Sunday, September 16, 2007

New frontier for DNA team: A bar code for every animal


To build and develop career www.careerbd.net




perfume presents personality www.perfumeplus.zlio.com





Step into a forest in southern Ontario and a dizzying array of diversity pummels the senses: ferns line a stream, songbirds flit overhead, lichen pepper a tree stump, a mosquito finds the soft flesh on your arm.


Unless you have a degree in taxonomy, identifying all of the flora and fauna is an insurmountable task.


University of Guelph scientists hope to change that using something retail stores have relied on for years: bar codes. Researchers at the Biodiversity Institute of Ontario are starting to assign a unique DNA identifier in the form of a genetic bar code to every animal species on the planet.


They are not alone in their quest. Since the idea was first published in 2003 by University of Guelph professor Paul Hebert, DNA bar coding has been adopted by 160 organizations in 50 countries and more than 31,000 species have been coded.


Experts believe it has a host of applications, from catching agricultural pests at the border to quickly identifying disease-carrying mosquitos.


It will help researchers discover species and trace evolutionary patterns, says David Schindel, executive secretary of the Consortium for the Barcode of Life, at the Smithsonian Institution in Washington, D.C. and host of next week's second international Barcode of Life conference in Taipei.


Scientists are bar-coding as many species as possible in an effort to create a global reference library, says Schindel.


Much like a fingerprint database, DNA bar-coding only works if there is a comprehensive catalogue from which to compare samples.


Barcoding will soon allow scientists to quickly identify hard-to-distinguish species within hours, rather than days. Taxonomists usually use physical characteristics, such as colour markings, to classify an animal. But that won't always work; scientists may only have a small piece of an organism to work with.


When dead birds carrying avian flu washed up on the shores of Scotland, it took weeks to identify the species as swans because they were so decomposed, Schindel says.


"If we could have bar-coded the species, we would have known what they were within a day and, possibly, where they came from," he says. "It would have been a big help for public health officials."


Hebert, who holds a Canada Research Chair in molecular biology, had long thought DNA could be used to identify species.


Scanning an animal's entire genome would cost too much and take too long, so he pinpointed a short piece of DNA - a section of a gene called cytochrome c oxidase 1, or CO1 - that could distinguish one animal from an other. It was a successful hunch, though it can't be used for plants.


"The results of the first wave of studies have been so positive that the plan to bar code all life is simply irresistible," Hebert wrote in an email while travelling in Korea.


He believes 500,000 animal species will be bar-coded within five years.


The Biodiversity Institute of Ontario, which opened in May, houses the world's leading DNA bar-code facility. Robert Hanner, an assistant professor at the University of Guelph and co-ordinator of the Fish Barcode of Life Campaign, says the lab is able to code between 12,000 and 20,000 samples a month, for $2 a sample.


Agricultural groups have approached them to bar-code insects that affect Ontario crops, he says.


Critics say DNA bar-coding isn't nearly as accurate as promised.


Felix Sperling, a biology professor at the University of Alberta, points out bar coding seems to work best for identifying species, such as birds, that are easy to distinguish by physical characteristics.


It does not work as well for other plant and animal groups, such as lichen, fungi and parasitic insects, he adds.


That doesn't bother Spencer Barrett, a University of Toronto professor of evolutionary biology, who is looking for a piece of DNA that can be used to distinguish plant species.


"The next big frontier, the next big scientific question, is to identify all of the biodiversity on Earth," he says, noting only 1.7 million species have been named of some 20 million to 30 million species.


HOW IT WORKS



Scientists only need DNA from a single gene to identify most species of animals on Earth.


• First, a tissue sample is collected and sent to a lab, where DNA can be extracted.


• The target piece of DNA - a portion of a gene called cytochrome c oxidase 1 (CO1) - is copied many times, using a technique called polymerase chain reaction.


• The copies are sequenced to determine the exact order of the four base pairs (A,T,C,G) within the strand of DNA, which generates the specific barcode for that species.


• The barcode information, along with the animal's taxonomic name, photos, GPS co-ordinates of where it was found, and other distinguishing characteristics, are entered into the Barcode of Life data system. It's accessible to anyone at www.barcodinglife.org.




PROMISING APPLICATIONS



• Quickly identifying species of mosquitos that carry diseases, including those that carry West Nile virus or malaria.


• Checking for consumer products made from endangered plants or animals.


• Identifying invasive insect pests on agricultural shipments going in and out of Canada


• Environmental monitoring - mapping how birds shift breeding territories in response to global warming, for example.


• Tracing unwanted plant and animal ingredients in foods.






Technorati :

The ecosystem of the mobile phone and iPhone,


To build and develop career www.careerbd.net




perfume presents personality www.perfumeplus.zlio.com



Just 74 days after launching its iPhone, Apple announced it had already sold 1 million of the things - a milestone that its previous blockbuster product, the iPod, took almost two years to reach.

And yet, to judge by the industry's chatter, the iPhone is already old news. More excitement swirls around rumours that Google, the Web-search giant that is Apple's neighbour in Silicon Valley, could enter the market with its own "gPhone." Google's boss, Eric Schmidt, has already said that the firm plans to bid for a prime slice of the wireless spectrum in a forthcoming auction, something Apple is also said to be considering.


In short, both mobile operators and handset-makers could soon be confronted with two of the world's sexiest brands as direct rivals. Publicly, Apple and Google are being diplomatic.


The industry is a stool with three legs - network service, devices, and the software and content that goes on them - and "I don't think any player in the ecosystem trying to glue it all together will be very successful," says Dipchand Nishar, who leads Google's mobile-phone strategy.


By this he may simply be conceding the obvious, which is that Google would not build hardware, even if it made the other two legs.


But Google seems to be up to something. It bought a company called Android in 2005 that specializes in mobile-phone software. It has Google Talk, a free Internet-calling service. In July it bought GrandCentral Communications, a firm that gives users one single phone number for life. And it recently filed a patent application for a new mobile-payment technology.


It would certainly be tempting to tie all these bits together into a new software "platform" for mobile phones and offer it to handset-makers as an alternative to existing smart-phone operating systems such as Symbian, Palm or Microsoft's Windows Mobile.


Naturally, Google's search, email and document services would be tightly integrated, along with its advertising technologies, which might pave the way for mobile service that is partly or wholly subsidized by advertising.


As a strategy, this might be just different enough from Apple's to assure harmony with its ally.


It would suit neither firm to open hostilities. So Google may concentrate on software for cheaper, mass-market devices, leaving Apple to make elegant, high-end hardware.




Technorati :

IBM researchers arrange 60-nanometer gold particles to re-create a work of Renaissance art


sponsored by:career builder and developer careerbd.net


IBM researchers arrange 60-nanometer gold particles to re-create a work of Renaissance art


sponsored by:career builder and developer careerbd.net


New Negatively-Charged Molecule Discovered


New Negatively-Charged Molecule Discovered


Astronomers using data from the National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT) have found the largest negatively-charged molecule yet seen in space. The discovery of the third negatively-charged molecule, called an anion, in less than a year and the size of the latest anion will force a drastic revision of theoretical models of interstellar chemistry, the astronomers say.


"This discovery continues to add to the diversity and complexity that is already seen in the chemistry of interstellar space," said Anthony J. Remijan of the National Radio Astronomy Observatory (NRAO). "It also adds to the number of paths available for making the complex organic molecules and other large molecular species that may be precursors to life in the giant clouds from which stars and planets are formed," he added.


A team of scientists from the Harvard-Smithsonian Center for Astrophysics (CfA) found negatively-charged octatetraynyl in a cold, dark cloud of molecular gas. A second team headed by Remijan found octatetraynyl in the envelope of gas around an old, evolved star. In both cases the molecule, a chain of eight carbon atoms and one hydrogen atom, had an extra electron, giving it a negative charge.


About 130 neutral and about a dozen positively-charged molecules have been discovered in space, but the first negatively-charged molecule was not discovered until late last year. The largest previously-discovered negative ion found in space has six carbon atoms and one hydrogen atom.


Ultraviolet light from stars can knock an electron off a molecule, creating a positively-charged ion. Astronomers had thought that molecules would not be able to retain an extra electron, and thus a negative charge, in interstellar space for a significant time. "That obviously is not the case," said Mike McCarthy of the CfA. "Anions are surprisingly abundant in these regions."


"Until recently, many theoretical models of how chemical reactions evolve in interstellar space have largely neglected the presence of anions. This can no longer be the case, and this means that there are many more ways to build large organic molecules in cosmic environments than have been explored," said Jan M. Hollis of NASA's Goddard Space Flight Center (GSFC).


Remijan and his colleagues found the octatetraynyl anions in the envelope of the evolved giant star IRC +10 216, about 550 light-years from Earth in the constellation Leo. They found radio waves emitted at specific frequencies characteristic of the charged molecule by searching archival data from the GBT, the largest fully-steerable radio telescope in the world.


Another team from the Harvard-Smithsonian Center for Astrophysics found the same characteristic emission when they observed a cold cloud of molecular gas called TMC-1 in the constellation Taurus. These observations also were done with the GBT. In both cases, preceding laboratory experiments by the CfA team showed which radio frequencies actually are emitted by the molecule, and thus told the astronomers what to look for.


"It is essential that likely interstellar molecule candidates are first studied in laboratory experiments so that the radio frequencies they can emit are known in advance of an astronomical observation," said Frank Lovas of the National Institute of Standards and Technology (NIST).


Both teams announced their results in the July 20 edition of the Astrophysical Journal Letters.


"With three negatively-charged molecules now found in a short period of time, and in very different environments, it appears that many more probably exist. We believe that we can discover more new species using very sensitive and advanced radio telescopes such as the GBT, once they have been characterized in the laboratory," said Sandra Bruenken of the CfA.


"Further detailed studies of anions, including astronomical observations, laboratory studies, and theoretical calculations, will allow us to use them to reveal new information about the physical and chemical processes going on in interstellar space," said Martin Cordiner, of Queen's University in Belfast, Northern Ireland.


"The GBT continues to take a leading role in discovering, identifying and mapping the distribution of the largest molecules ever found in astronomical environments and will continue to do so for the next several decades," said Phil Jewell of NRAO.


In addition to Hollis, Lovas, Cordiner and Jewell, Remijan worked with Tom Millar of Queen's University in Belfast, Northern Ireland, and Andrew Markwick-Kemper of the University of Manchester in the UK.


Bruenken worked with McCarthy, Harshal Gupta, Carl Gottlieb, and Patrick Thaddeus, all of the Harvard-Smithsonian Center for Astrophysics.


The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.



MORE NEWS.....


Astronomers have detected negatively charged molecules in space for the first time, suggesting the molecules may be more common than previously thought.


Previously, about 130 different neutral molecules and 14 positively charged molecules had been identified in space - but no negatively charged molecules were found.


Conventional wisdom held that these were rare because ultraviolet radiation from starlight would tend to strip away extra electrons, leaving behind only positive ions.


Now, astronomers from the Harvard-Smithsonian Center for Astrophysics (CfA) in Cambridge, Massachusetts, US, have found a negatively charged molecule in two nearby regions within the Milky Way. Composed of six carbon atoms, a hydrogen atom, and an extra electron, it is called a hexatriyne anion, or C6H-.


Curiously, the anion was found in two very different environments - a gas shell around the dying, red giant star IRC+10216 and the cold molecular cloud TMC-1, both of which lie about 500 light years from Earth.


Unknown cause


It is not yet clear what physical process actually led to the molecule's formation in those locations. "That's the point we're desperately eager to find out," says team member Patrick Thaddeus of the CfA.


The molecule may have formed in these gaseous regions after an extra proton was bumped off the neutral molecule hexatriyne, C6H2, or by an electron attaching to the neutral molecule C6H. The anion is present in both sources at a level of between 1% and 5% that of the neutral molecule C6H.


One clue to its formation may come from its size; C6H- is composed of more atoms than many of the neutral molecules that have been found in space.


"It was considered crazy that the first negatively charged molecule we found in space would be such a big molecule," Thaddeus says.


This large size may increase the molecule's stability. Previous research suggests electrons can attach themselves quite efficiently to carbon molecules when the molecules are composed of at least six carbon atoms.


Lurking undetected


To make the find, the CfA astronomers pored over data collected 11 years ago by Kentarou Kawaguchi at Okayama University in Japan. Kawaguchi's team found a series of spectral lines that could not be assigned to any known molecule in IRC+10216.


Back in the lab, the CfA team found the spectral lines matched C6H-. They then used the Green Bank Telescope to verify that the molecule was present in the red giant and in TMC-1.


The find suggests other negatively charged molecules are lurking in space and have not been detected because previous searches have focused on more diffuse gas clouds where the anions are not concentrated enough to produce a signal.


"This is a whole area of astrochemistry that we've just kind of been missing," says Robert McMahon, a chemist at the University of Wisconsin, Madison, US, who was not involved in the study.


Team member Michael McCarthy of the CfA says the researchers will search them out by first studying the spectral signatures of large anions, like C6H-, in the laboratory.


They have already found C4H- and C8H- in the lab and are now trying to find the molecules' signatures in space. The team says they may find these anions in IRC+10216 and TMC-1, since neutral or positively charged variations of these molecules have already been observed in the regions.










Technorati : , , ,

Prions May Activate Retroviruses In Infected Brain Cells


Prions May Activate Retroviruses In Infected Brain Cells


This micrograph of brain tissue reveals the cytoarchitectural histopathologic changes found in bovine spongiform encephalopathy.



In work originating from the Bavarian Research Cooperation Prions (FORPRION), which ended in 2007, a team led by the scientist Prof. Dr. Christine Leib-Mösch has been able to show that prion proteins may activate endogenous retroviruses in infected brain cells.


In the Institute of Molecular Virology of the GSF - National Research Center for Environment and Health in Neuherberg/Munich (Helmholtz Association of German Research Centres) the group is continuing to search for cellular components whose make-up is changed as a result of a prion infection. In collaboration with colleagues from the Technical University of Munich and the University of Heidelberg, the group used micro-array technologies - micro-arrays are chips with thousands or tens of thousands of DNA or protein probes - and could demonstrate that the expression of endogenous retroviruses is influenced by infectious prion proteins in tests with mouse cells.


Prions - an abbreviation for proteinaceous infectious particles - work as a trigger to a set of diseases of the brain and nervous system, the so-called spongiform encephalopathies. These include BSE in cattle, scrapie in sheep and Creutzfeldt Jakob's Disease in humans. Prions are structural variants of a normal protein found in healthy tissues - especially in the brain.



The devastating effect of infectious prions is that, once they have entered the organism, they can modify the normal "healthy" prion proteins to create more infectious prions, and thus cause the illness to progress. However, as yet, little is known about the molecular mechanisms of pathogenesis, the role of co-factors and the interaction of prion proteins with cellular components.


Retroviruses insert their genetic information into the genome of host cells. In the case of endogenous retroviruses, this involves retroviral infections from long ago, which were transmitted through many generations by means of the germ line. Nearly ten percent of the genome of mice and humans consists of endogenous retroviral sequences that have accumulated during the course of evolution. Indeed, most structural genes of endogenous retroviruses are inactive, but many regulatory elements, such as binding sites for transcription factors, often remain active and can influence neighbouring cellular genes.


The GSF scientists infected mouse neural cells kept in culture with infectious prion proteins and subsequently analysed the expression patterns of endogenous retroviruses. The results showed that the expression of a set of endogenous retroviral sequences is influenced by the prion infection: in comparison with uninfected cells, the expression partly increased but also partly decreased - depending on the cell line and the type of endogenous retroviruses. These effects could be suppressed by pentosan-polysulphate, an anti-prion drug, which means that the influence of the expression can be attributed to the prions and not to some secondary effects.


These observations suggest that prion proteins may stimulate the production of retroviral particles by activation of endogenous retroviruses. Subsequently, these retrovirus-like particles could transport prion proteins from cell to cell, and thus spread the infection.


These studies were carried out within the scope of the "Bavarian Research Cooperation Prions" (FORPRION) in the Association of Bavarian Research Cooperations. FORPRION was founded in 2001 following the appearance of the first BSE cases in Bavaria and was financed equally from the budgets of the Bavarian State Ministry for Science, Research and Art, and the Bavarian State Ministry of Health Food and Consumer Affairs.


Through basic and applied research the consortium aims to make progress in the diagnosis and therapy of human and animal prion diseases, as well as in the field of preventive consumer protection. FORPRION linked up 25 projects, based at five Bavarian universities and in institutes of the Max Planck Society. The financial support of the Bavarian Research Cooperation Prions FORPRION ended in June, 2007.



MORE NEWS......



A team led by the scientist Prof. Dr. Christine Leib-Mösch of the Bavarian Research Cooperation Prions (FORPRION), which ended in 2007, has confirmed that prion proteins may activate endogenous retroviruses in infected brain cells.



Prions - an abbreviation for proteinaceous infectious particles - work as a trigger to a set of diseases of the brain and nervous system, the so-called spongiform encephalopathies. These include BSE in cattle, scrapie in sheep and Creutzfeldt Jakob's Disease in humans. Prions are structural variants of a normal protein found in healthy tissues - especially in the brain.


The devastating effect of infectious prions is that, once they have entered the organism, they can modify the normal "healthy" prion proteins to create more infectious prions, and thus cause the illness to progress. However, as yet, little is known about the molecular mechanisms of pathogenesis, the role of co-factors and the interaction of prion proteins with cellular components.


Retroviruses insert their genetic information into the genome of host cells. In the case of endogenous retroviruses, this involves retroviral infections from long ago, which were transmitted through many generations by means of the germ line.


Nearly ten percent of the genome of mice and humans consists of endogenous retroviral sequences that have accumulated during the course of evolution. Indeed, most structural genes of endogenous retroviruses are inactive, but many regulatory elements, such as binding sites for transcription factors, often remain active and can influence neighbouring cellular genes.


The GSF scientists infected mouse neural cells kept in culture with infectious prion proteins and subsequently analysed the expression patterns of endogenous retroviruses. The results showed that the expression of a set of endogenous retroviral sequences is influenced by the prion infection: in comparison with uninfected cells, the expression partly increased but also partly decreased - depending on the cell line and the type of endogenous retroviruses. These effects could be suppressed by pentosan-polysulphate, an anti-prion drug, which means that the influence of the expression can be attributed to the prions and not to some secondary effects.



These observations suggest that prion proteins may stimulate the production of retroviral particles by activation of endogenous retroviruses. Subsequently, these retrovirus-like particles could transport prion proteins from cell to cell, and thus spread the infection.


These studies were carried out within the scope of the "Bavarian Research Cooperation Prions" (FORPRION) in the Association of Bavarian Research Cooperations. FORPRION was founded in 2001 following the appearance of the first BSE cases in Bavaria and was financed equally from the budgets of the Bavarian State Ministry for Science, Research and Art, and the Bavarian State Ministry of Health Food and Consumer Affairs.


Through basic and applied research the consortium aims to make progress in the diagnosis and therapy of human and animal prion diseases, as well as in the field of preventive consumer protection. FORPRION linked up 25 projects, based at five Bavarian universities and in institutes of the Max Planck Society. The financial support of the Bavarian Research Cooperation Prions FORPRION ended in June, 2007.




Technorati : , , , , ,