Dark Matter Could Transfer Energy in the Sun

Dark Matter Could Transfer Energy in the Sun

  10:05:00 AM    Science Lover

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Researchers from the Institute for Corpuscular Physics (IFIC) and other European groups have studied the effects of the presence of dark matter in the Sun. According to their calculations, low mass dark matter particles could be transferring energy from the core to the external parts of the Sun, which would affect the quantity of neutrinos that reach Earth.

Scientists believe that the majority of the dark matter 
particles gather together in the centre of the Sun, 
but in their elliptic orbits they also travel to the outer
part, interacting and exchanging with the solar atoms. 
In this way, the WIMPs transport the energy from the 
burning central core to the cooler peripheral
parts. (Credit: Hinode JAXA/NASA/PPARC)

"We assume that the dark matter particles interact weakly with the Sun's atoms, and what we have done is calculate at what level these interactions can occur, in order to better describe the structure and evolution of the Sun," Marco Taoso, researcher at the IFIC, a combined centre of the Spanish National Research Council and the University of Valencia, explains.

The astrophysical observations suggest that our galaxy is situated in a halo of dark matter particles. According to the models, some of these particles, the WIMPs (Weakly Interacting Massive Particles) interact weakly with other normal ones, such as atoms, and could be building up on the inside of stars. The study, recently published in the journal Physical Review D, carries out an in-depth study of the case of the Sun in particular.

"When the WIMPs pass through the Sun they can break up the atoms of our star and lose energy. This prevents them from escaping the gravitational force of the Sun which captures them, and they become trapped, orbiting inside it, with no way of escaping," the researcher points out.

The dark matter cools down the Sun's core

Scientists believe that the majority of the dark matter particles gather together in the centre of the Sun, but in their elliptic orbits they also travel to the outer part, interacting and exchanging with the solar atoms. In this way, the WIMPs transport the energy from the burning central core to the cooler peripheral parts.

"This effect produces a cooling down of the core, the region from where the neutrinos originate due to the nuclear reactions of the Sun," Taoso points out. "And this corresponds to a reduction in the flux of solar neutrinos, since these depend greatly on the temperature of the core."

The neutrinos that reach Earth can be measured by means of different techniques. These data can be used to detect the modifications of the solar temperature caused by the WIMPs. The transport of energy by these particles depends on the likelihood of them interacting with the atoms, and the "size" of these interactions is related to the reduction in the neutrino flux.

"As a result, current data about solar neutrinos can be used to put limits on the extent of the interactions between dark matter and atoms, and using numerical codes we have proved that certain values correspond to a reduction in the flux of solar neutrinos and clash with the measurements," the scientist reveals.

The team has applied their calculations to better understand the effects of low mass dark matter particles (between 4 and 10 gigaelectronvolts). At this level we find models that attempt to explain the results of experiments such as DAMA (beneath an Italian mountain) or CoGent (in a mine in the USA), which look for dark material using "scintillators" or WIMP detectors.

Debate about WIMP and solar composition

This year another study by scientists from Oxford University (United Kingdom) also appeared. It states that WIMPs not only reduce the fluxes of solar neutrinos, but also, furthermore, modify the structure of the Sun and can explain its composition.

"Our calculations, however, show that the modifications of the star's structure are too small to support this claim and that the WIMPs cannot explain the problem of the composition of the sun," Taoso concludes.

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The Future of Metabolic Engineering: Designer Molecules, Cells and Microorganisms

The Future of Metabolic Engineering: Designer Molecules, Cells and Microorganisms

  5:22:00 PM    Science Lover

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Will we one day design and create molecules, cells and microorganisms that produce specific chemical products from simple, readily-available, inexpensive starting materials? Will the synthetic organic chemistry now used to produce pharmaceutical drugs, plastics and a host of other products eventually be surpassed by metabolic engineering as the mainstay of our chemical industries? Yes, according to Jay Keasling, chemical engineer and one of the world's foremost practitioners of metabolic engineering.

Metabolic engineering - the practice of 
altering genes and metabolic pathways 
within a cell or microorganism -- could 
one day be used to mass-produce biofuels, 
pharmaceuticals and other chemical 
products from inexpensive and renewable 
starting materials. (Credit: Flavio Robles, 
Berkeley Lab Public Affairs)

In a paper published in the journal Science Keasling discusses the potential of metabolic engineering -- one of the principal techniques of modern biotechnology -- for the microbial production of many of the chemicals that are currently derived from non-renewable resources or limited natural resources. Examples include, among a great many other possibilities, the replacement of gasoline and other transportation fuels with clean, green and renewable biofuels.

"Continued development of the tools of metabolic engineering will be necessary to expand the range of products that can be produced using biological systems, Keasling says. "However, when more of these tools are available, metabolic engineering should be just as powerful as synthetic organic chemistry, and together the two disciplines can greatly expand the number of chemical products available from renewable resources."

Keasling is the chief executive officer for the Joint BioEnergy Institute, a U.S. Department of Energy (DOE) bioenergy research center. He also holds joint appointments with the Lawrence Berkeley National Laboratory (Berkeley Lab), where he oversees that institute's biosciences research programs, and the University of California (UC), Berkeley, where he serves as director of the Synthetic Biology Engineering Research Center, and is the Hubbard Howe Jr. Distinguished Professor of Biochemical Engineering.

Metabolic engineering is the practice of altering genes and metabolic pathways within a cell or microorganism to increase its production of a specific substance. Keasling led one of the most successful efforts to date in the application of metabolic engineering, when he combined it with synthetic organic chemistry techniques to develop a microbial-based means of producing artemisinin, the most potent of all anti-malaria drugs. He and his research group at JBEI are now applying that same combination to the synthesis of liquid transportation fuels from lignocellulosic biomass. In all cases, the goal is to engineer microbes to perform as much of the chemistry required to produce a desired final product as possible.

"To date, microbial production of natural chemical products has been achieved by transferring product-specific enzymes or entire metabolic pathways from rare or genetically intractable organisms to those that can be readily engineered," Keasling says. "Production of non-natural specialty chemicals, bulk chemicals, and fuels has been enabled by combining enzymes or pathways from different hosts into a single microorganism, and by engineering enzymes to have new function."

These efforts have utilized well-known, industrial microorganisms, but future efforts, he says, may include designer molecules and cells that are tailor-made for the desired chemical and production process.

"In any future, metabolic engineering will soon rival and potentially eclipse synthetic organic chemistry," Keasling says.

Keasling cites the production of active pharmaceutical ingredients as one area where metabolic engineering enjoys a distinct advantage over synthetic organic chemistry. This includes three specific classes of chemicals -- alkaloids, which are primarily derived from plants; polyketides and non-ribosomal peptides, which are produced by various bacteria and fungi; and isoprenoids, which also are typically produced by microbes.

"Many of these natural products are too complex to be chemically synthesized and yet have a value that justifies the cost of developing a genetically engineered microorganism," Keasling says. "The cost of starting materials is generally a small fraction of the complete cost of these products, and relatively little starting material is necessary so availability is not an issue."

Keasling also says that metabolic engineering could provide a valuable alternative means of producing variations of terpenes, the hydrocarbon compounds common to the resins of conifers, in a form that could yield pharmaceuticals that are more effective for the treatment of human disease than the forms that nature has provided.

Perhaps the ripest targets of opportunity for future metabolic engineering efforts are petroleum-based bulk chemical products, including gasoline and other fuels, polymers and solvents. Because such products can be inexpensively catalyzed from petroleum, microbial production has until now been rare, but with fluctuating oil prices, dwindling resources and other considerations, the situation, Keasling says, has changed.

"It is now possible to consider production of these inexpensive bulk chemicals from low-cost starting materials, such as starch, sucrose, or cellulosic biomass with a microbial catalyst," he says. "The key to producing these bulk chemicals in metabolically-engineered cells will be our ability to make the exact molecule needed for existing products rather than something 'similar but green' that will require extensive product testing before it can be used."

In his Science paper, Keasling discusses the formidable roadblocks that stand in the way of a future in which microorganisms and molecules can be tailor-made through metabolic engineering, including the need for "debugging routines" that can find and fix errors in engineered cells. However, he is convinced these roadblocks can and will be overcome.

"One can even envision a day when cell manufacturing is done by different companies, each specializing in certain aspects of the synthesis, with one company constructing the chromosome, one company building the membrane and cell wall bag, and one company filling this bag with the basic molecules needed to boot up the cell."

The Joint BioEnergy Institute (JBEI) is one of three Bioenergy Research Centers funded by the U.S. Department of Energy to advance the development of the next generation of biofuels. It is a scientific partnership led by Berkeley Lab and including the Sandia National Laboratories, the University of California campuses of Berkeley and Davis, the Carnegie Institution for Science, and the Lawrence Livermore National Laboratory.

The Synthetic Biology Engineering Research Center (SynBERC) is a multi-institution partnership, funded by the National Science Foundation, that is aimed at "making biology easier to engineer." The SynBERC partnership is led by UC Berkeley and includes UC San Francisco, Harvard, MIT, Stanford, and Prairie View A&M University.

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Antibacterial Soaps: Being Too Clean Can Make People Sick, Study Suggests

Antibacterial Soaps: Being Too Clean Can Make People Sick, Study Suggests

  9:57:00 AM    Science Lover

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Young people who are overexposed to antibacterial soaps containing triclosan may suffer more allergies, and exposure to higher levels of Bisphenol A among adults may negatively influence the immune system, a new University of Michigan School of Public Health study suggests.

Young people who are overexposed to antibacterial 
soaps containing triclosan may suffer more allergies, and 
exposure to higher levels of Bisphenol A among adults 
may negatively influence the immune system, a new 
University of Michigan School of Public Health study 
suggests. (Credit: iStockphoto/Jorge Salcedo)

Triclosan is a chemical compound widely used in products such as antibacterial soaps, toothpaste, pens, diaper bags and medical devices. Bisphenol A (BPA) is found in many plastics and, for example, as a protective lining in food cans. Both of these chemicals are in a class of environmental toxicants called endocrine-disrupting compounds (EDCs), which are believed to negatively impact human health by mimicking or affecting hormones.

Using data from the 2003-2006 National Health and Nutrition Examination Survey, U-M researchers compared urinary BPA and triclosan with cytomegalovirus (CMV) antibody levels and diagnosis of allergies or hay fever in a sample of U.S. adults and children over age 6. Allergy and hay fever diagnosis and CMV antibodies were used as two separate markers of immune alterations.

"We found that people over age 18 with higher levels of BPA exposure had higher CMV antibody levels, which suggests their cell-mediated immune system may not be functioning properly," said Erin Rees Clayton, research investigator at the U-M School of Public Health and first author on the paper.

Researchers also found that people age 18 and under with higher levels of triclosan were more likely to report diagnosis of allergies and hay fever.

There is growing concern among the scientific community and consumer groups that these EDCs are dangerous to humans at lower levels than previously thought.

"The triclosan findings in the younger age groups may support the 'hygiene hypothesis,' which maintains living in very clean and hygienic environments may impact our exposure to micro-organisms that are beneficial for development of the immune system," said Allison Aiello, associate professor at the U-M School of Public Health and principal investigator on the study.

As an antimicrobial agent found in many household products, triclosan may play a role in changing the micro-organisms to which we are exposed in such a way that our immune system development in childhood is affected.

"It is possible that a person can be too clean for their own good," said Aiello, who is also a visiting associate professor of epidemiology at Harvard.

Previous animal studies indicate that BPA and triclosan may affect the immune system, but this is the first known study to look at exposure to BPA and triclosan as it relates to human immune function, Aiello said.

One surprise finding is that with BPA exposure, age seems to matter, said Rees Clayton. In people 18 or older, higher amounts of BPA were associated with higher CMV levels, but in people younger than 18 the reverse was true.

"This suggests the timing of the exposure to BPA and perhaps the quantity and length of time we are exposed to BPA may be affecting the immune system response," Rees Clayton said.

This is just the first step, she said, but a very important one. Going forward, researchers would like to study the long-term effects of BPA and triclosan in people to see if they can establish a causal relationship.

One limitation of the study is that it measured disease and exposure simultaneously and thus shows only part of the picture, Aiello said.

"It is possible, for example, that individuals who have an allergy are more hygienic because of their condition, and that the relationship we observed is, therefore, not causal or is an example of reverse causation," Aiello said.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment.

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Same Face May Look Male or Female, Depending on Where It Appears in a Person's Field of View

Same Face May Look Male or Female, Depending on Where It Appears in a Person's Field of View

  9:42:00 AM    Science Lover

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Neuroscientists at MIT and Harvard have made the surprising discovery that the brain sees some faces as male when they appear in one area of a person's field of view, but female when they appear in a different location.

Neuroscientists at MIT and Harvard have made the
surprising discovery  that the brain sees some faces
as male when they appear in one area of a  person's
field of view, but female when they appear
in a different  location.

The findings challenge a longstanding tenet of neuroscience -- that how the brain sees an object should not depend on where the object is located relative to the observer, says Arash Afraz, a postdoctoral associate at MIT's McGovern Institute for Brain Research and lead author of a new paper on the work.

"It's the kind of thing you would not predict -- that you would look at two identical faces and think they look different," says Afraz. He and two colleagues from Harvard, Patrick Cavanagh and Maryam Vaziri Pashkam, described their findings in the Nov. 24 online edition of the journal Current Biology.

In the real world, the brain's inconsistency in assigning gender to faces isn't noticeable, because there are so many other clues: hair and clothing, for example. But when people view computer-generated faces, stripped of all other gender-identifying features, a pattern of biases, based on location of the face, emerges.

The researchers showed subjects a random series of faces, ranging along a spectrum of very male to very female, and asked them to classify the faces by gender. For the more androgynous faces, subjects rated the same faces as male or female, depending on where they appeared.

Study participants were told to fix their gaze at the center of the screen, as faces were flashed elsewhere on the screen for 50 milliseconds each. Assuming that the subjects sat about 22 inches from the monitor, the faces appeared to be about three-quarters of an inch tall.

The patterns of male and female biases were different for different people. That is, some people judged androgynous faces as female every time they appeared in the upper right corner, while others judged faces in that same location as male. Subjects also showed biases when judging the age of faces, but the pattern for age bias was independent from the pattern for gender bias in each individual.

Sample size
 
Afraz believes this inconsistency in identifying genders is due to a sampling bias, which can also be seen in statistical tools such as polls. For example, if you surveyed 1,000 Bostonians, asking if they were Democrats or Republicans, you would probably get a fairly accurate representation of these percentages in the city as a whole, because the sample size is so large. However, if you took a much smaller sample, perhaps five people who live across the street from you, you might get 100 percent Democrats, or 100 percent Republicans. "You wouldn't have any consistency, because your sample is too small," says Afraz.

He believes the same thing happens in the brain. In the visual cortex, where images are processed, cells are grouped by which part of the visual scene they analyze. Within each of those groups, there is probably a relatively small number of neurons devoted to interpreting gender of faces. The smaller the image, the fewer cells are activated, so cells that respond to female faces may dominate. In a different part of the visual cortex, cells that respond to male faces may dominate.

"It's all a matter of undersampling," says Afraz.

Michael Tarr, codirector of the Center for the Neural Basis of Cognition at Carnegie Mellon University, says the findings add to the growing evidence that the brain is not always consistent in how it perceives objects under different circumstances. He adds that the study leaves unanswered the question of why each person develops different bias patterns. "Is it just noise within the system, or is some other kind of learning occurring that they haven't figured out yet?" asks Tarr, who was not involved in the research. "That's really the fascinating question."

Afraz and his colleagues looked for correlations between each subject's bias pattern and other traits such as gender, height and handedness, but found no connections.

He is now doing follow-up studies in the lab of James DiCarlo, associate professor of neuroscience at MIT, including an investigation of whether brain cells can be recalibrated to respond to faces differently.

Admin's Note: This article is not intended to provide medical advice, diagnosis or treatment.

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Do Brain's 'Traffic Lights' Direct Our Actions?

Do Brain's 'Traffic Lights' Direct Our Actions?

  1:42:00 PM    Science Lover

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In every waking minute, we have to make decisions -- sometimes within a split second. Neuroscientists at the Bernstein Center Freiburg have now discovered a possible explanation how the brain chooses between alternative options. The key lies in extremely fast changes in the communication between single nerve cells.

The timing of exciting (red curve) and inhibiting 
(blue curve) signals could be a way to control the 
"traffic flow" of activity in the brain. (Illustration: 
Bernstein Center Freiburg) (Credit: Illustration 
courtesy of Bernstein Center Freiburg)

The traffic light changes from green to orange -- should I push down the accelerator a little bit further or rather hit the brakes? Our daily lives present a long series of decisions we have to make, and sometimes we only have a split second at our disposal. Often the problem of decision-making entails the selection of one set of brain processes over multiple others seeking access to same resources. Several mechanisms have been suggested how the brain might solve this problem. However, up to now, it is a mystery what exactly happens when during a rapid choice between two options.

In the current issue of the Journal of Neuroscience, Jens Kremkow, Arvind Kumar, and Ad Aertsen from the Bernstein Center Freiburg propose a mechanism how the brain can choose between possible actions -- already at the level of single nerve cells.

As the structure and activity of the brain are just too complex to answer this question through a simple biological experiment, the scientists constructed a network of neurons in the computer. An important aspect of the model in this context is the property of nerve cells to influence the activity of other nerve cells, either in an excitatory or inhibitory manner. In the constructed network, two groups of neurons acted as the senders of two different signals. Further downstream in the network, another group of neurons, the "gate" neurons, were to control which of the signals would be transmitted onward.

As the cells within the network were connected both with exciting and inhibiting neurons, the signals reached the gate as excitatory and, after a short delay, inhibitory activity. In their simulations, the scientists found that the key for the gate neurons' "decision" in favour of one signal over the other was the time delay of the inhibitory signal relative to the excitatory signal. If the delay was set to be very small, the activity of the cells in the gate was quenched too quickly for the signal to be propagated.

Conversely, a larger delay caused the gate to open for the signal. Results from neurophysiological experiments have already shown that a change in delay properties is possible in real neurons. These findings therefore support the hypothesis of Kremkow and colleagues that such temporal gating can form the basis for selecting one of several alternative options in our brain.

Admin's Note: This article is not intended to provide medical advice, diagnosis or treatment.

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Stem Cells from Amniotic Fluid: Reprogrammed Amniotic Fluid Cells Can Generate All Types of Body Cells

Stem Cells from Amniotic Fluid: Reprogrammed Amniotic Fluid Cells Can Generate All Types of Body Cells

  10:06:00 AM    Science Lover

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Reprogrammed amniotic fluid cells can generate all types of body cells. High hopes rest on stem cells: one day, they may be used to treat many diseases. To date, embryos are the main source of these cells, but this raises ethical problems. Scientists at the Max Planck Institute for Molecular Genetics in Berlin have now managed to convert amniotic fluid cells into pluripotent stem cells. These amniotic fluid-derived iPS cells are hardly distinguishable from embryonic stem cells. However, they "remember" where they came from.

Top: Before their reprogramming into amniotic fluid iPS cells, 
human amniotic fluid cells are outwardly distinguishable from 
embryonic stem cells. Bottom left: Amniotic fluid iPS cells 
produce OCT4 (green), one of the most important marker 
proteins for embryonic stem cells. Bottom right: Starting from 
this embryonic stem cell phase, the amniotic fluid iPS cells can 
form hepatocyte-like cells and others. They produce the plasma
protein alpha-fetoprotein (red), which is abundant in fetal 
liver. (Credit: Max Planck Institute for Molecular Genetics)

The research appears in the online journal PLoS ONE, published by the Public Library of Science.

The special abilities of embryonic stem cells can today be used in multiple "grown-up" cells (e.g. skin and hair cells). This is done by reprogramming the cells and converting them to "induced pluripotent stem cells" (iPS cells). These then possess the typical properties of embryonic stem cells, meaning they can generate any of the cell types of the human body (pluripotency), and they can multiply endlessly.

Stem cells with memory
 
The scientists have shown that the amniotic fluid iPS cells can form different human cell types. They have also discovered that induced pluripotent stem cells can remember the original cell type from which they were generated. During cellular reprogramming, various genes that control the development of stem cells are apparently switched on or remain active. This confirms other current research results, which show that iPS cells derived from distinct tissues are prone to follow their pre-destined developmental path upon spontaneous differentiation. "We don't know just yet whether this donor-cell type memory will have an impact on possible medical treatment, or which type of somatic cell-derived iPS cell will be most suitable for treatment," cautions Katharina Wolfrum of the Max Planck Institute for Molecular Genetics.

Amniotic fluid cells have a number of advantages over other cell types. For one thing, amniotic fluid cells are routinely harvested in antenatal examinations to enable the early detection of disease. In most cases, more cells are obtained than are actually needed. In addition, the amniotic fluid mixture contains different types of cells from the unborn child, including stem-cell-like cells. As they are not very old, they have fewer environmentally-induced mutations, making them genetically more stable. "This may mean that it is possible to reprogram these amniotic fluid cells faster and more easily than other cell types, making amniotic fluid-derived iPS cells an interesting complement to embryonic stem cells," explains James Adjaye of the Max Planck Institute in Berlin.

Moreover, amniotic fluid cells could be extracted for cellular reprogramming before the birth of a child and be prepared for their intended use while the pregnancy is still ongoing. "This would make it possible to test which drugs work for a baby and whether they are tolerated, before that baby is born. Moreover, in the future, sick newborns can be treated with cells from their own body," says Adjaye.

Admin's Note: This article is not intended to provide medical advice, diagnosis or treatment.

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Early Universe Was a Liquid, Nuclei Collisions at the Large Hadron Collider Show

Early Universe Was a Liquid, Nuclei Collisions at the Large Hadron Collider Show

  9:47:00 AM    Science Lover

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In an experiment to collide lead nuclei together at CERN's Large Hadron Collider physicists from the ALICE detector team including researchers from the University of Birmingham have discovered that the very early Universe was not only very hot and dense but behaved like a hot liquid.

Another Real lead-lead collision in ALICE inner 
detector. (Credit: CERN)

By accelerating and smashing together lead nuclei at the highest possible energies, the ALICE experiment has generated incredibly hot and dense sub-atomic fireballs, recreating the conditions that existed in the first few microseconds after the Big Bang. Scientists claim that these mini big bangs create temperatures of over ten trillion degrees.

At these temperatures normal matter is expected to melt into an exotic, primordial 'soup' known as quark-gluon plasma. These first results from lead collisions have already ruled out a number of theoretical physics models, including ones predicting that the quark-gluon plasma created at these energies would behave like a gas.

Although previous research in the USA at lower energies, indicated that the hot fire balls produced in nuclei collisions behaved like a liquid, many expected the quark-gluon plasma to behave like a gas at these much higher energies.

Scientists from the University of Birmingham's School of Physics and Astronomy are playing a key role in this new phase of the LHC's programme which comes after seven months of successfully colliding protons at high energies. Dr David Evans, from the University of Birmingham's School of Physics and Astronomy, and UK lead investigator at ALICE experiment, said: "Although it is very early days we are already learning more about the early Universe."

He continues: "These first results would seem to suggest that the Universe would have behaved like a super-hot liquid immediately after the Big Bang."

The team has also discovered that more sub-atomic particles are produced in these head-on collisions than some theoretical models previously suggested. The fireballs resulting from the collision only lasts a short time, but when the 'soup' cools down, the researchers are able to see thousands of particles radiating out from the fireball. It is in this debris that they are able to draw conclusions about the soup's behaviour.

Two papers detailing this research have been submitted for publication and posted on: http://xxx.lanl.gov/abs/1011.3914| and http://xxx.lanl.gov/abs/1011.3916|.

This research is funded by the Science and Technology Facilities Council (STFC).

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Researchers Train Bacteria to Convert Bio-Wastes Into Plastic

Researchers Train Bacteria to Convert Bio-Wastes Into Plastic

  9:27:00 AM    Science Lover

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Researcher Jean-Paul Meijnen has 'trained' bacteria to convert all the main sugars in vegetable, fruit and garden waste efficiently into high-quality environmentally friendly products such as bioplastics.

Bacteria in training. (Credit: Image courtesy of B-Basic)

There is considerable interest in bioplastics nowadays. The technical problems associated with turning potato peel into sunglasses, or cane sugar into car bumpers, have already been solved. The current methods, however, are not very efficient: only a small percentage of the sugars can be converted into valuable products. By adapting the eating pattern of bacteria and subsequently training them, Meijnen has succeeded in converting sugars in processable materials, so that no bio-waste is wasted.

The favoured raw materials for such processes are biological wastes left over from food production. Lignocellulose, the complex combination of lignin and cellulose present in the stalks and leaves of plants that gives them their rigidity, is such a material. Hydrolysis of lignocellulose breaks down the long sugar chains that form the backbone of this material, releasing the individual sugar molecules. These sugar molecules can be further processed by bacteria and other micro-organisms to form chemicals that can be used as the basis for bioplastics. The fruit of the plant, such as maize, can be consumed as food, while the unused waste such as lignocellulose forms the raw material for bioplastics.

"Unfortunately, the production of plastics from bio-wastes is still quite an expensive process, because the waste material is not fully utilized," explains Jean-Paul Meijnen. (It should be noted here that we are talking about agricultural bio-wastes in this context, not the garden waste recycled by households.) The pre-treatment of these bio-wastes leads to the production of various types of sugars such as glucose, xylose and arabinose. These three together make up about eighty per cent of the sugars in bio-waste.

The problem is that the bacteria Meijnen was working with, Pseudomonas putida S12, can only digest glucose but not xylose or arabinose. As a result, a quarter of the eighty per cent remains unused. "A logical way of reducing the cost price of bioplastics is thus to 'teach' the bacteria to digest xylose and arabinose too."

The xylose has to be 'prepared' before Pseudomonas putida S12 can digest it. This is done with the aid of certain enzymes. The bacteria are genetically modified by inserting specific DNA fragments in the cell; this enables them to produce enzymes that assist in the conversion of xylose into a molecule that the bacteria can deal with.

Meijnen achieved this by introducing two genes from another bacterium (E. coli) which code for two enzymes that enable xylose to be converted in a two-stage process into a molecule that P. putida S12 can digest.

This method did work, but not very efficiently: only twenty per cent of the xylose present was digested. The modified bacteria were therefore 'trained' to digest more xylose. Meijnen did this by subjecting the bacteria to an evolutionary process, successively selecting the bacteria that showed the best performance.

"After three months of this improvement process, the bacteria could quickly digest all the xylose present in the medium. And surprisingly enough, these trained bacteria could also digest arabinose, and were thus capable of dealing with the three principal sugars in bio-wastes." Meijnen also incorporated other genes, from the bacterium Caulobacter crescentus. This procedure also proved effective and efficient from the start.

Finally, in a separate project Meijnen succeeded in modifying a strain of Pseudomonas putida S12 that had previously been modified to produce para-hydroxybenzoate (pHB), a member of the class of chemicals known as parabens that are widely used as preservatives in the cosmetics and pharmaceutical industries.

Meijnen tested the ability of these bacteria to produce pHB, a biochemical substance, from xylose and from other sources such as glucose and glycerol. He summarized his results as follows: "This strategy also proved successful, allowing us to make biochemical substances such as pHB from glucose, glycerol and xylose. In fact, the use of mixtures of glucose and xylose, or glycerol and xylose, gives better pHB production than the use of unmixed starting materials. This means that giving the bacteria pretreated bio-wastes as starting material stimulates them to make even more pHB."

Meijnen will be defending his doctoral thesis on this topic, which was carried out in the context of the NWO B-Basic programme, at TU Delft on Nov. 22, 2010.

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Scientists Identify Antivirus System in Host Cells

Scientists Identify Antivirus System in Host Cells

  10:13:00 AM    Science Lover

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Viruses have led scientists at Washington University School of Medicine in St. Louis to the discovery of a security system in host cells. Viruses that cause disease in animals beat the security system millennia ago. But now that researchers are aware of it, they can explore the possibility of bringing the system back into play in the fight against diseases such as sudden acute respiratory syndrome (SARS), West Nile virus, dengue and yellow fever.

West Nile virus (brown) infects neurons, whose nuclei 
are the round purple-blue spots. Scientists have 
discovered a new anti-virus system in host cells by 
studying how viruses like West Nile defeated the system. 
It may one day be possible to use pharmaceuticals
to bring this security system back online in the fight 
against diseases such as West Nile, sudden acute 
respiratory syndrome (SARS), dengue and yellow 
fever. (Credit: Michael Diamond, MD, PhD)

The findings, published in Nature, solve a 35-year-old mystery that began when National Institutes of Health researcher Bernard Moss, MD, PhD, noticed that poxviruses put chemical "caps" on particular spots in every piece of genetic material transcribed from their DNA. That transcribed material is RNA; to reproduce, viruses need to trick the host cell into making viral proteins from this RNA.

Noting evidence that the host cell puts caps on its own RNA in identical positions, Moss theorized that the caps might be a way for cells to distinguish between their RNA and that of an invader. He guessed the caps might serve as a sort of fake identification badge for the virus' RNA, allowing it to bypass host cell security systems primed to attack any RNA lacking the caps.

Since Moss's study, scientists have learned that some viruses have strategies for stealing RNA caps from host cells and putting them on their own RNA. Several disease-causing viruses have to make their own caps, including:

* poxviruses, which cause smallpox

* flaviviruses, which cause West Nile encephalitis, yellow fever and dengue;

* rhabdoviruses, which cause rabies;

* coronaviruses, which cause SARS;

* reoviruses, which cause mild respiratory distress or diarrhea.

Scientists also learned that one of the chemical caps added to RNA helps stabilize it, preventing the RNA from breaking down. However, despite years of research, the purpose of another cap, added near the beginning of every RNA strand in a position scientists refer to as 2' (two prime), was a persistent mystery.

The new paper from the laboratory of senior author Michael S. Diamond, MD, PhD, solves that puzzle and confirms Moss' speculation. The study used a mutant form of the West Nile virus created by Pei-Yong Shi, PhD, now a researcher at the Novartis Institute for Tropical Diseases. The mutant strain can attach the cap that keeps RNA stable but is unable to add the 2' cap. When Diamond, professor of medicine, pathology and immunology, and molecular microbiology at Washington University School of Medicine, infected mice with this mutant virus, it could not cause disease.

Next, scientists injected the mutant virus into mice lacking the receptors for interferons. These proteins are important players in defensive reactions to invading viruses within the cell, a branch of the immune system known as intrinsic immunity. The mutant virus made these mice sick, suggesting that intrinsic immunity stops the mutant viruses in normal mice, and that the 2' cap was helping normal viruses evade this part of the immune system.

Researchers recently identified a gene, IFIT2, that is activated by interferons, has mild antiviral effects against West Nile virus and seems to have potential connections to translation of RNA into proteins. When Diamond turned IFIT2 levels up in cell culture and exposed it to the mutant West Nile virus, the mutant virus could barely replicate. Tests of a mutant poxvirus and a mutant coronavirus that could not attach the 2' cap produced similar results. Knocking out a related gene in mice, IFIT1, allowed the mutant virus to evade intrinsic immunity and cause infection when it was injected into the brain.

"Now that we know what this cap is used for, we can look at the question of whether the human and viral enzymes that put the cap on are sufficiently different," says Diamond. "If they are, we may be able to design inhibitors that prevent viruses from capping their RNA and make it much harder for them to replicate once the intrinsic immune system is activated."

Special Note: This article is not intended to provide medical advice, diagnosis or treatment.

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Quantum Memory for Communication Networks of the Future

Quantum Memory for Communication Networks of the Future

  2:25:00 AM    Science Lover

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Researchers from the Niels Bohr Institute at the University of Copenhagen have succeeded in storing quantum information using two 'entangled' light beams. Quantum memory or information storage is a necessary element of future quantum communication networks. The new findings are published in Nature Physics.

The illustration shows the two quantum memories. Each 
memory consists of a glass cell filled with caesium atoms, 
which are shown as small blue and red balls. The light 
beam is sent through the atoms and the quantum 
information is thus transferred from the light to the atoms. 
(Credit: Quantop)

Quantum networks will be able to protect the security of information better than the current conventional communication networks. The cornerstone of quantum communication is a phenomenon called entanglement between two quantum systems, for example, two light beams. Entanglement means that the two light beams are connected to each other, so that they have well defined common characteristics, a kind of common knowledge. A quantum state can -- according to the laws of quantum mechanics, not be copied and can therefore be used to transfer data in a secure way.

In professor Eugene Polzik's research group Quantop at the Niels Bohr Institute researchers have now been able to store the two entangled light beams in two quantum memories. The research is conducted in a laboratory where a forest of mirrors and optical elements such as wave plates, beam splitters, lenses etc. are set up on a large table, sending the light around on a more than 10 meter long labyrinthine journey. Using the optical elements, the researchers control the light and regulate the size and intensity to get just the right wavelength and polarisation the light needs to have for the experiment.

The two entangled light beams are created by sending a single blue light beam through a crystal where the blue light beam is split up into two red light beams. The two red light beams are entangled, so they have a common quantum state. The quantum state itself is information.

The two light beams are sent on through the labyrinth of mirrors and optical elements and reach the two memories, which in the experiment are two glass containers filled with a gas of caesium atoms. The atoms' quantum state contains information in the form of a so-called spin, which can be either 'up' or 'down'. It can be compared with computer data, which consists of the digits 0 and 1. When the light beams pass the atoms, the quantum state is transferred from the two light beams to the two memories. The information has thus been stored as the new quantum state in the atoms.

"For the first time such a memory has been demonstrated with a very high degree of reliability. In fact, it is so good that it is impossible to obtain with conventional memory for light that is used in, for example, internet communication. This result means that a quantum network is one step closer to being a reality," explains professor Eugene Polzik.

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