Thursday, September 3, 2009


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It appears that bacteria can squeeze through practically anything. In extremely small nanoslits they take on a completely new flat shape. Even in this squashed form they continue to grow and divide at normal speeds. This has been demonstrated by research carried out at TU Delft's Kavli Institute of Nanoscience.

Using nanofabrication, Delft scientists made minuscule channels, measuring a micrometer or less in width and 50 micrometer in length, on a silicon chip between tiny chambers containing bacteria. Subsequently they studied the behaviour of Escherichia. coli and Bacillus. subtilis bacteria in this artificial environment. The bacteria were genetically modified so that they were fluorescent and could easily be followed using a special microscope.

Under normal circumstances these bacteria swim and this research showed that they retain this motility in surprisingly narrow channels. They swam just as actively as usual even in channels that were only 30 percent wider than their own diameter (of about 1 micrometer). In even narrower submicron channels the bacteria stopped swimming, and an unexpected effect took place: The bacteria were able to make their way through ultra-narrow passageways in another manner, that is by growing and dividing. The researchers found that this way, E. coli bacteria could squeeze through narrow slits that were only half their own diameter in width. Post-doctoral researcher, Jaan Männik: "This took us totally by surprise. The bacteria become completely flattened. They have all sorts of peculiar shapes both in the channels and when they finally come out at the other side. What is really remarkable, however, is that in the channels, and therefore under extreme confinement, they continue to grow and divide at normal speeds. Apparently their shape is not a determining factor for these activities."

The flat bacteria form a new phenotype,. According to the researchers, this form may be more common than one might think. The bulk of the biomass on Earth is to be found under the ground. Here, bacteria often live in spaces that measure around a micrometer. The study suggests that many more bacteria may be present in small spaces than was always thought. This may have direct consequences, for example for membrane filters (with tiny pores) for water treatment and for medical applications, such as pacemakers or other implants, where bacteria must be excluded as much as possible. The results of the study also provide more fundamental understanding of the behaviour of bacteria that are 'locked up' in nanosized environments.

Little is known about the effect of this sort of confinement on the behaviour of bacteria as yet. According to Prof. Cees Dekker, this has to do with the required combination of very different disciplines: "Microbiologists do not generally engage in nanofabrication, which enables us to examine this area under controlled conditions, and nanoscientists usually know little about the behaviour of bacteria. My colleague, Juan Keymer, an evolutionary biologist, and I are now trying to combine these disciplines in our new Department of Bionanoscience. And this is leading to all sorts of new discoveries."

(Photo: Kavli TU Delft / Tremani)

Delft University of Technology


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A single evolutionary event appears to explain the short, curved legs that characterize all of today's dachshunds, corgis, basset hounds and at least 16 other breeds of dogs, a team led by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, reported today. In addition to what it reveals about short-legged dogs, the unexpected discovery provides new clues about how physical differences may arise within species and suggests new approaches to understanding a form of human dwarfism.

In a study published in the advance online edition of the journal Science, the researchers led by NHGRI's Elaine Ostrander, Ph.D., examined DNA samples from 835 dogs, including 95 with short legs. Their survey of more than 40,000 markers of DNA variation uncovered a genetic signature exclusive to short-legged breeds. Through follow-up DNA sequencing and computational analyses, the researchers determined the dogs' disproportionately short limbs can be traced to one mutational event in the canine genome - a DNA insertion - that occurred early in the evolution of domestic dogs.

"Every species, including canine and human, carries an amazing record of evolution scripted in its genome that can teach us about the mechanisms at work in biology, as well as about human health and disease," said NHGRI Scientific Director Eric Green, M.D., Ph.D. "This work provides surprising evidence of a new way in which genome evolution may serve to generate diversity within a species."

Specifically, the researchers found that in contrast to other dog breeds, all short-legged dog breeds have an extra copy of the gene that codes for a growth-promoting protein called fibroblast growth factor 4 (FGF4). Although functional, the extra gene lacks certain parts of the DNA code, called introns, found in normal genes. These characteristics led researchers to conclude that the extra gene is a so-called retrogene that was inserted into the dog genome some time after the ancestor of modern dog breeds diverged from wolves.

To understand retrogenes, one first needs to understand how the cell normally makes proteins. To produce a protein, a gene's DNA code is transcribed into a molecule called messenger RNA (mRNA). The mRNA then leaves the cell's nucleus and enters the outer region of the cell, called the cytoplasm. There the mRNA is read by tiny molecular machines, called ribosomes, which use the information to assemble proteins.

Retrogenes are formed when the mRNA encounters something - often a type of virus called a retrovirus - that turns it back into DNA through a process referred to as reverse transcription. This new piece of DNA, which contains the same protein-coding information as the gene that produced the mRNA, may then be inserted back into the genome, usually at a much different place than the original gene. Depending on where it is inserted, this piece of DNA may or may not be capable of producing proteins. If it is functional, it is called a retrogene.

In the case of short-legged dogs, the inserted retrogene results in the overproduction of the FGF4 protein, which researchers hypothesize may turn on key growth receptors at the wrong times during fetal development. Veterinary researchers already know that in certain dog breeds the development of long bones is curtailed due to calcification of growth plates, resulting in short legs with a curved appearance. The trait, called disproportional dwarfism, or chondrodysplasia, is an American Kennel Club standard for more than a dozen domestic dog breeds, including the dachshund, corgi, Pekingese and basset hound. This trait is distinct from the uniformly miniature size of toy breeds, such as the toy poodle.

"Our findings suggest that retrogenes may play a larger role in evolution than has been previously thought, especially as a source of diversity within species," said the study's first author, Heidi G. Parker, Ph.D. of NHGRI. "We were surprised to find that just one retrogene inserted at one point during the evolution of a species could yield such a dramatic physical trait that has been conserved over time."

In the past, retrogenes have been recognized as an important source of changes that have fueled the divergence of species. However, the dog findings are the first example of a retrogene that has spurred significant and long-lasting variation within a single species.

The findings also may have implications for understanding human biology and disease. Researchers note that some people are affected by a similar appearing growth disorder, called hypochondroplasia, which belongs to a group of conditions commonly referred to as dwarfism. While about two-thirds of cases of human hypochondroplasia have been linked to a different gene, the cause of the other one-third remains a mystery.

"This study points to a new gene that should be investigated for its possible role in human hypochondroplasia," said Dr. Ostrander, the study's senior author and a senior investigator in NHGRI's Division of Intramural Research. "Our findings may prove valuable to scientists studying other aspects of human growth and development. The work also underscores the value of canine studies for uncovering new biological mechanisms that are likely relevant to human disease."

(Photo: Tyrone Spady, NHGR)


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Using tiny crystals called quantum dots, Johns Hopkins researchers have developed a highly sensitive test to look for DNA attachments that often are early warning signs of cancer. This test, which detects both the presence and the quantity of certain DNA changes, could alert people who are at risk of developing the disease and could tell doctors how well a particular cancer treatment is working.

The new test was reported in a paper called “MS-qFRET: a quantum dot-based method for analysis of DNA methylation,” published in the August issue of the journal Genome Research. The work also was presented at a conference of the American Association of Cancer Research.

“If it leads to early detection of cancer, this test could have huge clinical implications,” said Jeff Tza-Huei Wang, an associate professor of mechanical engineering whose lab team played a leading role in developing the technique. “Doctors usually have the greatest success in fighting cancer if they can treat it in its early stage.”

Wang and his students developed the test over the past three years with colleagues at the Johns Hopkins Kimmel Cancer Center. Stephen B. Baylin, deputy director of the center and a co-author of the Genome Research study, said the test represents “a very promising platform” to help doctors detect cancer at an early stage and to predict which patients are most likely to benefit from a particular therapy.

The recent study, which included the detection of DNA markers in the sputum from lung cancer patients, was designed to show that the technology was sound. Compared to current methods, the test appeared to be more sensitive and delivered results more quickly, the researchers said. “The technique looks terrific, but it still needs to be tested in many real-world scenarios,” Baylin said. “Some of these studies are already under way here. If we continue to see exciting progress, this testing method could easily be in wide use within the next five years.”

The target of this test is a biochemical change called DNA methylation, which occurs when a chemical group called methyl attaches itself to cytosine, one of the four nucleotides or base building blocks of DNA. When methylation occurs at critical gene locations, it can halt the release of proteins that suppress tumors. When this occurs, it is easier for cancer cells to form and multiply. As a result, a person whose DNA has this abnormal gene DNA methylation may have a higher risk of developing cancer. Furthermore, these methylation changes appear to be an early event that precedes the appearance of genetic mutations, another precursor to cancer.

To detect this DNA methylation, the Johns Hopkins team found a way to single out the troublesome DNA strands that have a methyl group attached to them. Through a chemical process called bisulfite conversion, all segments that lack a methyl group are transformed into another nucleotide.

Then, another lab process is used to make additional copies of the remaining target DNA strands that are linked to cancer. During this process, two molecules are attached to opposite ends of each DNA strand. One of these molecules is a protein called biotin. The other is a fluorescent dye. These partner molecules are attached to help researchers detect and count the DNA strands that are associated with cancer.

To do this, these customized DNA strands are mixed with quantum dots, which are crystals of semiconductor material whose sizes are in the range of only few nanometers across. (A nanometer is one-billionth of a meter, far too small to see with the naked eye.).These dots are usually employed in electronic circuitry, but they have recently proved to be helpful in biological applications as well. Quantum dots are useful because they possess an important property: They easily transfer energy. When light shines on a quantum dot, the dot quickly passes this energy along to a nearby molecule, which can use the energy to emit a fluorescent glow. This behavior makes the cancer-related DNA strands light up and identify themselves.

In the Johns Hopkins cancer test, the quantum dots have been coated with a chemical that is attracted to biotin–one of the two molecules that were attached to the DNA strands. As a result, up to 60 of the targeted DNA strands can stick themselves to a single quantum dot, like arms extending from an octopus. Then, an ultraviolet light or a blue laser is aimed at the sample. The quantum dots grab this energy and immediately transfer it to the fluorescent dyes that were attached earlier to the targeted DNA strands. These dye molecules use the energy to light up.

These signals, also called fluorescence, can be detected by a machine called a spectrophotometer. By analyzing these signals, the researchers can discover not only whether the sample contains the cancer-linked DNA but how much of the DNA methylation is present. Larger amounts can be associated with a higher cancer risk.

“This kind of information could allow a patient with positive methylation to undergo more frequent cancer screening tests. This method could replace the traditionally more invasive ways for obtaining patient samples with a simple blood test,” said Vasudev J. Bailey, a biomedical engineering doctoral student from Bangalore, India, who was one of the two lead authors on the Genome Research paper. “It’s also important because these test results could possibly help a doctor determine whether a particular cancer treatment is working. It could pave the way for personalized chemotherapy.”

In addition, because different types of cancer exhibit distinctive genetic markers, the researchers say the test should be able to identify which specific cancer a patient may be at risk of developing. Markers for lung cancer, for example, are different from markers for leukemia.

(Photo: Johns Hopkins U.)


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Researchers at the Leipzig Max Planck Institute for Human Cognitive and Brain Sciences and the Wellcome Trust Centre for Neuroimaging in London have now developed a mathematical model which could significantly improve the automatic recognition and processing of spoken language. In the future, this kind of algorithms which imitate brain mechanisms could help machines to perceive the world around them.

Many people will have personal experience of how difficult it is for computers to deal with spoken language. For example, people who 'communicate' with automated telephone systems now commonly used by many organisations need a great deal of patience. If you speak just a little too quickly or slowly, if your pronunciation isn’t clear, or if there is background noise, the system often fails to work properly. The reason for this is that until now the computer programs that have been used rely on processes that are particularly sensitive to perturbations. When computers process language, they primarily attempt to recognise characteristic features in the frequencies of the voice in order to recognise words.

'It is likely that the brain uses a different process', says Stefan Kiebel from the Leipzig Max Planck Institute for Human Cognitive and Brain Sciences. The researcher presumes that the analysis of temporal sequences plays an important role in this. 'Many perceptual stimuli in our environment could be described as temporal sequences.' Music and spoken language, for example, are comprised of sequences of different length which are hierarchically ordered. According to the scientist’s hypothesis, the brain classifies the various signals from the smallest, fast-changing components (e.g., single sound units like 'e' or 'u') up to big, slow-changing elements (e.g., the topic). The significance of the information at various temporal levels is probably much greater than previously thought for the processing of perceptual stimuli. 'The brain permanently searches for temporal structure in the environment in order to deduce what will happen next', the scientist explains. In this way, the brain can, for example, often predict the next sound units based on the slow-changing information. Thus, if the topic of conversation is the hot summer, 'su…' will more likely be the beginning of the word 'sun' than the word 'supper'.

To test this hypothesis, the researchers constructed a mathematical model which was designed to imitate, in a highly simplified manner, the neuronal processes which occur during the comprehension of speech. Neuronal processes were described by algorithms which processed speech at several temporal levels. The model succeeded in processing speech; it recognised individual speech sounds and syllables. In contrast to other artificial speech recognition devices, it was able to process sped-up speech sequences. Furthermore it had the brain’s ability to 'predict' the next speech sound. If a prediction turned out to be wrong because the researchers made an unfamiliar syllable out of the familiar sounds, the model was able to detect the error.

The 'language' with which the model was tested was simplified - it consisted of the four vowels a, e, i and o, which were combined to make 'syllables' consisting of four sounds. 'In the first instance we wanted to check whether our general assumption was right', Kiebel explains. With more time and effort, consonants, which are more difficult to differentiate from each other, could be included, and further hierarchical levels for words and sentences could be incorporated alongside individual sounds and syllables. Thus, the model could, in principle, be applied to natural language.

'The crucial point, from a neuroscientific perspective, is that the reactions of the model were similar to what would be observed in the human brain', Stefan Kiebel says. This indicates that the researchers’ model could represent the processes in the brain. At the same time, the model provides new approaches for practical applications in the field of artificial speech recognition.

Max Planck Institute


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Scientists at the University of Calgary have found that methane emission by plants could be a bigger problem in global warming than previously thought.

A U of C study says that when crops are exposed to environmental factors that are part of climate change-increased temperature, drought and ultraviolet-B radiation-some plants show enhanced methane emissions. Methane is a very potent greenhouse gas; 23 times more effective in trapping heat than carbon dioxide.

"Most studies just look at one factor. We wanted to mix a few of the environmental factors that are part of the climate change scenario to study a more true-to-life impact climate change has on plants," says David Reid, a professor in the Department of Biological Sciences who co-authored a paper with research associate Mirwais Qaderi in the advanced on-line edition of the journal Physiologia Plantarum.

Reid and Qaderi, who received funding from the University Research Grants Committee (URGC) and Natural Sciences and Engineering Research Council of Canada (NSERC), analyzed methane emissions from six important Canadian crops-faba bean, sunflower, pea, canola, barley and wheat-that were exposed to combinations of three components of global climate change: temperature, ultraviolet-B radiation and water stress (drought). What they found they say is troubling. These stresses caused plants to emit more methane. In a warmer, drier world methane might be a bigger contributor in global warming than previously thought.

When it comes to the greenhouse effect, methane could be considered the misunderstood and often overlooked orphan greenhouse gas. Much of the attention has been focused on carbon dioxide but more recently it has been realized that methane should also be considered as a very significant greenhouse gas. Its concentrations have more than doubled since pre-industrial times. While the growth rate of methane concentrations has slowed since the early 1990s, some scientists say this is only a temporary pause.

"Our results are of importance in the whole climate warming discussion because methane is such a potent greenhouse warming gas, says Qaderi. "It points to the possibility of yet another possible feedback phenomena which could add to global warming."

Since elevated levels of carbon dioxide has been observed to counteract the negative effects of some environmental stresses, Qaderi and Reid are now studying the effect of increased carbon dioxide with factors such as drought, higher temperature and UVB on methane production in crops.

(Photo: U. Calgary)

University of Calgary


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The Department of Energy's Pacific Northwest National Laboratory has developed a reusable organic liquid that can pull harmful gases such as carbon dioxide or sulfur dioxide out of industrial emissions from power plants. The process could directly replace current methods and allow power plants to capture double the amount of harmful gases in a way that uses no water, less energy and saves money.

"Power plants could easily retrofit to use our process as a direct replacement for existing technology," said David Heldebrant, PNNL's lead research scientist for the project.

Harmful gases such as carbon dioxide or sulfur dioxide are called "acid gases." The new scrubbing process uses acid gas-binding organic liquids that contain no water and appear similar to oily compounds. These liquids capture the acid gases near room temperature. Scientists then heat the liquid to recover and dispose of the acid gases properly.

These recyclable liquids require much less energy to heat but can hold two times more harmful gases by weight than the current leading liquid absorbent used in power plants. It is a combination of water and monoethanolamine, a basic organic molecule that grabs the carbon dioxide.

PNNL's previous work with the all-organic liquids focused on pulling only carbon dioxide out of emissions from power plants. New work will show how the process can be applied to other acid gases such as sulfur dioxide.

"Current methods used to capture and release carbon dioxide emissions from power plants use a lot of energy because they pump and heat an excess of water during the process," said Heldebrant. He notes the monoethanolamine component is too corrosive to be used without the excess water.

In PNNL's process called "Reversible Acid Gas Capture," the molecules that grab onto the acid gases are already in liquid form, and don't contain water. The acid gas-binding organic liquids require less heat than water does to release the captured gases.
Heldebrant and colleagues demonstrated the process in previous work with a carbon dioxide-binding organic liquid, called CO2BOL. In this process, scientists mix the CO2BOL solution into a holding tank with emissions that contain carbon dioxide. The CO2BOL chemically binds with the carbon dioxide to form a liquid salt solution.

In another tank, scientists reheat the salt solution to strip out the carbon dioxide. Non-hazardous gases such as nitrogen would not be captured and are released back into the atmosphere. The toxic compounds are captured separately for storage. At that point, the CO2BOL solution is back in its original state and ready for reuse.

(Photo: PNNL)

Pacific Northwest National Laboratory


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According to a recent study published in Psychological Science, a journal of the Association for Psychological Science, it appears humans are not actually capable of "turning off" another language entirely. Psychologists Eva Van Assche, Wouter Duyck, Robert Hartsuiker and Kevin Diependaele from Ghent University found that knowledge of a second language actually has a continuous impact on native-language reading.

The researchers selected 45 Ghent University students whose native-language was Dutch and secondary language was English. The psychologists asked the students to read several sentences containing control words - plain words in their native-language - and cognates. Cognates are words that have a similar meaning and form across languages, often descending from the same ancient language; for example, "cold" is a cognate of the German word "kalt" since they both descended from Middle English.

While the students read the sentences, their eye movements were recorded and their fixation locations were measured--that is, where in the sentence their eyes paused. The researchers found that the students looked a shorter period of time at the cognates than at the controls. So in the example sentence "Ben heeft een oude OVEN/LADE gevonden tussen de rommel op zolder" (Ben found an old OVEN/DRAWER among the rubbish in the attic), the bilingual students read over "oven" more quickly than "lade."

According to the psychologists, it is the overlap of the two languages that speeds up the brain's activation of cognates. So even though participants did not need to use their second language to read in their native-language, they still were unable to simply "turn it off." It appears, then, that not only is a second language always active, it has a direct impact on reading another language--even when the reader is more proficient in one language than another.

Psychological Science


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Microscopic magnetic particles have been used to bring stem cells to sites of cardiovascular injury in a new method designed to increase the capacity of cells to repair damaged tissue, BBSRC-funded scientists at UCL announced recently.

The cross disciplinary research, published in The Journal of the American College of Cardiology: Cardiovascular Interventions, demonstrates a technique where endothelial progenitor cells - a type of stem cell shown to be important in vascular healing processes - have been magnetically tagged with a tiny iron-containing clinical agent, then successfully targeted to a site of arterial injury using a magnet positioned outside the body.

Following magnetic targeting, there was a five-fold increase in cell localisation at a site of vascular injury in rats. The team also demonstrated a six-fold increase in cell capture in an in vitro flow system (where microscopic particles are suspended in a stream of fluid and examined to see how they behave).

Although magnetic fields have been used to guide cellular therapies, this is the first time cells have been targeted using a method directly applicable to clinical practice. The technique uses an FDA (U.S. Food and Drug Administration) approved agent that is already used to monitor cells in humans using MRI (magnetic resonance imaging).

Dr Mark Lythgoe, UCL Centre for Advanced Biomedical Imaging, the senior author of the study, said: "Because the material we used in this method is already FDA approved we could see this technology being applied in human clinical trials within 3-5 years. It's feasible that heart attacks and other vascular injuries could eventually be treated using regular injections of magnetised stem cells. The technology could be adapted to localise cells in other organs and provide a useful tool for the systemic injection of all manner of cell therapies. And it's not just limited to cells - by focusing tagged antibodies or viruses using this method, cancerous tumours could be much more specifically targeted."

Panagiotis Kyrtatos, also from the UCL Centre for Advanced Biomedical Imaging and lead researcher of the study, added: "This research tackles one of the most critical challenges in the biomedical sciences today: ensuring the effective delivery and retention of cellular therapies to specific targets within the body.

"Cell therapies could greatly benefit from nano-magnetic techniques which concentrate cells where they are needed most. The nano-magnets not only assist with the targeting, but with the aid of MRI also allow us to observe how the cells behave once they're injected."

(Photo: BBSRC)



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Researchers have modified nanoparticles known as "Cornell dots" to make the world's tiniest laser -- so small it could be incorporated into microchips to serve as a light source for photonic circuits. The device may also have applications for sensors, solar collectors and in biomedicine.

The original Cornell dots, created by Ulrich Wiesner, the Spencer T. Olin Professor of Engineering at Cornell, consist of a core of dye molecules enclosed in a silica shell to create an unusually luminous particle. The new work by researchers at Norfolk (Virginia) State University (NSU), Purdue University and Cornell uses what Wiesner calls "hybrid Cornell dots," which have a gold core surrounded by a silica shell in which dye molecules are embedded.

The research is reported in the Aug. 16 online issue of the journal Nature and will appear in a coming print issue.

Using nanoparticles 44 nanometers (nm -- one billionth of a meter or about three atoms in a row) wide, the device is the smallest nanolaser reported to date, and the first operating in visible light wavelengths, the researchers said.

"This opens an interesting playground in terms of miniaturization," said Wiesner. "For the first time we have a building block a factor of 10 smaller than the wavelength of light."

An optical laser this small is impossible because a laser develops its power by bouncing light back and forth in a tuned cavity whose length must be at least half the wavelength of the light to be emitted. In the first tests of the new device, the light emitted had a wavelength of 531 nm, in the green portion of the visible spectrum.

In a conventional laser, molecules are excited by an outside source of energy, which may be light, electricity or a chemical reaction. Some molecules spontaneously release their energy as photons of light, which bounce back and forth between two reflectors, in turn triggering more molecules to emit photons.

In the new device, dye molecules in the nanoparticle are excited by a pumping laser. A few molecules spontaneously release their added energy to generate a plasmon -- a wave motion of free electrons at an optical frequency -- in the gold core. In the tiny space, the dye molecules and the gold core are coupled by electric fields, explains Purdue co-author Vladimir Shalaev.

Oscillations of the plasmon in turn trigger more dye molecules to release their energy, which further pumps up the plasmon, creating a "spaser" (surface plasmon amplification by stimulated emission of radiation). When the energy of the system reaches a threshold the electric field collapses, releasing its energy as a photon. The size of the core -- 14 nm in diameter -- is chosen to set up a resonance that reinforces a wave corresponding to the desired 531 nm light output.

Tests at NSU indicate that the lasing effect occurs within each Cornell dot and is not a phenomenon of a collection of the nanoparticles working together, making this unquestionably the world's smallest laser.

"Some people argue that the ability to produce a surface plasmon in this way will be even more useful," added NSU professor and lead author Mikhail Noginov. It has been suggested that plasmons could be used to send signals across a microchip at the speed of light -- much faster than electrons in wires -- but in less space than photonic circuits need.

(Photo: Wiesner Lab, Cornell University)

Cornell University




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