Category Archives: DNA

Mar. 29, 2013 A chromosome is rarely found in the shape we are used to seeing in biology books, that is to say the typical double rod shape (the X pattern, to put it simply). It is usually "diluted" in the nucleus and creates a bundle that under the microscope appears as a messy tangle. In the last few years such chaos, however, has been "measured" and scientists have unveiled their secret: the genes in the tangle are actually arranged in regions that may perform a functional role.

A research coordinated by the scientists at SISSA of Trieste has now developed and studied a numeric model of the chromosome that supports the experimental data and provides a hypothesis on the bundle's function.

A chromosome spends most of its life "diluted" in the nuclear cytoplasm. To the untrained eye it may look like a randomly entangled thread, yet biologists claim the opposite: although a chaotic component does exist in the bundle, experimental measurements have identified regions that tend to contain specific genes. Thanks to such measurements, researchers have obtained maps of the chromosome in its diluted form, the one in which the DNA transcription processes occur.

Cristian Micheletti, a physicist of SISSA, the International School for Advanced Studies of Trieste, has coordinated an international research team -- in which Marco Di Stefano and Angelo Rosa stand out -- that has devised an ingenious method which, on one hand, has allowed to verify the already known experimental measures and, on the other, to find data in support of a theory which explains why the DNA bundle is arranged in regions. "Employing the vast amount of publicly available data on gene expression, we have identified families of genes co-regulated within a chromosome" explains Micheletti. The co-regulated genes codify "in accord," but how such synchronization occurs is a mystery, since often the genes are located very far from one another on the DNA filament. "Two main hypotheses may be considered: either 'messengers' exist that travel back and forth from one gene to the other and coordinate the activity, or the DNA filament folding up inside the tangle brings the genes belonging to the same family physically close."

On the basis of the second assumption Micheletti and his colleagues have used the computer to induce the DNA numeric model to bring the co-regulated genes closer. "The outcome of the simulation has provided a map of chromosome arrangement that is very close to the one obtained through experimentation," explains Micheletti. "Besides, the model has successfully brought closer the genes belonging to the same family, as we had asked for, in 80% of cases, that is without too much effort, which corroborates the validity of the hypothesis and the effectiveness of the simulation."

The article was chosen by PLoS Computational Biology journal as the cover story for the March issue.

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The above story is reprinted from materials provided by Sissa Medialab, via AlphaGalileo.

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DNA : How to unravel the tangle

AUSTIN (KXAN) - A DNA match leads Austin police to arrest the man they believe sexually assaulted a woman near the Huston-Tillotson University campus two weeks ago.

According to police, Michael Broughton, 28, sexually assaulted the victim, who was riding her bicycle in the 1900 block of College Row around 1 a.m. on March 16 .

According to an affidavit, the victim was on College Row when four-door white truck drove past her and parked. She said she turned her bike around and started peddling away but a man from the truck jumped out and grabbed her and pushed her into the truck. While grabbing her, the victim said she heard Broughton say to his friend, "Should we get the gun?"

The victim said the suspect told her that he would not hurt her if she did what he demanded. When the suspect finished with the assault, the victim was allowed to sit up in the vehicle. At that time, she noticed there were emergency lights in the distance -- she was able to open the door and get out of the vehicle.

Victim said she ran away as fast as possible as the truck fled the scene. Victim was able to flag down an officer at 12th Street and IH-35.

On March 27, the Austin Police Department was notified of a DNA match in the Combined DNA Identification System (CODIS). The DNA was linked to Broughton, who is currently living in Killeen.

Police said when they interviewed Broughton, he admitted to kidnapping and sexually assaulting the victim.

Another person was identified and interviewed as a person of interest, detectives believe he is the second suspect in the truck. His involvement is still being investigated and he has not been charged.

Broughton is currently in the Bell County jail and has been charged with aggravated kidnapping and sexual assault.

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DNA match leads to sex assault suspect

A new study finds that coffees, teas and "liquid smoke" flavoring could be activating a repair gene in our bodies.

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(TIME.com) -- Plants are all-natural sources of all things good for us, right? It turns out some of our favorite plant-based flavorings may do more harm than good.

Scientists from Johns Hopkins Kimmel Cancer Center report in the journal Food and Chemical Toxicology that teas, coffees and "smoky flavoring" could be damaging our DNA at levels comparable to that caused by chemotherapy drugs.

The food chemistry and biology researchers tested the effects of some popular foods and food flavorings on cell cultures in the lab and discovered that a well-known repair gene called p53 that protects cells from becoming cancerous, was highly activated by compounds in black and green teas, coffee and liquid smoke flavoring, which is used to add smokey flavor to sausages and meat substitutes.

The foods caused a 30-fold increase in p53 activity when they were added to the cells, which is comparable to the effect that the chemotherapy drug etoposide can have on the cancer-suppressing gene.

p53 is stimulated when DNA is damaged, and the gene triggers a series of responses that attempt to repair the affected DNA. The greater the damage to the DNA, the more p53 becomes activated, and researchers have come to view p53 levels as a marker for DNA in distress.

To measure the p53 activity, the researchers tagged the gene in a bunch of human cells to a fluorescent marker that would glow when the gene was activated, and then added diluted amounts of the foods and flavorings.

They let the cultures sit for 18 hours. Cultures with the black and green teas, coffee and liquid smoke all began to glow, indicating that p53 was hard at work doing damage control. Tests with other flavorings, including fish and oyster sauces, smoked paprika, wasabi powder and kim chee, didn't activate p53 to the same levels.

TIME.com: How exercise can change your DNA

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Could our favorite flavorings be damaging our DNA ?

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Espresso Coffee Short Black

Plants are all-natural sources of all things good for us, right? It turns out some of our favorite plant-based flavorings may do more harm than good.

Scientists from Johns Hopkins Kimmel Cancer Center report in the journalFood and Chemical Toxicology that teas, coffees and smoky flavoring could be damaging our DNA at levels comparable to that caused by chemotherapy drugs.

The food chemistry and biology researchers tested the effects of some popular foods and food flavorings on cell cultures in the lab and discovered that a well-known repair gene called p53 that protects cells from becoming cancerous, was highly activated by compounds in black and green teas, coffee and liquid smoke flavoring, which is used to add smokey flavor to sausages and meat substitutes. The foods caused a 30 fold increase in p53 activity when they were added to the cells, which is comparable to the effect that the chemotherapy drug etoposide can have on the cancer-suppressing gene.

p53 is stimulated when DNA is damaged, and the gene triggers a series of responses that attempt to repairthe affected DNA. The greater the damage to the DNA, the more p53 becomes activated, and researchers have come to view p53 levels as a marker for DNA in distress. To measure the p53 activity, the researchers tagged the gene in a bunch of human cells to a fluorescent marker that would glow when the gene was activated, and then added diluted amounts of the foods and flavorings. They let the cultures sit for 18 hours. Cultures with the black and green teas, coffee and liquid smoke all began to glow, indicating that p53 was hard at work doing damage control. Tests with other flavorings, including fish and oyster sauces, smoked paprika, wasabi powder and kim chee, didnt activate p53 to the same levels.

(MORE: How Exercise Can Change Your DNA)

It turns out that these foods and flavorings share in common some chemicals pyrogallol and gallic acid that the researchers believe are responsible for damaging the DNA and setting off p53. Pyrogallol is found in smoked foods as well as hair dye, tea, cigarette smoke, and coffee. Gallic acid is a type of pyrogallol and is primarily found in coffees and teas. Its not clear how these agents act on DNA, but the harm is concerning enough to raise the alarm for p53 to swoop in and attempt to right the genetic wrongs.

Previous studies have documented similar DNA damage from liquid smoke on the stomach lining in rats, but whether it has the same effect on humans isnt known. On human cells, at least, the effect was striking. We found that liquid smoke, when diluted a thousand fold, was still as strong as the concentration of etoposide in a cancer patient being treated with etoposide. In fact, it works much the same way. Etoposide in cancer patients damages DNA, thats how you get rid of the cancers, but it also has side effects, says study author Dr. Scott Kern, the Kovler Professor of Oncology and Pathology at the Johns Hopkins University School of Medicine.

Why would plants harbor such potentially damaging agents? Its possible they help to protect them, primarily from herbivores looking for their next meal. Plants have been trying to keep animals from eating them for a long time. The plants make poisons, and animals develop defense mechanisms to take on the poisons. They have done this to such a great extent that some of these initial poisons can be considered nutrients and just food, says Kern.

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From Green Tea to Liquid Smoke, Food Flavoring Could Be Damaging Our DNA

The transistor revolutionized electronics and computing. Now, researchers have made a biological transistor from DNA that could be used to create living computers.

A transistor is a device that controls the flow of electrons in an electrical circuit, which acts as an on-off switch. Similarly, the biological transistor termed a transcriptor controls the flow of an enzyme as it moves along a strand of DNA (deoxyribonucleic acid). These cellular building blocks could be used to do anything from monitoring their environment to turning processes on and off in the cells. The findings were reported today (March 28) in the journal Science.

"Transcriptors are the key component behind amplifying genetic logic," lead author Jerome Bonnet, a bioengineer at Stanford University, said in a statement. On their own, these devices do not represent a computer, but they allow for logical operations, such as "if this-then that" commands, one of three basic functions of computers (the other two being storing and transmitting information).

To make the transcriptors, the researchers took a group of natural proteins, the workhorses of cells, and used them to control how the enzyme known as RNA polymerase zipped along a DNA molecule. The team used these transcriptors to create the mathematical operators that perform computations using Boolean logic.

1s and 0s

Boolean logic, named for the 19th-century mathematician George Boole, refers to a branch of math in which variables can have a true or false value (a 1 or a 0). In a Boolean circuit, the logic gates are like traffic conductors, deciding which of these values gets transmitted. [Album: The World's Most Beautiful Equations]

For example, the "AND" gate takes in two values as input, and only outputs 1 (a true value) if both inputs are 1. An "OR" gate, by contrast, outputs a 1 if either of its inputs is 1. Combining these simple gates in different ways gives rise to even the most complex forms of computing.

The scientists created biological versions of these logic gates, by carefully calibrating the flow of enzymes along the DNA (just like electrons inside a wire). They chose enzymes that would be able to function in bacteria, fungi, plants and animals, so that biological computers might be made with a wide variety of organisms, Bonnet said.

Living Computers

Like the transistor, one main function of the transcriptor is to amplify signals. Just as transistor radios amplify weak radio waves into audible sound, transcriptors can amplify a very small change in the production of an enzyme to produce large changes in the production of other proteins. Amplification allows signals to be carried over large distances, such as between a group of cells.

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Digital Evolution: DNA May Bring Computers to Life

The transistor revolutionized electronics and computing. Now, researchers have made a biological transistor from DNA that could be used to create living computers.

A transistor is a device that controls the flow of electrons in an electrical circuit, which acts as an on-off switch. Similarly, the biological transistor termed a transcriptor controls the flow of an enzyme as it moves along a strand of DNA (deoxyribonucleic acid). These cellular building blocks could be used to do anything from monitoring their environment to turning processes on and off in the cells. The findings were reported Thursday, March 28, in the journal Science.

"Transcriptors are the key component behind amplifying genetic logic," lead author Jerome Bonnet, a bioengineer at Stanford University, said in a statement. On their own, these devices do not represent a computer, but they allow for logical operations, such as "if this-then that" commands, one of three basic functions of computers (the other two being storing and transmitting information).

To make the transcriptors, the researchers took a group of natural proteins, the workhorses of cells, and used them to control how the enzyme known as RNA polymerase zipped along a DNA molecule. The team used these transcriptors to create the mathematical operators that perform computations using Boolean logic.

1s and 0sBoolean logic, named for the 19th-century mathematician George Boole, refers to a branch of math in which variables can have a true or false value (a 1 or a 0). In a Boolean circuit, the logic gates are like traffic conductors, deciding which of these values gets transmitted. [Album: The World's Most Beautiful Equations]

For example, the "AND" gate takes in two values as input, and only outputs 1 (a true value) if both inputs are 1. An "OR" gate, by contrast, outputs a 1 if either of its inputs is 1. Combining these simple gates in different ways gives rise to even the most complex forms of computing.

The scientists created biological versions of these logic gates, by carefully calibrating the flow of enzymes along the DNA (just like electrons inside a wire). They chose enzymes that would be able to function in bacteria, fungi, plants and animals, so that biological computers might be made with a wide variety of organisms, Bonnet said.

Living ComputersLike the transistor, one main function of the transcriptor is to amplify signals. Just as transistor radios amplify weak radio waves into audible sound, transcriptors can amplify a very small change in the production of an enzyme to produce large changes in the production of other proteins. Amplification allows signals to be carried over large distances, such as between a group of cells.

The new technology offers some electric possibilities: sensing when a cell has been exposed to sugar or caffeine, for example, and storing that information like a value in computer memory. Or telling cells to start or stop dividing depending on stimuli in their environment.

The researchers have made their biological logic gates available to the public to encourage people to use and improve them.

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Biological computer created with human DNA

The biggest-ever trawl of the human genome for cancer-causing DNA errors has netted more than 80 tiny mutations, a finding that could help people at high risk, researchers say.

The results, which double the number of known genetic alterations linked to breast, ovarian and prostate cancer, were unveiled in a dozen scientific papers published in journals in Europe and the United States.

The three hormone-related cancers are diagnosed in over 2.5 million people every year and kill one in three patients, said a Nature press statement.

Teams from more than 100 research institutes in Europe, Asia, Australia and the United States said the work should in the future help doctors to calculate an individual's cancer risk long before any symptoms emerge.

People with high-susceptibility mutations could be counselled against lifestyle choices that further increase their risk, given regular screening and drug treatment, or even preventative surgery.

"We have examined 200,000 areas of the genome in 250,000 individuals. There is no (other) study of cancer of this size," Per Hall, coordinator of the Collaborative Oncological Gene-environment Study (COGS), told AFP of the research.

The studies compared the DNA of more than 100,000 patients with breast, ovarian and prostate cancer to that of an equal number of healthy individuals. Most were of European ancestry.

Everyone has inherited alterations in their DNA, but whether these mutations are dangerous or not is determined by where on the code they lie.

And carrying a mutation does not necessarily mean a person will develop cancer, a disease that may have multiple causes.

The researchers said further study is needed to allow scientists to translate these DNA telltales into tests for predicting cancer risk. A more distant goal is using the knowledge for better treatments.

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DNA testing to identify cancer risk

DNA vs K-SHINE TRAILER (FULL BATTLE 3-31-13)
SMACK/ URL does it again with another crazy battle between DNA K-Shine. This battle drops March 31st Easter Sunday at 4PM. Log on to http://www.urltv.tv and subsc...

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DNA vs K-SHINE TRAILER (FULL BATTLE 3-31-13) - Video

Brain activity from experiences as common as exploring new locations surprisingly damages the noggin's DNA, hinting that such disruptions may be a key part of thinking, learning and memory, researchers say.

This damage normally heals rapidly, but abnormal proteins seen in Alzheimer's disease can increase this damage further, perhaps overwhelming the ability of brain cells to heal it. Further research into preventing this damage might help treat brain disorders, scientists added.

Explorer mice

Scientists analyzed young adult mice after they were placed into new, larger cages with different toys and odors that they were allowed to explore for two hours. They measured brain levels of a protein known as gamma-H2A.X, which accumulates when breaks occur in double-stranded molecules of DNA.

"DNA comes in double strands, and has the shape of a twisted ladder," said researcher Lennart Mucke, a neurologist and neuroscientist at the Gladstone Institute of Neurological Disease and the University of California at San Francisco. "Breaks in one strand, in one rail of the ladder, occur quite frequently, but breaking both takes quite a bit of damage and, in the brain, was thought to happen mostly in the context of disease." [10 Odd Facts About the Brain]

Unexpectedly, the researchers found such breaks also happened in the neurons of perfectly healthy mice, with up to six times more breaks in the neurons of explorer mice than in mice that remained in their home cages.

"Breaks of double strands of DNA seem to be a part of normal healthy brain activity," Mucke told LiveScience.

These DNA breaks occurred in various brain regions, especially in the dentate gyrus, an area necessary for spatial memory.

"It is both novel and intriguing, [the] team's finding that the accumulation and repair of DSBs [double-strand breaks] may be part of normal learning," said neuroscientist Fred Gage, of the Salk Institute, who did not take part in this study.

Mystery of DNA breaks

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Normal Brain Activity Linked to DNA Damage

A Brooklyn man accused of shooting an Italian tourist has been tied to the crime by DNA found on the gun used in the shooting and a blue Yankee cap he left behind, law-enforcement sources said yesterday.

Career criminal Tyron Lovick, 37, snatched a necklace worn by Eleonora Giuliani, 29, and then blasted Luciano Giuliani, 62, in the stomach after the brave father grabbed him on a Fort Greene Street in May 2012, prosecutors charge.

The gun and the hat definitely match the defendant, said the law-enforcement source. Its a solid case.

Eleonora said she expected the DNA evidence to match up with Lovick.

Im very glad they found the DNA, Eleonora said. I hope hes going to get a bigger sentence.

Lovick, who has been charged with multiple counts of assault and robbery, has 12 prior arrests.

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DNA , Yankee cap link thug to tourist’s shooting