Tag Archives: dna

We’re all hosts on a viral planet: yes, bacteria too

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Given that phages are able to destroy bacteria, they are of particular interest to science. Basic researchers from the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) in Berlin are especially interested in the tube used by phages to implant their DNA (or RNA – dp) into bacteria. In collaboration with colleagues from Forschungszentrum Jülich and Jena University Hospital, they have now revealed the 3D structure of this crucial phage component in atomic resolution. The key to success was combining two methods – solid-state NMR and cryo-electron microscopy. The study has just been published in the journal Nature Communications.

With growing antibiotic resistance, phages have increasingly become the focus of research. Phages are naturally occurring viruses with a very useful property: they implant their DNA into bacteria and proliferate there until the bacterial cell is ultimately destroyed. This is why they are also referred to as bacteriophages (bacteria eaters).
This approach has already been shown to fight multidrug-resistant bacteria. Last year, the case of a girl from England hit the headlines, when she was cured from a serious antibiotic-resistant infection using engineered phages.

However, the widespread use of phage therapy is still a long way off. Many of the underlying principles that are key to advancing this therapy are not yet understood. For example, little was previously known about the appearance of the exact architecture of the tube used by phages to implant their DNA into bacteria. Now scientists from the Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) in Berlin, together with colleagues from Forschungszentrum Jülich and Jena University Hospital, have managed to reveal the 3D structure of this crucial phage component in atomic resolution.

“The structure and flexibility of the DNA tube attached to the icosahedron-shaped capsid is somewhat reminiscent of a spinal column,” stated FMP’s Professor Adam Lange, describing one of the new findings. “It seems to be perfectly designed for transporting DNA.”

The researchers were able to gain insights into the structure and function of this sophisticated DNA transport pathway – in this case, from a variant of phage SPP1 – by combining solid-state NMR with cryo-electron microscopy (cryo-EM). Lange’s research group further developed nuclear magnetic resonance spectroscopy (NMR) especially for this task under an ERC Grant; cryo-EM expert Professor Gunnar Schröder from Forschungszentrum Jülich performed the electron-microscopic investigations. In addition, new modeling algorithms were required for the computer-based combination of the two data sets for structure determination. These algorithms were developed by Professor Michael Habeck from Jena University Hospital. “The key to success was combining the two methods, representing a methodological milestone,” commented Professor Lange.

While solid-state NMR is ideal for visualizing flexible structures and tiny details, cryo-EM provides insight into the overall architecture. The resulting image shows that six gp17.1 proteins organize into stacked rings, forming a hollow tube. The rings are connected by flexible linkers, making the tube very bendable. “We are now able to understand how negatively charged DNA is repelled from the likewise negatively charged interior wall of the flexible tube, passing through it smoothly,” explained FMP’s Maximilian Zinke, lead author of the study now published in Nature Communications. “The bacteria are ultimately destroyed via this pathway.”

Body to be exhumed for paternity test: Elementary Drawing with Salvador Dali

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I tried not to post this, but it brought back so many happy memories of watching SCTV in Canada as a teenager, and the awesome manscaping of Salvador Dali.

The food safety hook would be the Salmonella cross-contamination with the eggs.

AP reports a  Spanish judge has ordered the remains of artist Salvador Dali be exhumed to settle a paternity suit, despite opposition from the state-run foundation that manages the artist’s estate.

Dali, considered one of the ­fathers of surrealist art, died in 1989 and is buried in his museum in the northeast town of ­Figueres.

Pilar Abel, a tarot-card reader from the nearby city of Girona who was born in 1956, says she is the offspring of an affair between Dali and her mother, Antonia.

At the time of the alleged ­affair, Dali was married to his muse, Gala, who died seven years before the painter. Gala had a daughter from an earlier marriage but the couple had no children of their own. Upon his death, at age 84, Dali bestowed his estate to the Spanish state.

On Monday, a Madrid court statement said that tests with DNA from Dali’s embalmed body were necessary because there were no other existing biological remains with which to make a genetic comparison.

Burglar takes a dump on victim’s bedroom floor, police use the poop to track him down

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When you gotta go, you gotta go.

Unfortunately for one Chinese thief, that moment came when he was in the middle of robbing a house.

panda-poopThe 39-year-old man surnamed Zhang from Henan told a Beijing court that he simply couldn’t hold it, the Beijing Times reports. Rather than try to make it to the bathroom, Zhang took a dump right beside the poor victim’s bed. Think of it as a trade?

This being the age of CSI, the critical clump of evidence turned out to be Zhang’s downfall. Beijing police extracted DNA from the poop and matched it to Zhang, who already had a criminal record, receiving a 3-year prison sentence for theft in 2008.

This time, it doesn’t look like Zhang will get off so easy. Thanks to that fateful dump, he has been charged with a whopping 286 cases of theft and 1 case of robbery over the past 4 years. It’s not clear how Beijing police managed to link Zhang to 300 odd thefts, we assume that he didn’t leave his calling card at each one.

We’re all hosts on a viral planet: Meet Luca, the ancestor of all living things

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Some people look to the stars. Some look to themselves. I’ve always been interested in the cosmic goings on of DNA and RNA and their minuscule hosts.

dogma-jesusAccording to science writer legend Nicholas Wade of The New York Times life first emerged on Earth via a single-cell, bacterium-like organism, known as Luca, the Last Universal Common Ancestor, and is estimated to have lived some four billion years ago, when Earth was a mere 560 million years old.

The new finding sharpens the debate between those who believe life began in some extreme environment, such as in deep sea vents or the flanks of volcanoes, and others who favor more normal settings, such as the “warm little pond” proposed by Darwin.

The nature of the earliest ancestor of all living things has long been uncertain because the three great domains of life seemed to have no common point of origin. The domains are those of the bacteria, the archaea and the eukaryotes. Archaea are bacteria-like organisms but with a different metabolism, and the eukaryotes include all plants and animals.

Specialists have recently come to believe that the bacteria and archaea were the two earliest domains, with the eukaryotes emerging later. That opened the way for a group of evolutionary biologists, led by William F. Martin of Heinrich Heine University in Düsseldorf, Germany, to try to discern the nature of the organism from which the bacterial and archaeal domains emerged.

Their starting point was the known protein-coding genes of bacteria and archaea. Some six million such genes have accumulated over the last 20 years in DNA databanks as scientists with the new decoding machines have deposited gene sequences from thousands of microbes.

Genes that do the same thing in a human and a mouse are generally related by common descent from an ancestral gene in the first mammal. So by comparing their sequence of DNA letters, genes can be arranged in evolutionary family trees, a property that enabled Dr. Martin and his colleagues to assign the six million genes to a much smaller number of gene families. Of these, only 355 met their criteria for having probably originated in Luca, the joint ancestor of bacteria and archaea.

Genes are adapted to an organism’s environment. So Dr. Martin hoped that by pinpointing the genes likely to have been present in Luca, he would also get a glimpse of where and how Luca lived. “I was flabbergasted at the result, I couldn’t believe it,” he said.

The 355 genes pointed quite precisely to an organism that lived in the conditions found in deep sea vents, the gassy, metal-laden, intensely hot plumes caused by seawater interacting with magma erupting through the ocean floor.

Yes: Do you really want to know what’s in your burger?

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Is there meat in your veggie burger? It’s possible, according to Clear Labs, a company that genetically tests food products.

meatwad.raw.hamburgerThe company, which gave consumers a peek into the hot dog industry last October, revealed on Tuesday just what consumers are getting when they purchase burger products.

Clear Labs examined 258 samples from 79 brands and 22 different retailers. The samples included ground meat, frozen patties, veggie burgers and fast food burgers.

The company determined that 6.6 percent of the products contained an ingredient that was not listed on the label. In fact, there was beef DNA found in five products that were not supposed to contain beef, including two vegetarian burger products.

In addition, there were 14 products — all vegetarian — that were missing ingredients that were listed on the label. This includes a black bean burger that didn’t have any black beans in it. Altogether, 23.6 percent of vegetarian products were determined to have some discrepancy between the final product and the ingredients listed on the label.

That’s not where the trouble ends for veggie products, however. One vegetarian burger was determined to contain human DNA. The company notes that it was unable to uncover the source of the DNA, but it was likely from hair or skin cells.

Clear Labs also found issues with the meat samples that it tested. A fast food burger and a ground meat sample both contained rat DNA, in addition to one vegetarian burger.

In addition, seven of the 258 samples of meat tested contained a pathogen that had the potential to cause a foodborne illness. The report notes that the pathogens found in the cooked burgers were less likely to be alive and pose a smaller health risk.

“Although we did find several surprising quality issues, signaling that there are gaps in food safety and quality protocols that should be addressed, our findings suggest that the beef industry as a whole has benefited from stringent regulation and aggressive testing requirements,” Clear Labs said in the report.

cartmaburgerprocessjpg“I don’t think this report is helpful for a consumer to know if the food that they are choosing is safe or not,” Mandy Carr, the senior executive director of science and product solutions for the National Cattlemen’s Beef Association, told CNBC.

She raised concerns as to when the DNA discovered on the products was added, noting that the samples could have been contaminated in the lab it was tested in. Carr also noted that the study did not delve into whether the pathogens found in the meat were alive or benign, something that could have been tested.

‘Not in our culture to eat horse meat’; horse, pig DNA found in Irish supermarket burgers

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Traces of horse meat have been found in burgers on sale in some of the country’s busiest supermarkets, food safety chiefs have revealed.

Scientific tests on beef products sold in Tesco, Dunnes Stores, Lidl, Aldi and Iceland uncovered low levels of the animal’s DNA.

Professor Alan Reilly, chief executive of the Food Safety Authority of Ireland (FSAI), said there was no health risk but also no reasonable horse.meat.09explanation for horse meat to be found.

“The products we have identified as containing horse DNA and/or pig DNA do not pose any food safety risk and consumers should not be worried,” he said.

According to the research by the FSAI, one sample of burger goods, Tesco Everyday Value Beef Burgers, showed about 29% horse meat relative to beef content.

“Whilst there is a plausible explanation for the presence of pig DNA in these products due to the fact that meat from different animals is processed in the same meat plants, there is no clear explanation at this time for the presence of horse DNA in products emanating from meat plants that do not use horse meat in their production process,” Prof Reilly said.

“In Ireland, it is not in our culture to eat horse meat and therefore, we do not expect to find it in a burger.”

Food fraud growing in America

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I went on a date with my wife last week.

Not like that new movie, Date Night, which looks horrible, but at 1 p.m., when we have a babysitter. Anything later than that is too tiring to contemplate.

Being in Kansas, I ordered the mussels from Prince Edward Island (that’s in Canada) and the featured white wine from Australia, which, to our ultimate surprise, cost $15 a glass. The extent to which restaurants will go to rip people off, especially in a crappy economy, apparently knows no bounds. I take responsibility, but won’t be going back.

I’m also not alone.

The Washington Post reported yesterday that the expensive "sheep’s milk" cheese in a Manhattan market was really made from cow’s milk. And a jar of "Sturgeon caviar" was, in fact, Mississippi paddlefish.

Some honey makers dilute their honey with sugar beets or corn syrup, their competitors say, but still market it as 100 percent pure at a premium price.

And last year, a Fairfax man was convicted of selling 10 million pounds of cheap, frozen catfish fillets from Vietnam as much more expensive grouper, red snapper and flounder. The fish was bought by national chain retailers, wholesalers and food service companies, and ended up on dinner plates across the country.

"Food fraud" has been documented in fruit juice, olive oil, spices, vinegar, wine, spirits and maple syrup, and appears to pose a significant problem in the seafood industry. Victims range from the shopper at the local supermarket to multimillion companies, including E&J Gallo and Heinz USA.

Such deception has been happening since Roman times, but it is getting new attention as more products are imported and a tight economy heightens competition. And the U.S. food industry says federal regulators are not doing enough to combat it.