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Posts tagged "dna"

kqedscience:

Testing Complete DNA Sequences Yields Only Partial Info but Could Still Save Your Life

"For a while now, we have been told that soon we will be able to learn a whole lot about our health risks from studying our complete DNA sequence. Our future health will be read by scientists in the tea leaves that are DNA.

new study out of Stanford University in the Journal of the American Medical Association (JAMA) shows just how far we are from that brave new world. For around $15,000 or so per patient, these researchers managed to only get a partial read of key health genes and to only catch around half of a certain class of DNA differences in twelve patients. Not only that, but they also struggled to understand what many parts of these DNA reads meant.  We are not yet at a point where we can cheaply and easily get and interpret the complete set of instructions for a single person.

Still, it isn’t all doom and gloom. You may not be able to learn everything from your DNA but as one patient in the study found, you can still find things that just might save your life.”

Learn more from Dr. Barry Starr of thetechstaff: http://goo.gl/yxrEJE

yaleuniversity:

Yale engineers have developed a method for designing temperature adaptive enzymes, an innovation believed to be the first of its kind. Read on 

(via kenobi-wan-obi)

melodiebenford:

Bacteriophage phi 29 DNA polymerase. The bacteriophage phi 29 DNA polymerase is involved both in the protein-primed initiation and elongation steps of viral DNA replication and displays a very processive 3’,5’-exonuclease activity acting preferentially on single-stranded DNA. 

DNA Polymerase is the essential enzyme used in polymerase chain reaction (PCR). PCR is a revolutionary technique that amplifies DNA sequences, crucial for completion of the Human Genome Project and its creator, Kary B. Mullis, was awarded the Nobel Prize for Chemistry.

Alternatively phi29 DNA Polymerase (pictured above) is the replicative polymerase from the Bacillus subtilis phage phi29 (Φ29). It is being increasingly used for multiple displacement DNA amplification (MDA) procedures, a non-PCR based DNA amplification technique.

MDA can rapidly amplify minute amounts of DNA samples to a reasonable quantity for genomic analysis. Compared to conventional PCR amplification techniques, MDA generates larger sized products with a lower error frequency. This method has been actively used in whole genome amplification (WGA) and is a promising method for application to single cell genome sequencing and sequencing-based genetic studies.

DNA amplification techniques also permit early diagnosis of malignant diseases such as leukemia and lymphomas. It is also valuable in newly emerging laboratory and clinical techniques, including DNA fingerprinting, detection of bacteria or viruses (particularly AIDS), and diagnosis of genetic disorders.

Sources (1, 2, 3, 4, 5)

(via kenobi-wan-obi)

breakingnews:


DNA study suggests dogs originated in Europe
AP: A new DNA study published Thursday indicates dogs originated in Europe some 19,000 to 32,000 years ago.
This large DNA study aligns with the earliest known doglike fossils, which also came from Europe. Other DNA studies have suggested that dogs originated in east Asia and the Middle East. Scientists agree that dogs became the first domesticated animals after emerging from wolves.
Photo: This photo provided by the Center for American Archaeology on Nov. 12, 2013 shows canine bones buried at the Koster site in Greene County, Ill.(AP Photo/Center for American Archaeology, Del Baston)

breakingnews:

DNA study suggests dogs originated in Europe

AP: A new DNA study published Thursday indicates dogs originated in Europe some 19,000 to 32,000 years ago.

This large DNA study aligns with the earliest known doglike fossils, which also came from Europe. Other DNA studies have suggested that dogs originated in east Asia and the Middle East. 

Scientists agree that dogs became the first domesticated animals after emerging from wolves.

Photo: This photo provided by the Center for American Archaeology on Nov. 12, 2013 shows canine bones buried at the Koster site in Greene County, Ill.(AP Photo/Center for American Archaeology, Del Baston)

(via cindyburkeoriginals)

anthrocentric:

A History of Slavery and Genocide Is Hidden in Modern DNA

There are plenty of ways to study history. You can conduct archaeological digs, examining the artifacts and structures buried under the ground to learn about past lifestyles. You can read historical texts, perusing the written record to better understand events that occurred long ago.

But an international group of medical researchers led by Andrés Moreno-Estrada and Carlos Bustamante of Stanford and Eden Martin of the University of Miami are looking instead at a decidedly unconventional historical record: human DNA.

Hidden in the microscopic genetic material of people from the Caribbean, they’ve found, is an indelible record of human history, stretching back centuries to the arrival of Europeans, the decimation of Native American populations and the trans-Atlantic slave trade. By analyzing these genetic samples and comparing them to the genes of people around the world, they’re able to pinpoint not only the geographic origin of various populations but even the timing of when great migrations occurred.

As part of a new project, documented in a study published yesterday in PLOS Genetics, the researchers sampled and studied the DNA of 251 people living in Florida who had ancestry from one of six countries and islands that border the Caribbean—Cuba, Haiti, Dominican Republic, Puerto Rico, Honduras and Colombia—along with 79 residents of Venezuela who belong to one of three Native American groups (the YukpaWarao and Bari tribes). Each study participant was part of a triad that included two parents and one of their children who were also surveyed, so the researchers could track which particular genetic markers were passed on from which parents.

The researchers sequenced the DNA of these participants, analyzing their entire genomes in search of particular genetic sequences—called single-nucleotide polymorphisms (SNPs)—that often differ between unrelated individuals and are passed down from parent to child. To provide context for the SNPs they found in people from these groups and areas, they compared them to existing databases of sequenced DNA from thousands of people globally, such as data from the HapMap Project.

[read more]

(via kenobi-wan-obi)

danidoroi:

Fast-Mutating DNA Sequences Shape Early Development; Guided Evolution of Uniquely Human Traits

What does it mean to be human? According to scientists the key lies, ultimately, in the billions of lines of genetic code that comprise the human genome. The problem, however, has been deciphering that code. But now, researchers at the Gladstone Institutes have discovered how the activation of specific stretches of DNA control the development of uniquely human characteristics — and tell an intriguing story about the evolution of our species.

In the latest issue of Philosophical Transactions of the Royal Society B, researchers in the laboratory of Gladstone Investigator Katherine Pollard, PhD, use the latest sequencing and bioinformatics tools to find genomic regions that guide the development of human-specific characteristics. These results offer new clues as to how the activation of similar stretches of DNA — shared between two species — can sometimes result in vastly different outcomes.

"Advances in DNA sequencing and supercomputing have given us the power to understand evolution at a level of detail that just a few years ago would have been impossible," said Dr. Pollard, who is also a professor of epidemiology and biostatistics at the University of California, San Francisco’s (UCSF’s) Institute for Human Genetics. "In this study, we found stretches of DNA that evolved much more quickly than others. We believe that these fast-evolving stretches were crucial to our human ancestors becoming distinct from our closest primate relatives."

These stretches are called human accelerated regions, or HARs, so-called because they mutate at a relatively fast rate. In addition, the majority of HARs don’t appear to encode specific genes. The research team hypothesized that HARs instead acted as “enhancers,” controlling when and for how long certain genes were switched on during embryonic development. Through experiments in embryonic animal models, combined with powerful computational genomics analyses, the research team identified more than 2,600 HARs. Then, they created a program called EnhancerFinder to whittle down that list to just the HARs were likely to be enhancers.

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thenewenlightenmentage:

This is the most accurate model yet of what DNA looks like

This is a stunning 3D map that shows how six feet of of DNA can be crammed inside a single chromosome — a space that’s only a hundredth of a millimeter across. Not surprisingly, it looks like something that would go well with meatballs.

Chromosomes, those packages of genetic material found in our cells, were discovered way back in the late 1800s, but scientists have struggled to understand the exact way DNA molecules fold into them across three-dimensions. But a new study conducted by researchers at MIT and the University of Massachusetts Medical school has resulted in the world’s first comprehensive model of the 3D organization of condensed human chromosomes.

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laboratoryequipment:

Scientists See DNA Repair Protein in ActionErrors in the human genetic code that arise from mismatched nucleotide base pairs in the DNA double helix can lead to cancer and other disorders. In microbes, such errors provide the basis for adaption to environmental stress. As one of the first responders to these genetic errors, a small protein called MutS – for “Mutator S” – controls the integrity of genomes across a wide range of organisms, from microbes to humans. Understanding the repair process holds importance for an equally impressive range of applications, including synthetic biology, microbial adaption and pathogenesis.Read more: http://www.laboratoryequipment.com/news/2013/10/scientists-see-dna-repair-protein-action

laboratoryequipment:

Scientists See DNA Repair Protein in Action

Errors in the human genetic code that arise from mismatched nucleotide base pairs in the DNA double helix can lead to cancer and other disorders. In microbes, such errors provide the basis for adaption to environmental stress. As one of the first responders to these genetic errors, a small protein called MutS – for “Mutator S” – controls the integrity of genomes across a wide range of organisms, from microbes to humans. Understanding the repair process holds importance for an equally impressive range of applications, including synthetic biology, microbial adaption and pathogenesis.

Read more: http://www.laboratoryequipment.com/news/2013/10/scientists-see-dna-repair-protein-action

laboratoryequipment:

Drug Attacks HIV Before it Integrates with Human DNA

Thirty-four million people are living with human immunodeficiency virus, or HIV, worldwide and each year some 2.5 million more are infected, according to the World Health Organization.

New medicine developed at the Univ. of Georgia attacks the virus before it integrates with human DNA, understood by researchers as the point of no return.

Read more: http://www.laboratoryequipment.com/news/2013/10/drug-attacks-hiv-it-integrates-human-dna

(via kenobi-wan-obi)

New, Incurable Botulinum Strain Has Top Secret DNA

Image above: 

Botulinum Toxin-Producing Clostridium botulinum and Spores 
CDC

It’s one of the most toxic substances known to science. You would die from inhaling 13/1,000,000,000 of a gram of it. And some folks inject small amounts of it in their faces to get rid of their wrinkles. (Go figure.) Botulinum toxins are fascinating, all-natural chemicals—they’re made by bacteria—and just last week, a team of scientists discovered a new type of the toxin, as well as a new strain of the bacterium that makes it, Clostridium botulinum.

Yet because the toxin type is new, scientists have not yet discovered an antidote to it, so they’ve restricted how much information they’re publishing about it. They’re withholding the DNA sequence that codes for for the toxin, out of fear that terrorists could use that information to make a potent bioweapon. This is the first time biologists have held back a DNA sequence because of security concerns, New Scientist reports

NPR’s Morning Edition covered some of the debate over this withholding of scientific information. Everyone Morning Edition talked with agreed it was a good idea not to publish the DNA sequence of this new type of botulinum toxin. Such cases aren’t always so clear-cut, however. Bird flu research sparked debate last year among scientists and health officials about how much science to publish and how much to keep secret when it comes to dangerous diseases.

Two scientists from the California Department of Public Health discovered the new botulinum toxin and bacterium in fecal samples taken from a baby who had botulism, the disease that results from exposure to the toxin. Babies are more susceptible to botulism, which they can get from eating improperly canned vegetables or honey contaminated with Clostridium botulinum spores. The California pair published their work in two papers in The Journal of Infectious Diseases. 

[NPR Morning Edition]

(via femscinerd)

This is how Francis Crick dealt with unwanted solicitations following the discovery of DNA.

When James Watson and Francis Crick unveiled the double-helical structure of DNA, the pair became international celebrities. But with celebrity, can come a lot of unwanted personal attention.

One of the ways Crick dealt with the barrage of letters, personal requests and solicitations that he received throughout the 1960s was the pre-printed, catch-all reply card featured up top.

According to The Francis Crick Archive at the Wellcome Library, the seventeen reply options you see listed here “are a faithful reflection of the requests [Crick] regularly received,” though there was also space to add more if he felt like it. Apparently, unsolicited solutions to “the coding problem” (the question of how just four nucleotides could code for a polypeptide containing up to twenty different amino acids) were pretty common… just not common enough to earn them a spot on the reply card. [For the Record: The Francis Crick Archive at the Wellcome Library via Futility Closet]

Dino-DNA Art Honors the 20th Anniversary of ‘Jurassic Park’ Today

DINO-DNA: A tribute to Jurassic Park” is an online art tribute to Michael Crichton’s novel and Steven Spielberg’s movie masterpiece, which premiered 20 years ago on this date in 1993. The show is curated & presented by Chogrin (Facebook.com/chogrinart), who’s love for Jurassic Park was born in a movie theater back in 1993.

All of the art above (and on the Dino-DNA blog) can be purchased through the Dino-DNA exhibit site where you’ll find artist information and e-mail addresses to contact them and purchase a print.

(via FirstShowing)

42violethill:

“Molecular structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid” was an article published by James D. Watson and Francis Crick in the scientific journal Nature in its 171st volume on pages 737–738 (dated April 25, 1953). It was the first publication which described Rosalind Franklin’s discovery of the double helix structure of DNA. This discovery had a major impact onbiology, particularly in the field of genetics.

This article is often termed a “pearl” of science because it is brief and contains the answer to a fundamental mystery about living organisms. This mystery was the question of how it was possible thatgenetic instructions were held inside organisms and how they were passed from generation to generation. The article presents a simple and elegant solution, which surprised many biologists at the time who believed that DNA transmission was going to be more difficult to detail and understand.

Image Credit: DNA Replication Animation

Happy Birthday DNA!!!!

Apart from the structure itself the only feature of the [first Nature] paper which has excited comment was the short sentence: ‘It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.’ This has been described as ‘coy,’ a word that few would normally associate with either of the authors …. In fact it was a compromise …. I was keen that the paper should discuss the genetic implications. Watson was against it. He suffered from periodic fears that the structure might be wrong and that he had made an ass of himself. I yielded … but insisted that something be put in … otherwise someone else would certainly write to make the suggestion, assuming we had been too blind to see it….

Francis Crick, writing in Nature (April 26, 1974) on the 21st birthday of the original Nature paper (April 25, 1953) proposing the Watson-Crick structure of DNA

21st Birthday Rites for Double Helix

Chemical & Engineering News, May 27, 1974

(via cenwatchglass)

Electronic zippers control DNA strands

A research team from NPL and the University of Edinburgh have invented a new way to zip and unzip DNA strands using electrochemistry.

The DNA double helix has been one of the most recognisable structures in science ever since it was first described by Watson and Crick almost 60 years ago (paper published in Nature in 25 April 1953). The binding and unbinding mechanism of DNA strands is vital to natural biological processes and to the polymerase chain reactions used in biotechnology to copy DNA for sequencing and cloning.

The improved understanding of this process, and the discovery of new ways to control it, would accelerate the development of new technologies such as biosensors and DNA microarrays that could make medical diagnostics cheaper, faster and simpler to use.

The most common way of controlling the binding of DNA is by raising and lowering temperature in a process known as heat cycling. While this method is effective, it requires bulky equipment, which is often only suitable for use in laboratories. Medicine is moving towards personalised treatment and diagnostics which require portable devices to quickly carry out testing at the point of care, i.e. in hospitals rather than laboratories. The development of alternative methods to control the DNA binding process, for example with changes in acidity or the use of chemical agents, would be a significant step towards lab-on-a-chip devices that can rapidly detect disease.

However, until now, no method has been shown to enable fast, electrochemical control at constant temperatures without the need for dramatic changes in solution conditions or modifying the nucleotides, the building blocks of DNA.

A research team from NPL and the University of Edinburgh have invented a new way of controlling DNA using electrochemistry. The team used a class of molecules called DNA intercalators which bind differently to DNA, depending on whether they are in a reduced or oxidised state, altering its stability. These molecules are also electroactive, meaning that their chemical state can be controlled with an electric current.

A paper published in the Journal of the American Chemical Society explains how the process works. Electrodes apply a voltage across a sample containing double strands of DNA which are bonded to the electroactive chemicals. This reduces the chemicals (they gain electrons), decreasing the stability of the DNA and unzipping the double helix into single strands. Removing the voltage leads to the oxidisation of the chemicals and the DNA strands zip back up to re-form the familiar double helix structure. Put simply, with the flick of a switch, the oxidation state of the molecules can be changed and the DNA strands are zipped together or pulled apart.