Viruses and Bioinformatics from Virology.uvic.ca
92.6K views | +0 today
Follow
Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Rescooped by Kathleen McLeod from Amazing Science
Scoop.it!

Cleaning Up Ancient Human DNA for Next Generation Sequencing

Cleaning Up Ancient Human DNA for Next Generation Sequencing | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

With the genomes of Ötzi, the 5300-year-old iceman, and even Neandertals pouring out of DNA sequencing labs lately, you might think that it’s now a piece of cake to glean the entire genetic code of an ancient human. But it turns out that those studies used exceptionally pure samples of DNA taken from human bone, tooth, hair, or other tissue typically preserved in frozen soil, ice, or a chilly cave. More often, human remains found by scientists have been sitting in soil warm enough to harbor bacteria, which swamp out the human DNA with their genes and make it too costly to analyze. A clever new method for purifying ancient human DNA samples—reported here last week at the annual meeting of the American Society of Human Genetics—could change that, however.

 

The average ancient DNA sample taken from, say, a human tooth or bone is often less than 1% short, degraded pieces of human DNA; the rest is bacterial DNA. Although scientists could sequence this gemisch, they would have to run the samples through their sequencing machines many times to zoom in on the human DNA portion, and it’s not worth the cost. Instead, researchers often prepare stretches of modern human DNA that roughly match the genes or sequences they’re interested in and use these so-called probes to filter the sample. (Modern and ancient human DNA are similar enough that the probes will stick to the ancient DNA.) But this is still expensive, and it reveals the sequence of only a subset of the genome.

A team at Stanford University has now come up with a better idea.

 

Postdoctoral researcher Meredith Carpenter and others in the lab of Carlos Bustamante made their probes from RNA instead of DNA, which is “super cheap,” Bustamante says. They found a way to make enough RNA probes to cover the entire genome of an average modern human. The probe has a chemical group that sticks to special beads, so when the researchers mix the probes with an ancient DNA sample, they can wash away the nonhuman DNA. The final step is to use an RNA-chewing enzyme to get rid of the probes, leaving only pure ancient human DNA that can then be fed into a genome sequencing machine.

 

When the researchers tested this filtering method on a dozen ancient bone, teeth, and hair DNA samples from 500 to 3500 years old, they gleaned twofold to 13-fold more human genetic sequence from the samples than they could have by simply sequencing the mixture the same number of times. This higher resolution yielded new information about the samples. For instance, while previously they could only say that a more than 2500-year-old Bronze Age tooth from Bulgaria was European, they could now narrow its ethnic origin down to central or southern European. The team was also able to determine that a more than 500-year-old Peruvian mummy did not have European ancestry, as Spanish explorers claimed.

 


Via Dr. Stefan Gruenwald
more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

PLOS Pathogens: A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

PLOS Pathogens: A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Plants and pathogens evolve in response to each other. This co-evolutionary arms race is fueled by genetic variation underlying the recognition of pathogen proteins by the host and the defeat of host defenses by the pathogen. Together with new mutations, genetic diversity in populations of both the host and pathogen represent a pool of possible variants to maintain adaptation via natural selection.

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Genomics, Medicine, and Pseudoscience: Whatever happened to swine flu?

Genomics, Medicine, and Pseudoscience: Whatever happened to swine flu? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

From a vial of mom's blood, a fetus's entire genome

NEW YORK (Reuters) - The days of pregnant women having a 3-inch-long (8-centimetre-long) hollow needle jabbed into their abdomens may be numbered.For the second time in a month, scientists have announced...
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Genomics, Evolution, and Pseudoscience: Evolution bugs me

Genomics, Evolution, and Pseudoscience: Evolution bugs me | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

+ Scary stats on who believes in evolution in USA

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

PLoS ONE: Single Virus Genomics: A New Tool for Virus Discovery

PLoS ONE: Single Virus Genomics: A New Tool for Virus Discovery | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
PLoS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
more...
No comment yet.
Rescooped by Bradford Condon from Genomics and metagenomics of microbes
Scoop.it!

Fungal genes in context: genome architecture reflects regulatory complexity and function

Fungal genes in context: genome architecture reflects regulatory complexity and function | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Gene context determines gene expression, with local chromosomal environment most influential. Comparative genomic analysis is often limited in scope to conserved or divergent gene and protein families, and fungi are well suited to this approach with low functional redundancy and relatively streamlined genomes. We show here that one aspect of gene context, the amount of potential upstream regulatory sequence maintained through evolution, is highly predictive of both molecular function and biological process in diverse fungi. Orthologues with large upstream intergenic regions are strongly enriched in information processing functions, such as signal transduction and sequence specific DNA binding, and, in the genus Aspergillus, include the majority of experimentally studied, high-level developmental and metabolic transcriptional regulators. Many uncharacterised genes are also present in this class and, by implication, may be of similar importance

more...
No comment yet.
Scooped by Bradford Condon
Scoop.it!

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi.

more...
Bradford Condon's curator insight, April 11, 2013 11:51 AM

Expansion of transposable elements in pathogenic compared to non-pathogenic isolates of Pyrenophora tritici-repentis.

Scooped by Chris Upton + helpers
Scoop.it!

BMC Genomics | De novo Assembly of highly diverse viral populations

Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data.

more...
No comment yet.
Scooped by Ben Hetman
Scoop.it!

PLoS Pathogens: The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

PLoS Pathogens: The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
From molecules to physiology...
more...
No comment yet.