Monthly Archives: September 2013

Using DNA to assemble a transistor from graphene

Posted: September 10, 2013 at 7:41 pm

DNA is the blueprint for life. Could it also become the template for making a new generation of computer chips based not on silicon, but on an experimental material known as graphene? Thats the theory behind a process that Stanford chemical engineering professor Zhenan Bao reveals in Nature Communications.

Bao and her co-authors, former post-doctoral fellows Anatoliy Sokolov and Fung Ling Yap, hope to solve a problem clouding the future of electronics: consumers expect silicon chips to continue getting smaller, faster and cheaper, but engineers fear that this virtuous cycle could grind to a halt. Why has to do with how silicon chips work.

Everything starts with the notion of the semiconductor, a type of material that can be induced to either conduct or stop the flow of electricity. Silicon has long been the most popular semiconductor material used to make chips.

The basic working unit on a chip is the transistor. Transistors are tiny gates that switch electricity on or off, creating the zeroes and ones that run software.

To build more powerful chips, designers have done two things at the same time: theyve shrunk transistors in size and also swung those gates open and shut faster and faster.

The net result of these actions has been to concentrate more electricity in a diminishing space. So far that has produced small, faster, cheaper chips. But at a certain point, heat and other forms of interference could disrupt the inner workings of silicon chips.

"We need a material that will let us build smaller transistors that operate faster using less power," Bao said.

Graphene has the physical and electrical properties to become a next-generation semiconductor material if researchers can figure out how to mass-produce it.

Graphene is a single layer of carbon atoms arranged in a honeycomb pattern. Visually it resembles chicken wire. Electrically this lattice of carbon atoms is an extremely efficient conductor.

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Using DNA to assemble a transistor from graphene

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Dallas Police Say DNA Links Suspect to Rapes

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Police are searching for a crime watch volunteer who they say has been connected by DNA to at least four sexual assaults in a South Dallas neighborhood in the past two months.

Authorities took Van Dralan Dixson, 38, into custody briefly last week and obtained a DNA sample from him, but lacked evidence to bring charges at the time, police Maj. Jeff Cotner said.

Three arrest warrants issued Monday and another on Saturday charge Dixson with aggravated sexual assault in four attacks in Fair Park, southeast of downtown Dallas. DNA test results from two other attacks were pending, while DNA evidence from two more in the inner-city neighborhood were not available, Cotner said.

Federal agents were assisting city police in the manhunt, and police have interviewed friends, family, and associates for clues to Dixson's whereabouts, Cotner said. Dixson's car was found abandoned in Garland, a northeastern Dallas suburb, and police have sought a warrant to search the vehicle, Cotner said.

As a crime-watch volunteer, Dixson would patrol the streets several times a week, neighbors said.

"He just walks every night, all night," one resident, Billy Washington, told Dallas television station WFAA. "Every time I would look out my window, or out my door, he was walking."

Dixson has been part of the area's neighborhood crime-watch group, the Mill City Community Association, since January. The group's president, Alendra Lyons, didn't return messages Monday from The Associated Press.

The group said Dixson's duties were limited to telling neighbors about the association, not patrolling at night. Neighbors told The Dallas Morning News that he was referred to as "neighborhood watch," and it seemed he was patrolling the area almost every night.

State criminal records show Dixson was arrested and convicted of aggravated robbery in 1993. He was also arrested as recently as last month on a deadly conduct charge, according to Dallas County records.

Authorities say they believe one man is responsible for the nine sexual assaults that have been reported in the Fair Park area since June. In each incident, the attacker approached his victims in the early morning hours, forced them to secluded areas nearby, then robbed and sexually assaulted them.

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Dallas Police Say DNA Links Suspect to Rapes

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Mouse Genome Informatics (MGI) – Video

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Mouse Genome Informatics (MGI)
Presented by Janan Eppig.

By: USC ISI

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Mouse Genome Informatics (MGI) - Video

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Dr. Daoud Meerzaman: Computational Tools for Cancer Genome Analysis – Video

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Dr. Daoud Meerzaman: Computational Tools for Cancer Genome Analysis
On July 24, 2013, NCI #39;s Dr. Daoud Meerzaman, Director of R D/Section Head of Computational Genomics Research (CGR) at the Center for Biomedical Informatics a...

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Dr. Daoud Meerzaman: Computational Tools for Cancer Genome Analysis - Video

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George Church – Keynote: Improving the Accuracy of Genome Sequencing and Interpretation – Video

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George Church - Keynote: Improving the Accuracy of Genome Sequencing and Interpretation
Our ability to view and alter biology is progressing at an exponential pace -- faster even than electronics. Next generation sequencing can be used to assess...

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George Church - Keynote: Improving the Accuracy of Genome Sequencing and Interpretation - Video

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Clinical Applications of Whole Exome and Whole Genome Sequencing – Video

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Clinical Applications of Whole Exome and Whole Genome Sequencing
Whole exome and whole genome sequencing are two very new testing techniques that are poised to change the current paradigm of clinical genetic testing. To ge...

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Clinical Applications of Whole Exome and Whole Genome Sequencing - Video

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Introduction to Whole Exome and Whole Genome Sequencing – Video

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Introduction to Whole Exome and Whole Genome Sequencing
Whole exome and whole genome sequencing are two very new testing techniques that are poised to change the current paradigm of clinical genetic testing. To ge...

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Introduction to Whole Exome and Whole Genome Sequencing - Video

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Forester XT EJ255 + TurboXS 3" StealthBack Catted + STI Genome Axelback – Video

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Forester XT EJ255 + TurboXS 3" StealthBack Catted + STI Genome Axelback
SSR Disculpenme el desenfoque, pero mi mina estaba grabando... Y disculpen lo sucio del escape... Sorry about the bad focus, but my chick was on cam... and s...

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Forester XT EJ255 + TurboXS 3" StealthBack Catted + STI Genome Axelback - Video

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How to Pronounce Genome Wide Association Study – Video

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How to Pronounce Genome Wide Association Study
https://www.youtube.com/EnglishPronounce - Study, English, Pronounce.

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Researchers reconstruct mitochondrial genome of Middle Pleistocene cave bear

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Javascript is currently disabled in your web browser. For full site functionality, it is necessary to enable Javascript. In order to enable it, please see these instructions. 4 hours ago by Marcia Malory Skull of Ursus deningeri. Credit: Wikipedia

(Phys.org) Researchers have reconstructed the mitochondrial genome of a Middle Pleistocene cave bear using a bone sample found in Spain. This is the first time anyone has reconstructed such an old genome from a sample found outside the tundra. To reproduce the genome, Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology in Leipzig and his team devised a new technique for stringing together small DNA strands. In addition to recreating the genome, the team were able to reconstruct the cave bear's phylogeny. The research appears in the Proceedings of the National Academy of Sciences.

DNA fragments over time, largely because of depurination, making it hard to analyze very old samples. The fragmentation rate is temperature-based; DNA from samples recovered from permafrost tends to be less fragmented than DNA from samples found elsewhere. Recently, for example, scientists were able to reconstruct the genome of an approximately 700,000 year old horse from a sample in Canada's Yukon Territory. Until now, however, scientists have only been able to generate sequences from non-permafrost samples about 120,000 years old or younger.

Meyer and his colleagues studied a bone sample from a Middle Pleistocene cave bear (Ursus deningeri). The sample, found at Spain's Sima de los Huesos cave site, was more than 300,000 years old. The researchers believed they could recreate the cave bear's genome by improving the method of DNA extraction.

As DNA samples age, intact sequences become smaller. However, DNA library purification techniques tend to cause the loss of DNA molecules less than 40 bp. To preserve smaller molecules, the team used a single-stranded DNA preparation method used recently in the sequencing of Neanderthal and Denisovan genomes. This method eliminates these purification steps. By combining this single-stranded method with a widely used silica-based DNA extraction technique, the researchers were able to recover and sequence DNA molecules as short as 30 bp.

Meyer's team were able to construct a phylogeny of cave bears, determining that Ursus deningeri diverged from the common ancestor of the Late Pleistocene cave bears Ursus spelaeus and Ursus ingressus at an early stage, to form a sister lineage.

The researchers say it may be possible to sequence DNA molecules even shorter than 30 bp in the future. This will allow geneticists to reconstruct even more Middle Pleistocene genomes, including those from hominin samples at the Sima Los Huesos site, which contains the largest collection of Middle Pleistocene hominin fossils in the world.

Explore further: German researchers publish full Neanderthal genome

More information: Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments, PNAS, Published online before print September 9, 2013, DOI: 10.1073/pnas.1314445110

Abstract Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.

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Researchers reconstruct mitochondrial genome of Middle Pleistocene cave bear

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