Category Archives: Transhuman News

Mouse Genome Informatics (MGI)
Presented by Janan Eppig.

By: USC ISI

Read the original here:
Mouse Genome Informatics (MGI) - Video

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...

By: KveldulvCL

Continue reading here:
Forester XT EJ255 + TurboXS 3" StealthBack Catted + STI Genome Axelback - Video

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...

By: TheWSGSC

See the rest here:
Introduction to Whole Exome and Whole Genome Sequencing - Video

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...

By: TheWSGSC

Follow this link:
Clinical Applications of Whole Exome and Whole Genome Sequencing - Video

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...

By: LabRoots

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

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.

See the article here:
Researchers reconstruct mitochondrial genome of Middle Pleistocene cave bear

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

By: English Pronounce

Link:
How to Pronounce Genome Wide Association Study - Video

A fossilized bear bone, from which the genetic material was extracted. / Javier Trueba(MADRID SCIENTIFIC FILMS)

An international team that includes Spanish researchers has sequenced the mitochondrial genome (special DNA passed on exclusively by mothers) of bears who lived about 400,000 years ago in Atapuerca, near Burgos in northern Spain. This brings scientists closer to sequencing the entire genome of pre-Neanderthal humans who lived at the same time, and who hold clues about the evolution of our species.

The small mtDNA fragments were found inside samples of bear bones that were mixed in with hominid fossils at Sima de los Huesos (Pit of the Bones) at the Atapuerca site, which contains the world's largest collection of human remains from the Middle Pleistocene. Until now, the oldest samples of DNA recovered in temperate areas - not frozen at high altitudes - were between 100,000 and 120,000 years old.

The breakthrough could have significant implications for human paleontology.

"Let us hope that the methodology that we are presenting here will help recover ancient DNA sequences from other organisms of the Middle Pleistocene. The fossils of Sima de los Huesos are the target of these efforts," write Jesse Dabney and his colleagues in Proceedings of the National Academy of Sciences (PNAS), which this week publishes the entire mitochondrial genome of those early cave inhabitants.

"Yes, of course I am optimistic about the possibility of obtaining DNA from human fossils at the pit; if it is there in the bear bones, it can be there in the human bones, which are contemporary to the latter," says Juan Luis Arsuaga, co-director of the Atapuerca site and one of the authors of the new study.

The rest is here:
Bear genome at Atapuerca paves way for earliest hominid sequencing at site

Research team will look at medical and social consequences

Computational Biologist Steven Brenner will be part of an ambitious effort toassess whether large-scale gene sequencing aimed at detecting disorders and conditions can and should become a routine part of newborn testing.

Brenner, a professor in the Department of Plant & Microbial Biology at UC Berkeley, is part of a UC San Francisco team granted $6 million by the National Institutes of Health to identify the accuracy and feasibility of providing genetic sequencing as part of, or instead of, the current newborn screening that relies on biochemical changes in the blood. It also will assess what additional information would be useful to have at birth and the ethics and public interest in having such tests performed.

"Genome sequencing has the potential to reduce costs and improve theeffectiveness of newborn screening," Brenner said, allowing early intervention for infants and fundamental changes in the tehcnology for screening newborns.

The project has three broad goals:

The cost of genome sequencing has plummeted but the ethical and moral questions surrounding genetic testing loom large.

The first genome sequenced, about a decade ago, cost nearly $3 billion.Today scientists can sequence all of anindividual's genes for a few hundred dollars. The Brenner Lab, experts at computational biology, are at the forefront of this new area of science.

Visit link:
Should genome sequencing for newborns be routine?

Sep. 9, 2013 A wide range of biologically inspired materials may now be possible by combining protein studies, materials science and RNA sequencing, according to an international team of researchers.

"Biological methods of synthesizing materials are not new," said Melik C. Demirel, professor of engineering science and mechanics, Penn State. "What is new is the application of these principles to produce unique materials."

The researchers looked at proteins because they are the building blocks of biological materials and also often control sequencing, growth and self-assembly. RNA produced from the DNA in the cells is the template for biological proteins. Materials science practices allow researchers to characterize all aspects of how a material functions. Combining these three approaches allows rapid characterization of natural materials and the translation of their molecular designs into useable, unique materials.

"One problem with finding suitable biomimetic materials is that most of the genomes of model organisms have not yet been sequenced," said Demirel who is also a member of the Materials Research Institute and Huck Institutes of Life Sciences, Penn State. "Also, the proteins that characterize these materials are notoriously difficult to solubilize and characterize."

The team, lead by Ali Miserez, assistant professor, School of Materials Science and Engineering, Nanyang Technological University, Singapore, looked at mollusk-derived tissues that had a wide range of high-performance properties including self-healing elastomeric membranes and protein-based polymers. They combined a variety of approaches including protein sequencing, amino acid composition and a complete RNA reference database for mass spectrometry analysis. They present their results in a recent issue of Nature Biotechnology.

The researchers looked at three model systems. The protein containing egg case membranes of a tropical marine snail are intriguing because they have unusual shock-absorbing qualities and elasticity. Investigation using the variety of methods showed this material has a coiled structure with crosslinking that absorbs energy. This information can be applied to biomimetic engineering of robust yet permeable coiled, protein-based membranes with precisely tailored mechanical properties.

The array of techniques applied toanalysis of a mussel foot showed that a species-to-species variation exists in mussel, including unusual variation in the protein. These variations suggest that protein engineering could produce a range of self-healing properties.

The final model used jumbo squid sucker ring teeth (SRT), grappling-hook-like structures used for predatory attacks. Analysis of the squid teeth showed nanotubular structure and strong polymers. While there was some similarity to silk and oyster shell matrix proteins, the protein was novel and the researchers named it Suckerin-39. Further analysis showed that Suckerin-39's structure allowed it to be reprocessed into a variety of shapes.

"While some biological materials have interesting properties, they cannot be reshaped or remolded because they do not soften upon heating," said Demirel. "The SRT is an elastomer, which is moldable, it is a thermoplastic and can be reshaped."

The materials properties of SRT do not change after heating and reshaping.

Go here to see the original:
Genome of elastomeric materials creates novel materials