Category Archives: DNA

A year after a Globe investigation found restaurants and stores across Massachusetts were routinely selling cheaper, lower-quality fish than they promised customers, a new round of DNA testing shows the vast majority are still mislabeling seafood.

Kens Steak House in Framingham again served Pacific cod instead of a more expensive Atlantic species. Slices of fish sold as white tuna at Sea To You Sushi in Brookline were again actually escolar, an oily species nicknamed the ex-lax fish by some in the industry because it can cause digestion problems. H Mart, an Asian supermarket chain found to have sold mislabeled red snapper last year, this time was selling inexpensive freshwater Nile perch as pricier ocean grouper at its Burlington store.

The results underscore an ongoing lack of regulation in the nations seafood trade oversight so weak restaurants and suppliers know they will not face punishment for mislabeling fish. Over the past several months, the Globe collected 76 seafood samples from 58 of the restaurants and markets that sold mislabeled fish last year. DNA testing on those samples found 76 percent of them werent what was advertised.

Some restaurant operators who repeatedly mislabeled fish blamed suppliers. Others said naming inconsistencies were the result of clerical errors. Several made only partial revisions to their menus. Some, like at Hearth n Kettle in Attleboro, corrected their menus, but waitstaff still wrongly described the fish as local. And a few said the issue was not a priority.

Were too busy to deal with such silliness, Janet Cooper, of Kens Steak House, said after several phone interviews during which she could not explain why the restaurant was still selling far less expensive Pacific cod as locally caught fish.

After the Globes Fishy Business series last fall, state and federal lawmakers pledged quick action to strengthen oversight of the seafood industry. US Representative Ed Markey, Democrat of Malden, filed a bill in July to require traceability of fish from the boat to the dinner plate, but the legislation hasnt moved out of House subcommittees.

Elsewhere, little progress has been made to protect consumers from paying too much for inferior fish. The Food and Drug Administration, which maintains a list of acceptable market names for fish species, has historically focused efforts on food safety, rather than economic fraud such as seafood substitution. The agency recently began conducting its own DNA testing, but the results so far have provided little insight into where mislabeling occurs in the supply chain.

The Globe hired the Biodiversity Institute of Ontario at the University of Guelph to conduct DNA testing on the fish samples, as it did for the initial round of tests in 2011. The testing focused on certain species, such as red snapper and cod, because they have been identified by regulators as more likely to be substituted.

Seafood mislabeling persisted at the Sand Bar & Grille on Marthas Vineyard, where the Globe last year found farmed hybrid bass was switched for striped bass, and tilapia was misrepresented as red snapper.

Mike Wallace, who runs the Oak Bluffs restaurant, said he talked with his sushi chef after the Globes initial investigation and believed the issue was resolved. But DNA testing this year showed samples of albacore and red snapper were both tilapia, one of the cheapest farmed fish on the market.

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New round of DNA tests finds dozens of repeat offenders in fish mislabeling

By Ed Yong | November 29, 2012 1:17 pm

For tens of thousands of years, humans have created sculptures by carving pieces from a solid block. They have chipped away at stone, metal, wood and ceramics, creating art by subtracting material. Now, a group of scientists from Harvard University have figured out how to do the same thing with DNA.

First, Yonggang Ke builds a solid block of DNA from individual Lego-like bricks. Each one is a single strand of the famous double helix that folds into a U-shape, designed to interlock with four neighbours. You can see what happens in the diagram below, which visualises the strands as two-hole Lego bricks. Together, hundreds of them can anneal into a solid block. And because each brick has a unique sequences, it only sticks to certain neighbours, and occupies a set position in the block.

This means that Ke can create different shapes by leaving out specific bricks from the full set, like a sculptor removing bits of stone from a block. Starting with a thousand-brick block, he carved out 102 different shapes, with complex features like cavities, tunnels, and embossed symbols. Each one is just 25 nanometres wide in any direction, roughly the size of the smallest viruses.

Kes work, led by Harvards Peng Yin, is the latest achievement from the growing field of DNA origami. Its forefather was the chemist Ned Seeman, who created a DNA cube in 1991 by annealing separate strands together. He followed this with a simple tubes and lattices, but his technique was laborious and inefficient.

Paul Rothemund greatly improved it in 2006. He showed that you can fold a long 7,000-letter strand of viral DNA into a specific shape by using hundreds of shorter snippets. These match different part of the viruss genome and staple it into place. Mix the strands togetherthe long scaffold and short staplesand they spontaneously fold into the right shape. Rothemund and others used the origami technique to create miniature maps, smiley faces, the word NED (in honour of Seeman), and more elaborate shapes like boxes.

Last year, Yins team broke off from the scaffold-and-staples tradition. I wrote about their work for Nature News:

Bryan Wei and his colleagues make shapes out of single strands of DNA just 42 letters long. Each strand is unique, and folds to form a rectangular tile. When mixed, neighbouring tiles stick to each other in a brick-wall pattern, and shorter boundary tiles lock the edges in place.

In their simplest configuration, the tiles produce a solid 64-by-103-nanometre rectangle, but Wei and his team can create more complex shapes by leaving out specific tiles. Using this strategy, they created 107 two-dimensional shapes, including letters, numbers, Chinese characters, geometric shapes and symbols. They also produced tubes and rectangles of different sizes, including one consisting of more than 1,000 tiles.

The team designed a robot to pick the tiles. The desired shape is drawn using a graphical interface, and the robot picks out and mixes the required strands. It can produce 48 shapes in as many hours. Millions of shapes can be crafted from the same set of tiles simply by leaving some out. Once you have a pre-synthesized library, you dont need any new DNA designs, says Yin. You just pick your molecules.

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DNA Lego bricks produce nano-sculptures

Fifty-nine years after James Watson and Francis Crick deduced the double-helix structure of DNA, a scientist has captured the first direct photograph of the twisted ladder that props up life.

Enzo Di Fabrizio, a physics professor at the Magna Graecia University in Catanzaro, Italy, snapped the picture using an electron microscope.

Previously, scientists had only seen DNA's structure indirectly. The double-corkscrew form was first discovered using a technique called X-ray crystallography, in which a material's shape is reconstructed based on how X-rays bounce after they collide with it.

But Di Fabrizio and his colleagues developed a plan to bring DNA out of hiding. They built a nanoscopic landscape of extremely water-repellant silicon pillars. When they added a solution that contained strands of DNA into this scene, the water quickly evaporated and left behind cords of bare DNA that stretched like tightropes between the tiny mesas.

They then shone beams of electrons through holes in the silicon bed, and captured high-resolution images of the illuminated molecules.

Di Fabrizio's images actually show a thread of several interwoven DNA molecules, as opposed to just two coupled strands. This is because the energy of the electrons used would be enough to destroy an isolated double helix, or a single strand from a double helix.

But with the use of more sensitive equipment and lower energy electrons, Di Fabrizio thinks that snapshots of individual double helices will soon be possible, reports New Scientist.

Molecules of DNA, or deoxyribonucleic acid, store the genetic instructions that govern all living organisms' growth and function.

Di Fabrizio's innovation will allow scientists to vividly observe interactions between DNA and some of life's other essential ingredients, such as RNA (ribonucleic acid). The results of Di Fabrizio's work were published in the journal NanoLetters.

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DNA Directly Photographed for First Time

Two Twins Dancing
Do we have a #39;music #39; DNA gene? If you are connected to the music business, register at http://www.musicalexchanges.com - "The fastest-growing music network on the planet!"From:TheMusicalExchangesViews:0 0ratingsTime:00:54More inMusic

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Two Twins Dancing - Video

Happy Birthday Mommy Gigi
Happy happy birthday Mother! Thank you for all the love, care and understanding even when Daddy #39;s DNA is getting the better of me. We love you so so much. We can soon move to a place we can call our own. Stay beautiful and healthy. I love you!From:TheBabelsOutcastViews:1 0ratingsTime:05:53More inPeople Blogs

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Happy Birthday Mommy Gigi - Video

Cancer Heterogeneity Analysis With Ion AmpliSeq Cancer Panel - Prof Aldo Scarpa, ARC-NET, Verona
Learn more at http://www.lifetechnologies.com Evaluation of tumor heterogeneity by NGS, using the Ion PGM and Ion AmpliSeq cancer panel. The team at ARC-NET, Verona use 10ng FFPE DNA samples to profile genomic sequence variations, revealing specific DNA variants that are associated with different tumor morphologies.From:LifeTechnologiesCorpViews:0 0ratingsTime:04:43More inScience Technology

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Cancer Heterogeneity Analysis With Ion AmpliSeq Cancer Panel - Prof Aldo Scarpa, ARC-NET, Verona - Video

Transcripted Gameplay (PC/1080p HD)
Transcripted Gameplay (PC/1080p HD) More gameplay videos here: http://www.youtube.com Transcripted is a mixture of two incredibly addictive and vastly popular casual gaming styles: the dual-stick shooter and the match three puzzle game. In Transcripted players take control of the Nano Probe, a microscopic apparatus used to combat disease. With the aid of a skill tree that improves ship equipment, health, shields and the Nano Probe #39;s arsenal of upgradeable weapons, players must successfully navigate through hordes of deadly pathogens to destroy the disease #39;s pseudo-DNA as it twines perilously on its endless path to infection. Along the way players must defeat gigantic boss colonies the pathogen has evolved with the sole purpose of stopping the Nano Probe from completing its mission. Difficulty levels of both puzzle and shooting segments can be adjusted independently to suit every play style, making Transcripted an amazingly replayable experience.From:PalmSmashViews:0 0ratingsTime:05:37More inGaming

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Transcripted Gameplay (PC/1080p HD) - Video

HOUSTON, Nov. 29, 2012 /PRNewswire/ --The world's largest processor of full mitochondria sequences, Gene By Gene, Ltd., today announced the launch of DNA DTC to offer highly reliable and competitively priced genomic testing solutions to institutional customers as well as to the Direct-to-Consumer market.

Genomic investigators at life science companies, contract research organizations, academic institutions and public-sector research facilities now have access to the company's Genomics Research Center, a CLIA registered lab, which has processed more than 5 million discrete DNA tests for more than 700,000 individuals and organizations since it was established 12 years ago.

"Given the explosive demand for accurate, timely, and large-scale next generation sequencing, we're pleased to make our Genomics Research Center available to investigators exploring the cutting edge of research to pioneer and enhance treatment of disease, enhance quality of life, break new ground in genealogical inquiry and otherwise advance the science of genomics," Gene By Gene President Bennett Greenspan said. "The launch of DNA DTC is the perfect complement to our other divisions, through which we make genetic testing advances every day in the fields of ancestry, health and relationship testing."

DNA DTC's Houston research center offers a wide range of Research Use Only (RUO) tests, utilizing next generation sequencing including the entire exome (at 80x coverage) and the whole genome. The company offers several products at various levels of analysis and price-points, from cost effective and powerful tools like the Illumina Human OmniExpress BeadChip for genome-wide association studies (GWAS), to human mitochondrial tests, to the comprehensive results delivered by DNA DTC's Exome and Whole Genome Sequencing products.

"Gene By Gene is a truly unique organization in their ability to drive advancements and discoveries in research, clinical applications, and consumer products. We are very excited to be involved in building such a well rounded offering," said Matt Posard, Senior Vice President and General Manager of Illumina's Translational and Consumer Genomics business.

DNA DTC's automated laboratory and processes allow highly reliable testing with remarkable processing times and the most competitive prices in the industry. For example, DNA DTC offers introductory pricing of $695 for Exome Sequencing 80x, using the Illumina HiSeq platform recognized for its high degree of accuracy in identifying variations in any individual's DNA sequence.

With the launch of DNA DTC, institutional customers may take full advantage of Gene By Gene's proven Genomics Research Center, which has already served the needs of researchers from France's Institut Pasteur, Israel's Rabin Medical Center, University of Utah and the National Geographic Society's Genographic Project. The facility processes more than 200 types of DNA tests for customers, is a leading discoverer of Y-chromosome Single Nucleotide Polymorphisms (SNPs), and is the largest processor of human mitochondria sequences submitted to the National Institute of Health's (NIH) National Center for Biotechnology Information (NCBI) GenBank.

The company employs experienced scientists, including Chief Scientist Doron Behar MD, PhD., whose academic background, combined with his dual degrees in Internal Medicine and Critical Care Medicine, gives him unique expertise in evolutionary genomics, ancestry, phylogenetics and translational genomics. Behar leads a multi-disciplinary team of experts working together to develop robust, competitively-priced genetic testing for consumers and institutional customers worldwide.

Customer Inquiries

Prospective institutional customers interested in more information on DNA DTC's RUO offering may visit http://www.dnadtc.com or contact the DNA DTC customer service team at info@dnadtc.com or 713-868-1438.

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Gene By Gene Launches DNA DTC

ScienceDaily (Nov. 30, 2012) DNA lesions are really common -- about one million individual molecular lesions per cell per day -- because its long strands usually have one missing base or are damaged. These lesions can stall the DNA replication process, what can lead to the cell death. To avoid it, there are several pathways to bypass lesions in order to continue with the process of DNA replication. One of these processes has been entirely reproduced in vitro using some techniques of manipulation of single-molecules in a study published November 30 in Science, led by the researcher of the University of Barcelona Maria Maosas.

"This pathway was proposed in the seventies and now we have been able to prove it on a bacteriophage through the manipulation of single-molecules that, oppositely to the traditional biochemical techniques that work with a great number of molecules, allows to study how a protein works on a molecule in real time," explains Maosas, professor at the Department of Fundamental Physics of the UB, affiliated with the campus of International excellence, BKC.

To study a single-molecule, we used magnetic tweezers, a technique which consists on tethering a DNA hairpin between a glass surface and a magnetic bead. A magnetic system generates a magnetic field which allows manipulating the beads and generates magnetic forces. This system can be used in order to measure the extension changes of DNA strands through the screening of the magnetic beads. According to Maosas, "proteins' activity over DNA can be inferred from the changes in the extension of the molecule. The changes are due to the proteins' work."

The template switching strategy

In the DNA replication process, the two strands who act as a template to synthesise a complementary strand are separated, and the new complementary strand joins each of the initial strands in order to obtain two identical copies of the original DNA molecule. In this process take part the polymerases, a family of enzymes that carry out all forms of DNA replication. When in any of the two derived strands there is a lesion, especially in the leading strand, the polymerase stops synthetizing the bases, so the replication process is stalled. "To stall this process can entail some problems in cellular growth," explains Maosas. "When the replication mechanism (replisome) is disassembled, the bypass process analysed in this study starts," points out the author, member of the Biomedical Research Networking center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) and researcher at the University of Paris.

The studied process begins with the action of a helicase protein (UvsW) which promotes the binding of DNA strands, a phenomenon named DNA hybridization. This protein is also able to build an intermediate structure (Holliday junction) taking as a model the not damaged replicated strand and, together with the action of polymerase, drive the system to its departure point, once "jumped" the lesion, and then restart the DNA replication process. "Therefore, the information lost when one strand is damaged can be recovered from the other intact strand which acts as a backup; this process is named "the template switching strategy." In the study, we have also observed the regulation mechanisms of this pathway, as well as the rate of annealing of helicase UvsW, 1500 bases per second, one the largest known," concludes Maosas.

DNA repair is essential in a great number of diseases. A deeper knowledge of these phenomena will enable us to act over some proteins which have similar functions in humans. Maosas is working on this direction; she is carrying out a study on a human protein named HARP in order to know how it works, because it is known that it has a really important role in the genome conservation and its dysfunction is related to some types of cancer.

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Pathway to bypass DNA lesions in replication process is experimentally shown

Engineers have found a new and unexpected use for the code of lifeas a commonplace building material that can be used to fashion precise 3D structures, ranging from miniature smiley faces to cubes.

Most people think of DNA as the master blueprint that is carried in every cell, spelling out the essential traits of organisms. DNA is the building block of life only in the metaphorical sense. But scientists at the Wyss Institute for Biologically Inspired Engineering at Harvard University saw in the material an unexploited versatility, if it were to be used as a real brick. They described Thursday in the journal Science an array of molecular Legos that could one day provide a useful scaffold for building tiny electronic circuits and drug-delivery devices.

To show just how much control they had over structures made of DNA, the team of researchers built a demonstration set of 100 figures. Those ranged from practical engineering feats, such as joining together two structures with a narrow connection, to the whimsicalthe alphabet, or a heart.

When Hendrik Dietz, who leads the Laboratory for Biomolecular Nanotechnology at Technische Universitt Mnchen in Germany, received a copy of the paper from a colleague at Harvard a few weeks ago, he was full of enthusiasm for the work. It represents a new level of control over building precisely tailored objects at the tiniest scales, he wrote in an e-mail. But Dietz said he also had an almost instantaneous emotional response.

The 3D thing is so awesome, he wrote to his colleague. I almost got tears in my eyes because of the joy. I love the Lego figures. When looking at this, one cannot help but submit to the power of DNA.

Peng Yin, a core faculty member of the Wyss Institute who led the research, said it was helpful for the researchers to think of the DNA as Lego bricks rather than as molecules. The code of DNA involves four lettersC, G, T, and Awhich abide by precise pairing rules: A matches up with T, and C with G. To build the structures, researchers started with short strands of DNA, each carrying eight-letter fragments that acted like the prongs on a Lego block. Each eight-letter fragment was like a Lego prong that would only fit one other predetermined Lego.

But unlike a kit that keeps kids busy for hours, these DNA structures required little assembly, once the structures had been designed, Yin said.

You just add some water and salt and increase the temperature to 90 degrees and let it cool down gradually over three daysthats it, Yin said. In one test tube, there are billions of copies of these individual objects, but they all look the same.

The work, he said, demonstrates that DNA, essential for life, can have other uses. It builds on earlier research, in which Yins team found it could stack DNA bricks on one another in two dimensions. And earlier this year, Yins colleague at Harvard, George Church, showed that it was possible to turn DNA into a more conventional storage material. He took the text of his 284-page book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves, translated its words into binary codewords became a string of 0s and 1s. Then, they translated that binary into the letters of DNA, with As and Cs corresponding to 0 and Gs and Ts indicating a 1. They then they created 55,000 short strands of DNA that, read together and properly decoded, amounted to a genetic copy of the book.

Church, who is collaborating with Yin, said the new work would be helpful in any application in which precision was important.

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Harvard scientists build tiny structures with DNA Legos