Category Archives: DNA

Apr. 2, 2013 New study published in Reproductive Biomedicine Online shows that fluid-filled cavity in 5-day old human blastocysts may contain DNA from the embryo, allowing diagnosis of genetic disease without a biopsy.

Preimplantation genetic diagnosis (PGD) technologies allow identification of genetic disorders in human preimplantation embryos after in vitro fertilization (IVF) and before the embryo is transferred back to the patient. This technique allows couples with a high-risk of passing on inherited diseases, to increase their chances of having a healthy baby. Despite the theoretical benefits of PGD, clinical outcomes using these technologies vary, possibly because of the need to remove one or more cells from the embryo using biopsy.

In a recent study published in Reproductive Biomedicine Online, a group of researchers from Italy and the United Kingdom sought to achieve diagnose of genetic disease in embryonic DNA without the use of a biopsy. By extracting fluid from human embryos at the blastocyst stage they found that it contains DNA from the embryo. Blastocysts are 5 or 6 day old embryos and are at the last free-living stage that can be studied in the laboratory prior to transfer into the uterus. They contain between 50 and 300 cells that surround a fluid-filled cavity called the blastocoels. The researchers carefully removed fluid from the blastocoel, leaving the cells intact; the sampled blastocysts were subsequently cryopreserved. Analysis of this fluid showed that it contained cell-free DNA in a state good enough to determine several known genes of the sex chromosomes by polymerase chain reaction (PCR); whole genome amplification and followed by analysis using a specialized tool for genetic testing called a DNA microarray were also used and revealed whether the embryos had a normal number of chromosomes -- chromosome abnormalities are one of the main causes of miscarriage and failure of embryos to form pregnancies during IVF treatments.

"This is the first time that embryonic DNA has been detected in the human blastocyst without the use of biopsy," explained lead researchers Dr. Simone Palini Ph.D., from the IVF Unit at Cervesi Hospital in Cattolica, Italy and Dr. Galluzzi from University of Urbino in Italy and Dr. Dagan Wells from University of Oxford, United Kingdom.

"This is a technique that most embryologists can easily master," Dr. Buletti who directs the IVF team at Cervesi Hospital Cattolica and Prof. Magnani, Chairman of the Department of Biomolecular Sciences of the University of Urbino, added. "More work needs to be done to confirm our results, but we hope that this approach will ultimately help infertile couples achieve their dream of having a family. It may also improve the options for families affected by severe inherited conditions, helping them to have healthy babies."

"Even though it is only a preliminary finding, this approach may allow for genetic testing of the embryo without the complexity of cell sampling," Dr. Joe Leigh Simpson MD, Senior Vice President for Research Programs, March of Dimes Foundation and President, International Federation of Fertility Societies (IFFS), a pioneer in reproductive medicine and genetics, commented on the research.

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The above story is reprinted from materials provided by Elsevier.

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Sampling of embryonic DNA after IVF without biopsy

April 2, 2013

redOrbit Staff & Wire Reports Your Universe Online

Scientists at Penn State University have discovered how a vital step in the human DNA replication process the loading of molecular structures known as sliding clamps onto DNA molecules is performed.

The researchers say their work, the results of which were published in Tuesdays edition of the journal eLife, will help uncover some of the mystery surrounding this crucial part of the chemical replication process. This step had not previously been closely analyzed in human DNA replication, which is the basis for biological inheritance in all types of living organisms.

According to Mark Hedglin, a post-doctoral researcher in Penn States Department of Chemistry and one of the investigators behind the discovery, the sliding clamp is a ring-shaped protein which essentially encircles a DNA strand, latching around it much like a watch band. The sliding clamp then anchors polymerases enzymes involved in the synthesis of nucleic acids to ensure more efficient copying of the genetic material.

Without a sliding clamp, polymerases can copy very few bases the molecular letters that make up the code of DNA at a time. But the clamp helps the polymerase to stay in place, allowing it to copy thousands of bases before being removed from the strand of DNA, Hedglin explained in a statement.

However, because of the closed circular structure of those sliding clamps, another step in DNA replication the presence of a so-called clamp loader to latch and unlatch them at different stages of the process is required. Previously, researchers did not know exactly how the sliding clamp and the clamp loader interacted with one another, nor did they know exactly when the clamp was attached to or unattached from the DNA.

We know that polymerases and clamp loaders cant bind the sliding clamp at the same time, so the hypothesis was that clamp loaders latched sliding clamps onto DNA, then left for some time during DNA replication, returning only to unlatch the clamps after the polymerase left so they could be recycled for further use, Hedglin said.

In order to test their theory, they turned to a method known as Frster resonance energy transfer (FRET), which attaches fluorescent tags to human proteins and parts of DNA in order to monitor the interactions between them.

With those tags in place, Hedglin said he and his colleagues observed the formation of holoenzymes the active form of the polymerase involved in DNA replication, which consists of the polymerase itself along with any accessory factors that optimize its activity.

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Clamping Down On The Mystery Of Human DNA Replication

ST. LOUIS There is no physical evidence tying Rodney Lincoln to a gruesome attack three decades ago that left a mother dead and her two young daughters critically injured, new DNA tests show.

But theres nothing in those results that points to anyone else in the April 27, 1982, slaying, either.

Among the seven pieces of crime scene evidence sent to a Kansas City crime lab including three bloody knives and a bloody fingerprint left on a door frame no male DNA profiles were found. That means the blood is likely that of the victims: JoAnn Tate, 35, Melissa, 7, and Renee, 4.

What it means for Lincolns actual innocence claim, when paired with tests in 2010 that gave him hope, is disputed.

Lincolns lawyers, from the Midwest Innocence Project, argue the DNA results contradict faulty science and misleading testimony that was key to sending him to prison three decades ago on a double life sentence.

It kind of blows their whole case apart, said legal director Laura OSullivan, contending a jury would not convict if presented with the case anew.

But Circuit Attorney Jennifer Joyces office has argued the conviction never rested on science that eyewitness testimony of the two girls sealed Lincolns fate. Through a spokesperson for the office, prosecutors declined to speak about the case for this article.

St. Louis Circuit Court Judge Robin Vannoy has scheduled a three-day hearing in September to consider both sides. It will be the culmination of a seven-year battle under a state law that allows for post-conviction DNA testing in certain instances, and will be key to whether Lincolns convictions are overturned.

Lincolns case was one of six Joyce chose for testing in 2003 from among 1,400 pre-DNA-era convictions. But her office reversed course after learning more about the evidence in his case.

The Midwest Innocence Project got involved in 2005 to push for the DNA tests, setting the stage for the current battle.

Link:
New DNA tests in brutal 1982 slaying in St. Louis set the stage for a decisive hearing

If youve ever tried to decorate a room and have been frustrated because there werent pieces of furniture that were uniquely you, you might be in luck. Dutch design studio Tjep. will present its first exhibition of DNA furniture and jewelry, called Future Nostalgia,at Ventura Lambrate in Milan this month.Thats right furniture shaped by DNA data.

Frank Tjepkema,founder of Tjep. studio, is making these truly one-of-a-kind creations in collaboration with DutchDNAs Eric Wolthuis by taking genetic profiles, mapping them with 3-D imaging, and constructing pieces of furniture that literally capture a persons essence and stand as unique pieces of art.

Wolthuis initiated the idea of designing with DNA by producing jewelry through genetic mapping. After realizing the potential genetic data has to augment design, he reached out to Tjepkema with the idea to create furniture because he saw it as another extension of peoples bodies and personalities.

The signature piece of the first collection of DNA furniture is the Darwin Table, which, somewhat confusingly, isnt made from Darwins DNA, but rather that of Giulia Wolthuis, a contemporary dancer (and daughter of Eric Wolthuis). The tables 3-D design directly corresponds to its DNA mapping visual, capturing Giulias essence through form, according to Tjepkema. The table almost seems to mimic Giulias fluidity and motion as a dancer, with dips and curves that create a totally abstract shape. Some projects allow more artistic liberty, similar to how Tjepkema took the DNA mapping visuals and combined them with iconic symbols such as a heart and flowers for the jewelry collection.

The process to make one of their fittings starts at BaseClear Laboratories in the Netherlands, where they create a DNA profile from a sample of saliva taken with a swab. Rather than a DNA sequencing analysis, the DNA profile is similar to tests done in forensic analysis and paternity tests, creating a unique DNA fingerprint with 16 variable markers spread over the human genome.

Those markers are then translated by a design-mapping program created by Tjep. into a visual representation of the DNA. This DNA mapping serves as kind of a blueprint for the final projects design as Tjepkema takes the 2-D and 3-D forms of the DNA, along with his own artistic direction, and uses them to design a specific piece.

Figuring out the best way to marry genetic data and design was a challenge, but one that Tjepkema embraced from the beginning. Using data sets and numbers pushed him out of his comfort zone, but also allowed him to experiment with a new form of abstract design.

When I was asked to work with an abstract series of numbers I was thrown back into a world without cultural references and this was actually quite liberating, Tjepkema says. I had an excuse to make something abstract within a given conceptual framework. The resulting designs are either completely abstract, in which case the data itself was source of inspiration or a combination of a symbolic reference. The data in itself is very hard and raw but it opened up a whole new intuitive territory.

Tjepkema and Wolthuis seem to have tapped into a new way of humanizing data, giving us another way to seek out information that we might not have been interested in before and use it to create something beautiful and practical. After the Furniture Fair in Milan, DutchDNA and Tjep. will be opened to commissioned projectsno prices are listed yet for individual pieces, but you wont have to wait long to get that genetically-inspired coffee table youve always wanted.

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DNA -Mapped Furniture Imprints Your Genetic Profile in Your Living Room

The Darwin Table is created from a person's unique DNA profile.

The Darwin Table is created from a person's unique DNA profile.

Furnishing a new apartment or house can be tough; sometimes you just can't find that end table or couch that is uniquely "you."

Well, as Wired reports, a Dutch design studio is trying to change that.

Tjep. is expected to exhibit the first line of its DNA furniture and jewelry, called "Future Nostalgia," this month in Milan, Italy. The process takes genetic profiles, maps them with 3-D imaging and constructs pieces of furniture that, quite literally, capture a person's essence.

Wired has more:

"The signature piece of the first collection of DNA furniture is the Darwin Table, which, somewhat confusingly, isn't made from Darwin's DNA, but rather that of Giulia Wolthuis, a contemporary dancer (and daughter of Eric Wolthuis). The table's 3-D design directly corresponds to its DNA mapping visual, capturing Giulia's essence through form, according to Tjepkema. The table almost seems to mimic Giulia's fluidity and motion as a dancer, with dips and curves that create a totally abstract shape. Some projects allow more artistic liberty, similar to how Tjepkema took the DNA mapping visuals and combined them with iconic symbols such as a heart and flowers for the jewelry collection.

The process to make one of their fittings starts at BaseClear Laboratories in the Netherlands, where they create a DNA profile from a sample of saliva taken with a swab. Rather than a DNA sequencing analysis, the DNA profile is similar to tests done in forensic analysis and paternity tests, creating a unique "DNA fingerprint" with 16 variable markers spread over the human genome.

Those markers are then translated by a design-mapping program created by Tjep. into a visual representation of the DNA. This DNA mapping serves as kind of a blueprint for the final project's design as Tjepkema takes the 2-D and 3-D forms of the DNA, along with his own artistic direction, and uses them to design a specific piece."

After the exhibition, Tjep. and its partners will be opened for commissioned projects, though no prices have yet been set. But, if Ikea isn't cutting it and you want a genetically inspired bed, table or desk, this is your chance.

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DNA -Mapped Furniture Really Ties The Room Together ... With You

Published: March. 31, 2013 at 9:41 PM

BALTIMORE, March 31 (UPI) -- Liquid smoke flavoring, black and green teas and coffee activated the highest levels of the cancer-linked gene called p53, U.S. researchers say.

Dr. Scott Kern of the Johns Hopkins University School of Medicine in Baltimore said the p53 gene becomes activated when DNA is damaged. It makes repair proteins that mend DNA. The higher the level of DNA damage, the more p53 becomes activated, Kern said.

"We don't know much about the foods we eat and how they affect cells in our bodies," Kern said in a statement. "But it's clear that plants contain many compounds that are meant to deter humans and animals from eating them, like cellulose in stems and bitter-tasting tannins in leaves and beans we use to make teas and coffees, and their impact needs to be assessed."

Kern said he is not suggesting people stop using tea, coffee or flavorings, but he did suggest the need for further research.

Kern and graduate student Samuel Gilbert, used Kern's test for p53 activity, which makes a fluorescent compound that "glows" when p53 is activated. They mixed dilutions of the food products and flavorings with human cells and grew them in laboratory dishes for 18 hours.

Measuring and comparing p53 activity with baseline levels, the scientists found liquid smoke flavoring, black and green teas and coffee showed up to nearly 30-fold increases in p53 activity, which was on par with their tests of p53 activity caused by a chemotherapy drug called etoposide.

Other flavorings like fish and oyster sauces, Tabasco and soy sauces and black bean sauces showed minimal p53 effects in Kern's tests, as did soybean paste, kim chee, wasabi powder, hickory smoke powders and smoked paprika, the study said.

Many studies have linked coffee and green tea with reducing the risk of some cancers and other diseases.

The findings were published in the journal Food and Chemical Toxicology.

Excerpt from:
DNA -damaging toxins found in some foods

Apr. 1, 2013 For the first time, an elusive step in the process of human DNA replication has been demystified by scientists at Penn State University. According to senior author Stephen J. Benkovic, an Evan Pugh Professor of Chemistry and Holder of the Eberly Family Chair in Chemistry at Penn State, the scientists "discovered how a key step in human DNA replication is performed."

The results of the research will be published in the journal eLife on 2 April 2013.

Part of the DNA replication process -- in humans and in other life forms -- involves loading of molecular structures called sliding clamps onto DNA. This crucial step in DNA replication had remained somewhat mysterious and had not been well studied in human DNA replication. Mark Hedglin, a post-doctoral researcher in Penn State's Department of Chemistry and a member of Benkovic's team, explained that the sliding clamp is a ring-shaped protein that acts to encircle the DNA strand, latching around it like a watch band. The sliding clamp then serves to anchor special enzymes called polymerases to the DNA, ensuring efficient copying of the genetic material. "Without a sliding clamp, polymerases can copy very few bases -- the molecular 'letters' that make up the code of DNA -- at a time. But the clamp helps the polymerase to stay in place, allowing it to copy thousands of bases before being removed from the strand of DNA," Hedglin said.

Hedglin explained that, due to the closed circular structure of sliding clamps, another necessary step in DNA replication is the presence of a "clamp loader," which acts to latch and unlatch the sliding clamps at key stages during the process. "The big unknown has always been how the sliding clamp and the clamp loader interact and the timing of latching and unlatching of the clamp from the DNA," said Hedglin. "We know that polymerases and clamp loaders can't bind the sliding clamp at the same time, so the hypothesis was that clamp loaders latched sliding clamps onto DNA, then left for some time during DNA replication, returning only to unlatch the clamps after the polymerase left so they could be recycled for further use."

To test this hypothesis, the team of researchers used a method called Frster resonance energy transfer (FRET), a technique of attaching fluorescent "tags" to human proteins and sections of DNA in order to monitor the interactions between them. "With these tags in place, we then observed the formation of holoenzymes -- the active form of the polymerase involved in DNA replication, which consists of the polymerase itself along with any accessory factors that optimize its activity," Hedglin said. "We found that whenever a sliding clamp is loaded onto a DNA template in the absence of polymerase, the clamp loader quickly removed the clamp so that free clamps did not build up on the DNA. However, whenever a polymerase was present, it captured the sliding clamp and the clamp loader then dissociated from the DNA strand."

The team members also found that, during the moments when both the clamp loader and the clamp were bound to the DNA, they were not intimately engaged with each other. Rather, the clamp loader released the closed clamp onto the DNA, allowing an opportunity for the polymerase to capture the clamp, completing the assembly of the holoenzyme. Subsequently, the clamp loader dissociated from DNA. "Our research demonstrates that the DNA polymerase holoenzyme in humans consists of only a clamp and a DNA polymerase. The clamp loader is not part of it. It disengages from the DNA after the polymerase binds the clamp," Hedglin added.

Benkovic noted that this mechanism provides a means for the cell to recycle scarce clamps when they are not in use for productive replication.

In addition to Benkovic and Hedglin, other Penn State researchers who contributed to the paper include Senthil K Perumal and Zhenxin Hu.

The research was funded by the National Institutes of Health.

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Crucial step in human DNA replication observed for the first time

SMACK / URLTV PRESENTS DNA VS K-SHINE [FULL BATTLE]
SMACK/ URL does it again with another dope match up between DNA (Queens, NY) K-Shine (Harlem, NY) . This took place on March 9th which is the anniversary o...

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SMACK / URLTV PRESENTS DNA VS K-SHINE [FULL BATTLE] - Video

HOUSTON, March 26, 2013 /PRNewswire/ -- Gene By Gene, Ltd., the Houston-based genomics and genetics testing company, announced that a unique DNA sample submitted via National Geographic's Genographic Project to its genetic genealogy subsidiary, Family Tree DNA, led to the discovery that the most recent common ancestor for the Y chromosome lineage tree is potentially as old as 338,000 years. This new information indicates that the last common ancestor of all modern Y chromosomes is 70 percent older than previously thought.

The surprising findings were published in the report "An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree" in The American Journal of Human Genetics earlier this month. The study was conducted by a team of top research scientists, including lead scientist Dr. Michael F. Hammer of the University of Arizona, who currently serves on Gene By Gene's advisory board, and two of the company's staff scientists, Drs. Thomas and Astrid-Maria Krahn.

The DNA sample had originally been submitted to National Geographic's Genographic Project, the world's largest "citizen science" genetic research effort with more than 500,000 public participants to date, and was later transferred to Family Tree DNA's database for genealogical research. Once in Family Tree DNA's database, long-time project administrator Bonnie Schrack noticed that the sample was very unique and advocated for further testing to be done.

"This whole discovery began, really, with a citizen scientist someone very similar to our many customers who are interested in learning more about their family roots using one of our genealogy products," said Gene By Gene President Bennett Greenspan. "While reviewing samples in our database, she recognized that this specific sample was unique and brought it to the attention of our scientists to do further testing. The results were astounding and show the value of individuals undergoing DNA testing so that we can continue to grow our databases and discover additional critical information about human origins and evolution."

The discovery took place at Family Tree DNA's Genomic Research Center, a CLIA registered lab in Houston which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations, including participants in the Genographic Project. Drs. Thomas and Astrid-Maria Krahn of Family Tree DNA conducted the company's Walk-Through-Y test on the sample and during the scoring process, quickly realized the unique nature of the sample, given the vast number of mutations. Following their initial findings, Dr. Hammer and others joined to conduct a formal study, sequencing ~240 kb of the chromosome sample to identify private, derived mutations on this lineage, which has been named A00.

"Our findings indicate that the last common Y chromosome ancestor may have lived long before the first anatomically modern humans appeared in Africa about 195,000 years ago," said Dr. Michael Hammer. "Furthermore, the sample, which came from an African American man living in South Carolina, matched Y chromosome DNA of males from a very small area in western Cameroon, indicating that the lineage is extremely rare in Africa today, and its presence in the US is likely due to the Atlantic slave trade. This is a huge discovery for our field and shows the critical role direct-to-consumer DNA testing companies can play in science; this might not have been known otherwise."

Family Tree DNA recently dramatically reduced the price of its basic Y-DNA test by approximately 50%. By offering the lowest-cost DNA test available on the market today, Gene By Gene and Family Tree DNA are working to eliminate cost as a barrier to individuals introducing themselves to personal genetic and genomic research. They hope that expanding the pool of DNA samples in their database will lead to future important scientific discoveries.

About Gene By Gene, Ltd. Founded in 2000, Gene By Gene, Ltd. provides reliable DNA testing to a wide range of consumer and institutional customers through its four divisions focusing on ancestry, health, research and paternity. Gene By Gene provides DNA tests through its Family Tree DNA division, which pioneered the concept of direct-to-consumer testing in the field of genetic genealogy more than a decade ago. Gene by Gene is CLIA registered and through its clinical-health division DNA Traits offers regulated diagnostic tests. DNA DTC is the Research Use Only (RUO) division serving both direct-to-consumer and institutional clients worldwide. Gene By Gene offers AABB certified relationship tests through its paternity testing division, DNA Findings. The privately held company is headquartered in Houston, which is also home to its state-of-the-art Genomics Research Center.

Media Contacts:Kate Croft for Family Tree DNA and Gene By Gene, Ltd. Casteel Schoenborn 888-609-8351 croft@csirfirm.com

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Family Tree DNA 's Genomics Research Center Facilitates Discovery of Extremely Ancient Root to the Human Y Chromosome ...

Device Review: Droid DNA from a Consumer #39;s Perspective
To watch the other part of this video, the developer-oriented material, make sure to head over to http://www.youtube.com/watch?v=Kq43Xk5iyN8. If you liked th...

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Device Review: Droid DNA from a Consumer's Perspective - Video