERIA AS AN ART

Biophysicists are growing Petri dishes of different species of bacteria in order to develop new antibiotics. The bacteria are subjected to different temperatures and have limited food sources inside the dish. Despite these conditions, most colonies tend to communicate and reproduce. Their growth results in unique patterns of varying colors--a sort of "bacteria painting." Researchers are hoping to learn more about the strategies the bacteria use to thrive, in order to find weaknesses that new drugs could exploit.

There was a time when doctors thought antibiotics could cure all. It's a different story today as drug-resistant bacteria emerge in places like hospitals and schools. To keep up with changes in bacterial behavior, scientists are fighting bacteria using an artistic approach. Biophysicist Herbert Levine's Petri dishes look like an exhibit at a modern art museum. His beautiful images are actually made from bacteria similar to the ones that cause deadly diseases. Dr. Levine uses bacteria in Petri dishes in his quest to discover the next super drug. He's fighting a new generation of bacterial infections that includes MRSA, a flesh-eating disease resistant to antibiotics. Dr. Levine and his team have gone back to the basics of biology. They have created bacteria patterns by changing the temperature and limiting the food sources inside Petri dishes. Despite harsh conditions, the colonies find ways to communicate and reproduce. Through Dr. Levine's work, scientists have learned bacteria are very resourceful. They enclose themselves in areas antibiotics can't find. They also soak up antibiotics to keep the rest of their colony safe and transform themselves into new strains that are less sensitive to the drugs. Along the way, scientists turned the study of bacteria into an art form. Dr. Levine and his colleague, Eshel Ben-Jacob, use the patterns to create computer models. One day those models could be the basis for new medicines that fight all types of bacteria.

WHAT IS MRSA: MRSA is a common cause of skin infections; it can also cause pneumonia, ear infections and sinusitis. MRSA bacteria are sometimes dubbed 'superbugs' because they are highly resistant to common antibiotics like penicillin, making infections difficult to treat effectively. Bacteria are highly adaptive, and over time they naturally develop resistance, protecting them from incoming germs (and antibiotics) and making them harder to kill. If MRSA enters the body through the skin, it can cause irritating skin infections, but if it enters the lungs or bloodstream, it can cause serious blood infections, pneumonia, even death. MRSA infection rates in the US have been increasing since 1970, largely because surveillance programs to monitor its spread are not effective. Other countries, such as the Netherlands, Sweden and Denmark have all but eliminated MRSA from their hospitals through such surveillance programs, which focus on screening patients for MRSA at admission and isolating any carriers.

DRUG RESISTANCE: Bacteria are highly adaptive, and over time they naturally develop resistance, protecting them from incoming germs (and antibiotics), which makes them more difficult to kill. If someone has strep throat, for example, repeated exposure to penicillin and amoxicillin can result in a throat full of bacteria that can shield strep germs from the older drugs. The surviving bacteria then reproduce more and become more dominant. Sometimes parents discontinue antibiotic medication prematurely when they or their children begin to feel better, so the strep germ isn't entirely killed off, leading to much more severe infections requiring the use of even stronger drugs later on. This can also happen with many other infections inside the body and on the skin.

For Downloading Some more interesting Bacterial Patterns and Information Please visit:

http://star.tau.ac.il/~eshel/gallery.html

E. coli - Why is it a Master and Model of GENETIC EFFICIENCY
The bacterium Escherichia coli, one of the best-studied single-celled organisms around, is a master of industrial efficiency. This bacterium can be thought of as a factory with just one product: itself. It exists to make copies of itself, and its business plan is to make them at the lowest possible cost, with the greatest possible efficiency.

A bacterium like E. coli can be thought of as a self replicating factory, where inventory synthesis, degradation, and management is concerted according to a well-defined set of rules encoded in the organism’s genome. Since the organism’s survival depends on this set of rules, these rules were most likely optimized by evolution. Therefore, by writing down these rules, what could one learn about Escherichia coli? Scientists examined E. coli growing in the simplest imaginable environment, one constant in space and time and rich in resources, and attempted to identify the rules that relate the genome to the cell composition and self-replication time. With more than 4,400 genes, a full-scale model would be prohibitively complicated, and therefore they "coarse-grained" E. coli by lumping together genes and proteins of similar function. They used this model to examine measurements of strains with reduced copy number of ribosomal-RNA genes, and also to show that increasing this copy number overcrowds the cell with ribosomes and proteins. As a result, there appears to be an optimum copy number with respect to the wild-type genome, in agreement with observation. They hope that this model will improve and further challenge our understanding of bacterial physiology, also in more complicated environments.

Efficiency, in the case of a bacterium, can be defined by the energy and resources it uses to maintain its plant and produce new cells, versus the time it expends on the task. Dr. Tsvi Tlusty and research student Arbel Tadmor of the Physics of Complex Systems Department developed a mathematical model for evaluating the efficiency of these microscopic production plants. Their model, which recently appeared in the online journal PLoS Computational Biology, uses only five remarkably simple equations to check the efficiency of these complex factory systems.
The equations look at two components of the protein production process: ribosomes – the machinery in which proteins are produced – and RNA polymerase – an enzyme that copies the genetic code for protein production onto strands of messenger RNA for further translation into proteins. RNA polymerase is thus a sort of work ‘supervisor’ that keeps protein production running smoothly, checks the specs and sets the pace.

The first equation assesses the production rate of the ribosomes themselves; the second the protein output of the ribosomes; the third the production of RNA polymerase.
The last two equations deal with how the cell assigns the available ribosomes and polymerases to the various tasks of creating other proteins, more ribosomes or more polymerases. The theoretical model was tested in real bacteria. Do bacteria ‘weigh’ the costs of constructing and maintaining their protein production machinery against the gains to be had from being able to produce more proteins in less time? What happens when a critical piece of equipment is in short supply, say a main ribosome protein? Tlusty and Tadmor found that their model was able to accurately predict how an E. coli would change its production strategy to maximize efficiency following disruptions in the work flow caused by experimental changes to genes with important cellular functions. What’s the optimum? The model predicts that a bacterium, for instance, should have seven genes for ribosome production. It turns out that that’s exactly the number an average E. coli cell has. Bacteria having five or nine get a much lower efficiency rating. Evolution, in other words, is a master efficiency expert for living factories, meeting any challenges that arise as production conditions change.

For a detailed account download the following original research paper:
http://www.weizmann.ac.il/complex/tlusty/papers/PLoSCompBio2008.pdf

Fungi and Bacteria in Ventilation Systems
Fungi growing in ventilation systems may contaminate indoor environments and cause a variety of problems. Some fungi can cause lung infections. Many fungi can cause allergic reactions in susceptible people and respiratory irritation in non-allergic people.Inhalation of fungal spores by highly susceptible people can have fatal consequences. Some environmental bacteria can grow in ventilation systems, but these are raely a threat to healthy people. They can, however, be a nosocomial problem. Low levels of airborne fungi can be a primary or contributing cause of Sick Building Syndrome (SBS) and poor Indoor Air Quality (IAQ). The photomicrograph at the right shows lung tissue infected with a growing mycelium of aspergillus. Fungi differ significantly, in certain respects, from most other airborne pathogens, such as bacteria, viruses, and protozoa. Fungi do not cause secondary contagious infections; only the person inhaling the fungi is at risk. Fungi can exist outdoors and enter the building through the air intakes. No other respiratory pathogens can exist outdoors - viruses and bacteria are carried and transmitted indoors by human or animal hosts, with anthrax being the one exception. Fungi are normally harmless and non-parasitic. Fungal infections inevitably result from fungi being in the wrong place, often as the result of poor cleanliness or improper design of ventilation system components.
Fungi are actually plants that contain no chlorophyll -- see this chart.

The true fungi are the Eumycetes. Some of the fungi, the mushrooms, yeasts and some of the molds are extremely beneficial to us. They assist the production of cheese, antibiotics, yogurt, wine and beer. Some fungi, like the blights, can cause extensive crop damage. Dutch Elm disease is, in fact, a fungus. In buildings, the ones that cause problems when they get into the wrong place are usually certain of the ascomycetes.
Airborne Pathogenic Fungi
Only certain fungi can produce infections, and only a few of these have been noted to travel via the airborne route, or become entrained in the airflow of intake ducts. The following chart list those fungi which are of primary concern:

Fungi from Outdoors
Fungi produce spores, in much the same way as bacteria do, and this enables them to survive harsh conditions while they travel or lie dormant. Spores are usually what enter the building air intakes and what can travel through the ventilation airstream. Fungal spores are smaller than fungal cells and can vary in size from 1 micron to 100 microns. A well-maintained HEPA filter should be capable of intercepting the vast majority of fungal spores. At the right is an image of a colony of Candida albicans that has produced a number of large and small spores.
Fungi are ubiquitous in the outdoors, but occur in high concentrations only in hot Southern climates, especially during dry spells. Florida, Louisiana, Texas, New Mexico and southern California often experience high seasonal mold spore levels. Generally, when the ground dries after a period of moisture, the winds can overturn the top layers of soil and disperse large quantities of mold spores. These can be carried aloft into urban areas, where they are drawn into air intakes and building ventilation systems. The photo at left shows the long growing branches of mycelium that are characteristic of Nocardia asteroides, from a sputum sample of an infected patient. Nocardia are bacteria called actinomycetes, which greatly resemble fungi in characteristics, and they also produce spores.
Even though the problem is more common in southern states, it only takes the right conditions for microscopic quantities of fungi to gain a foothold in a ventilation system. This situation has occurred across the US, regardless of climate. Many, if not most, cases of poor IAQ and SBS can be tied directly to the occurrence of mold spores either in the ventilation ducts, or in the walls of buildings. Sometimes, fungi are merely a contributing factor when the ventilation is inadequate -- normal levels of airborne fungi are not removed from the building air.
Dealing with Fungi in Ventilation Systems
Filtration provides the primary defense against fungal spores entering a building ventilation system. Pre-filters can be effective against most fungi, even when in the spore form. If a higher degree of protection is required, HEPA filters can be very effective, provided they are tightly installed, and well maintained. Fungus can grow on HEPA filters as well as other ventilation components and, if unchecked, can actually contribute to the problem. The image at right shows a layer of actinomyces mycelium growing on a surface.
Fungus or fungal spores from the outdoors can be dealt with easily, as described above. If, however, the fungus is already growing inside the building or ventilation system, the problem becomes somewhat more difficult. Fungi require moisture for growth. The source of the moisture must be identified and then controlled.
Cooling coils, drains pans, and water pans for humidifiers are likely locations for fungal growth, especially when there is standing water. These must be treated as necessary with proper disinfectants. Some systems provide built-in UVGI lights for continuous disinfection. These components should be disassembled and cleaned with a strong disinfectant, such as chlorine, when fungal or bacterial growth is found. Clogged drains are often a cause for standing water.
Condensation on ductwork or other components is another likely source of moisture. The ductwork must be inspected for fungal growth and cleaned with a disinfectant. The cause of the condensation must be identified. Often, it results from inadequate insulation, or leakage into, or out of, the ductwork. Sometimes return air can leak into the supply air duct and result in localized condensation. Sometimes the insulation itself can absorb and hold moisture, resulting in fungus growth that may then directly or indirectly produce contamination of the building air. Smoke tests, or airflow measurements, and/or pressure tests can determine duct leakage.

In the absence of water they may reduce to spore form, which makes them even more subject to air entrainment. Therefore, a cycle of condensation and dehydration may exacerbate a fungal dispersion problem. In this case, the problem might be perplexing to isolate -- sometimes the duct and components will appear dry, while cases of respiratory irritation or infection may occur in irregular cycles that could ultimately depend on humidity variations. Every situation can be unique and must be studied carefully.
Air Sampling and Testing
Sampling of airborne microorganisms can be inconclusive. There are no absolute standards, and decisions on whether a building has a fungus problem or not are often made arbitrarily. Methods of collection can give divergent results and are therefore heavily subject to interpretation. Swabbing a sample from a duct or an exhaust grille will yield some concentration of fungal or bacterial cells, but doesn't exactly correlate with airborne concentrations.
Measuring airborne concentrations can likewise produce results that depend on interpretation. Often, the testing agencies will not identify the specific microorganisms, but will merely state that colonies were formed, or that there is a potential contamination problem. Most fungi are unique and have distinctive characteristics. The photomicrograph at right shows a colony of actinomyces, in which the radiating rays of the mycelium are clearly visible around the central granule.
Any studies contracted to be performed, such as on schools or office buildings, should be required both to state the types of microorganisms discovered, their probable airborne concentrations, and how these compare with standards or typical concentrations in normal, or "healthy," buildings.

For further information please follow the following Link:
http://www.cancerfungus.com/pdf/fungi-nexus.pdf
http://www.naima.org/pages/resources/library/pdf/RP032.PDF
http://www.library.ca.gov/crb/01/notes/v8n1.pdf

New Family Of Antibacterial Agents Uncovered
As bacteria resistant to commonly used antibiotics continue to increase in number, scientists keep searching for new sources of drugs. One potential new bactericide has now been found in the tiny freshwater animal Hydra.

The protein identified by Joachim Grötzinger, Thomas Bosch and colleagues at the University of Kiel, hydramacin-1, is unusual (and also clinically valuable) as it shares virtually no similarity with any other known antibacterial proteins except for two antimicrobials found in another ancient animal, the leech.
Hydramacin proved to be extremely effective though; in a series of laboratory experiments, this protein could kill a wide range of both Gram-positive and Gram-negative bacteria, including clinically-isolated drug-resistant strains like Klebsiella oxytoca (a common cause of nosocomial infections). Hydramacin works by sticking to the bacterial surface, promoting the clumping of nearby bacteria, then disrupting the bacterial membrane.
Grötzinger and his team also determined the 3-D shape of hydramacin-1, which revealed that it most closely resembled a superfamily of proteins found in scorpion venom; within this large group, they propose that hydramacin and the two leech proteins are members of a newly designated family called the macins.

For an Abstract of the above Research Please visit the following link: http://www.jbc.org/cgi/content/abstract/284/3/1896

MAGNETOTACTIC BACTERIA - Current research and Applications
Oxygen is essential for human life, but it is corrosive and poisonous to many bacteria. Magnetotactic bacteria evolved a clever method of using the Earth's magnetic field to orient itself and swim downward – exactly the direction a microbe must move to locate low oxygen areas in lakes and oceans. To find the direction of the magnetic field, these bacteria synthesize nanoscale cellular structures called magnetosomes that contain crystals of naturally occurring magnetic minerals.
The shape and composition of magnetosomes are species- and strain-specific, suggesting that magnetosome synthesis is biologically controlled. Magnetosomes are currently difficult to harvest in large quantities or synthesize artificially, therefore deciphering how cells form magnetosomes is crucial if they are to be useful in new technologies.
Genetic analyses have been performed in closely related magnetotactic bacteria, but because magnetosomes are also found in other classes of bacteria, scientists do not yet have a clear picture of the genetic components necessary for magnetosome formation. Tadashi Matsunaga of the Tokyo University of Agriculture and Technology and colleagues recognized that by analyzing the genome of more distantly related magnetotactic bacteria, researchers may be able to clearly define the minimal gene set needed for magnetosome synthesis.
In this work, Matsunaga's group sequenced the genome of Desulfovibrio magneticus strain RS-1, a more distant relative of other magnetotactic bacteria previously studied, and is also known for the unique bullet-shape of its magnetosomes. "This bacteria could be the key to opening up new applications for magnetosomes.

Comparing the RS-1 genome sequence to the genomes of other magnetotactic bacteria, the team determined that all magnetotactic bacteria contain three separate gene regions related to magnetosome synthesis. Surprisingly, they also found that magnetosome-related genes are very well conserved across different classes of bacteria. Matsunaga explained that this suggests that the core magentosome genes may have been established in these bacteria by several horizontal gene transfer events, rather than being passed down through a lineage.
In addition to illuminating core magnetosome genes, the group expects that their work on RS-1 will be a stepping-stone to manipulation of magnetosomes for new technologies. Further research with RS-1 could open doors to the synthesis of morphologically controlled magnetosomes, and provide opportunities to their applications in electromagnetic tapes, drug delivery, magnetic resonance imaging, and cell separation.
Magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) with well-controlled size and morphology. BacMPs are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. Recent molecular studies including genome sequence, mutagenesis, gene expression and proteome analyses indicated a number of genes and proteins which play important roles for BacMP biomineralization. Some of the genes and proteins identified from these studies have allowed us to express functional proteins efficiently onto BacMPs, through genetic engineering, permitting the preservation of the protein activity, leading to a simple preparation of functional protein–magnetic particle complexes. They were applicable to high-sensitivity immunoassay, drug screening and cell separation. Furthermore, fully automated single nucleotide polymorphism discrimination and DNA recovery systems have been developed to use these functionalized BacMPs. The nano-sized fine magnetic particles offer vast potential in new nano-techniques.

For observing the Research Paper on the above article visit the following link:
http://rsif.royalsocietypublishing.org/content/5/26/977.full.pdf+html

For downloading Full length Paper Right Click and "Save" the following link:
http://rsif.royalsocietypublishing.org/content/5/26/977.full.pdf

'Green' Energy From Algae

In view of the shortage of petrochemical resources and climate change, development of CO2-neutral sustainable fuels is one of the most urgent challenges of our times. Energy plants like rape or oil palm are being discussed fervently, as they may also be used for food production. Hence, cultivation of microalgae may contribute decisively to tomorrow’s energy supply. For energy production from microalgae, KIT scientists (Karlsruhe Institute of Technology, GERMANY) have developed closed photo-bioreactors and novel cell disruption methods.

Microalgae are monocellular, plant-like organisms engaged in photosynthesis and converting carbon dioxide (CO2) into biomass. From this biomass, both potential resources and active substances as well as fuels like biodiesel may be produced. While growing, algae take up the amount of CO2 that is later released again when they are used for energy production. Hence, energy from algae can be produced in a CO2-neutral manner contrary to conventional energy carriers.
Apart from CO2-neutral closed loop management, algae have an-other advantage: Industrial CO2 emissions may be used as a “resource”, as algae grow faster at high carbon dioxide concentrations and, hence, produce more biomass for energy production.
However, this is not their only advantage-According to Professor Clemens Posten, who directs this research activity at the KIT Institute of Life Science Engineering Compared to land plants, algae produce five times as much biomass per hectare and contain 30 to 40% oil usable for energy production. As the algae may also be cultivated in arid i.e. dry, areas not suited for agriculture, there is hardly any competition with agricultural areas. There, however, closed systems are required.

Presently, algae are being produced in open ponds in southern countries of relatively small productivity. This is where the new technology starts as the novelty is in using closed photobioreactors . Plants convert solar energy into biomass, the efficiency being five times higher than that in open ponds. The plates in usual photo-bioreactors are arranged vertically. Every alga sees a little bit less light, but the plant is operated at increased efficiency. Modern designs under investigation will find more intelligent ways to light distribution.
Consequently, algae production does not only work in countries with an extremely high solar irradiation. Most algae need a maximum of ten percent of the incident sunlight intensity. According to Posten, the remaining fraction would just be wasted. But there, the reactor contents would have to be cooled. Other advantages of the closed system are drastic savings of water and fertilizers. Double use of algae for the production of food or fine chemicals and subsequent energy production from the residual biomass may also be conceivable. Posten’s institute hosts one of the two KIT working groups focusing on research in the field of algae biotechnology and as far as the development of photobioreactors is concerned, it is among the three locations worldwide, where considerable progress is being achieved in both process technology and biology.
The researchers plan to convert the biomass remaining after extraction (60 – 70%) into other energy carriers like hydrogen or methane by means of the hydrothermal gasification process.

For More Information and Downloads Right Click and "Save":

www.physorg.com/pdf168769898.pdf

http://www.chemeurope.com/news/e/pdf/news_chemeurope.com_104460.pdf

http://www1.eere.energy.gov/biomass/pdfs/algalbiofuels.pdf

Ulcer-causing Bacteria: The Biochemical Mechanism which Enables Bacteria to Colonize Host
A team of researchers from Boston University, Harvard Medical School and Massachusetts Institute of Technology recently made a discovery that changes a long held paradigm about how bacteria move through soft gels. They showed that the bacterium that causes human stomach ulcers uses a clever biochemical strategy to alter the physical properties of its environment, allowing it to move and survive and further colonize its host.
The Proceedings of the National Academy of Sciences reports the findings in its most recent issue. Helicobacter pylori is a bacterium that inhabits various areas of the stomach where it causes chronic, low-level inflammation and is linked to gastric ulcers and stomach cancer. In order to colonize the stomach, H. pylori must cope with highly acidic conditions in which other bacteria are unable to survive. It is well known however, that the bacterium accomplishes this by producing ammonia to neutralize the acid in its surroundings. In addition, newly published research shows it does something else; it changes its environment to enable freer movement. Acidic conditions within the stomach also work against the bacteria's ability to move freely. This is due to a protein called "mucin," a crucial component of the protective mucus layer in the stomach. In the presence of acid mucin forms a protective gel, which acts as a physical barrier that stops harmful bacteria from reaching the cell wall. But, H. pylori increases the pH of its surroundings and changes this "mucin" gel to a liquid, allowing the bacterium to swim across the mucus barrier, establish colonies, attack surface cells and form ulcers. "Bacteria 'swim' through watery fluids using their tails to propel them," according to Boston University physicist Rama Bansil.
But it was not obvious how they move through a soft gel like mucus. Using video microscopes, the researchers found that when mucins extracted from mucus were in a liquid state, the bacteria could swim freely, but when mucins were in a gel state, the bacteria were stuck, even though their tails were rotating. More advanced imaging techniques revealed that pH changes directly correlated with the ability of the bacteria to move--the higher the pH, the greater the movement.
This study indicates that the H. pylori, which is shaped very much like a screw, does not bore its way through the mucus gel like a screw through a cork as has previously been suggested. Instead it achieves motility by using a clever biochemical strategy. Researchers hope that the work will pave the way for future studies in native mucus and live animals to devise strategies for preventing H. pylori infection. Such studies could be important to the design of new therapeutic approaches that prevent the bacteria from colonizing in the first place, and also may be relevant to the broader question of bacterial infections in mucus linings in other organs.

Full length paper of the Research work can be downloaded (Right Click and “Save”) at:
http://www.pnas.org/content/early/2009/08/11/0903438106.full.pdf
Real time Movies of the “Bacterial Swim” recorded by the scientists can be downloaded at:
http://www.pnas.org/content/early/2009/08/11/0903438106/suppl/DCSupplemental

HOW GRAM-NEGATIVE BACTERIA INFECT CELLS – Latest Findings

The bacteria that cause food poisoning, bubonic plague, and whooping cough all deploy the same weapon to infect the body. A MOLECULAR “SYRINGE” STICKS OUT OF THE BACTERIA, POKES A HOLE IN A NEARBY CELL, AND SQUIRTS IN VENOMOUS PROTEINS THAT HIJACK THE CELL'S MACHINERY.
For the first time, Howard Hughes Medical Institute researchers have captured a detailed picture of the large doughnut-shaped base of the syringe barrel embedded in the bacterial membranes. The findings are reported in a the journal Nature . This first atomic picture of a major structural component of the hazardous molecular hypodermic may help scientists develop a new kind of drug that can disable the syringe and render disease-causing bacteria harmless while sparing beneficial bacteria. Currently, doctors must fight bacterial infections with antibiotics, which kill all bacteria, good and bad. Furthermore, the researchers are optimistic that drugs of this type might be effective against pathogens that are resistant to existing antibiotics.
It is believed that this ring forms the foundation upon which all of the other components assemble, without this assembly, there is no pathogenesis. This provides a real potential point of intervention. The syringe is used almost exclusively by pathogenic bacteria, such as the Escherichia coli (E.coli) sometimes found in uncooked foods, the Pseudomonas that cause life-threatening infections in the lungs of people with cystic fibrosis, and the plague bacillus, Yersinia pestis , that causes so-called black death. Many major plant pathogens also use the same piercing needle to puncture plant cells.
The barrel of the syringe spans the inner and outer membranes of gram-negative bacteria, a major category of microbes that have multilayered cell walls. Two proteins at the tip of the needle drill into other cells. Each species of gram-negative bacteria injects a distinctive blend of proteins that do different things to the cell and result in diverse diseases. The shared molecular machinery that injects the customized protein is called a type III secretion system.
The new molecular model shows a circle of 24 identical interlocking molecules that hint at how the other syringe components may fit together. This large ring sits on top of the inner membrane of the gram-negative bacterium, the portal where infectious proteins gather to exit the cell.

The new model is based on experiments by first author Calvin Yip, a graduate student in Strynadka's lab, using a technique called x-ray crystallography. The number of molecules was confirmed by analysis of whole bacteria in the lab of co-author Sam Miller at the University of Washington. Together, these experiments revealed details that confirm and enhance the blurry picture of the secretion system previously reported by other researchers relying on an electron microscope.
The protein ring, called EscJ, is a large, fatty molecule that had defied repeated attempts to grow it into the orderly crystals needed for detailed structural studies. One of the problems was that the ring's surface is glazed with positively charged atoms that push clones of themselves away like magnets repelling each other.
The breakthrough in the lab came when Yip made a mutant version to reduce some of the surface charge. That allowed the mutant EscJ molecules to line up in orderly arrays in a crystal. Researchers in Finlay's lab confirmed that the mutant protein could still form a functional syringe in bacteria. Based on the way the EscJ molecule is packed in the crystal, the scientists suspect that EscJ forms a ring that functions as a molecular platform for the assembly of the secretion system. The greatest excitement about the new atomic structure comes from the potential to selectively target a type of disease-causing bacteria. Interestingly, several of those genes closely resemble another set of genes that make up the flagella, the beating hairs that propel some bacteria.

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http://www.hhmi.org/news/pdf/strynadka2.pdf

QUORUM SENSING Cell-to-Cell Communication in Bacteria
It has been discovered that Bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves.

Quorum sensing is the process of cell-cell communication in bacteria. Until recently, the ability of bacteria to communicate was considered an anomaly that occurred only in a few marine Vibrio species. It is now clear that cell-cell communication is ubiquitous in the bacterial world and that understanding this process is fundamental to all of microbiology, including industrial and clinical microbiology, and ultimately to understanding the development of higher organisms. Bacterial communication, combines genetics, biochemistry, structural biology, chemistry, microarray studies, bioinformatics, and modeling.
Quorum sensing, which involves the production, release, and subsequent detection of chemical signaling molecules called autoinducers, allows bacteria to regulate gene expression in response to changes in cell-population density. As a population of bacteria grows, the extracellular concentration of autoinducer increases. When a threshold is reached, the group responds with a population-wide alteration in gene expression. Processes controlled by quorum sensing are usually ones that are unproductive when undertaken by an individual bacterium but become effective when undertaken by the group. For example, Quorum sensing controls bioluminescence, secretion of virulence factors, biofilm formation, sporulation, and the exchange of DNA. Thus, quorum sensing is a mechanism that allows bacteria to function as multicellular organisms. Recent studies show that bacteria make, detect, and integrate information from multiple autoinducers, some of which exclusively facilitate intraspecies communication, while others enable communication between species. Study of quorum sensing is providing insight into intra- and interspecies communication, population-level cooperation, and the design principles underlying signal transduction and information processing at the cellular level. These investigations are leading to synthetic strategies for controlling quorum sensing. Objectives include development of antimicrobial drugs aimed at bacteria that use quorum sensing to control virulence, and improved industrial production of natural products such as antibiotics.

Please Click here to See a Lecture on QUORUM SENSING Cell-to-Cell Communication in Bacteria by its Discoverer Dr. Bonnie Bassler

http://www.ted.com/index.php/talks/bonnie_bassler_on_how_bacteria_communicate.html

Right Click and "Save" for and Elsevier paper titled "Quorum sensing and bacterial cross-talk in biotechnology by John C March and William E Bentley"

http://star.tau.ac.il/~eshel/papers/RNA-genome/quorum%20sensing-2004.pdf