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Virus hunting season open

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metagenomics

Virus hunting season open

New viruses have been popping up in industrial water-cooling towers, in Antarctica and salty deserts. Erwin van Meir, from Winship Cancer Institute of Emory University, and his collaborators managed to find two inside someone’s metastatic tumor.

Working with Terry Fei Fan Ng and Eric Delwart from UCSF, Van Meir identified two new species of anellovirus, a family of viruses first discovered in the 1990s. The new viruses come from a patient with a melanoma that had metastasized to the brain and was operated on at Emory University Hospital.

The results were recently published in Oncotarget.

“We have no evidence that these two viruses were involved in the tumor’s formation, but the data are proof of principle that the metagenomics method used can discover more unknown viruses in human brain tumors,” Van Meir says.

Erwin Van Meir, PhD

Metagenomics is the study of genetic material obtained directly from the environment. The approach is often used to study bacteria, but it is equally valid for viruses. In this paper, investigators used enzymes to chew up human and bacterial DNA, enriching for viral DNA protected by the viral capsid.

Estimates from the USAID’s PREDICT program point to thousands or even millions of viruses, present in mammals and birds, which remain unknown to humans. According to Annual Review of Virology from this summer, Viruses with Circular Single-Stranded DNA Genomes are Everywhere! – and that includes Anelloviridae, for which there is “still no convincing direct causal relation to any specific disease.”

Anelloviruses are relatively primitive in that they do not encode a viral polymerase (the enzyme that copies DNA) and thus need to rely upon the host cell and replicate inside the nucleus. The new ones were named Torque teno mini virus Emory1 (TTMV Emory1) and Torque teno mini virus Emory2 (TTMV Emory2). The research team gave a nod to Emory by using its colors in the virus genome cartoons accompanying the publication. Read more

Posted on by Quinn Eastman in Cancer Leave a comment

Metagenomics explainer

A term we heard a bunch at the Emory Microbiome Symposium in November was “metagenomics”. Time for an explainer, with some help from Emory geneticist Tim Read.

Nature Reviews Microbiology defines metagenomics as “genomic analysis of microbial DNA that is extracted directly from communities in environmental samples.”

This technology — genomics on a huge scale — enables a survey of the different microorganisms present in a specific environment, such as water or soil, to be carried out. Metagenomics is also emerging as a tool for clinical diagnosis of infectious diseases.

Read notes that the term specifically refers to “shotgun” sequencing of environmental DNA.

“The shotgun approach is to randomly sample small pieces of the DNA in the tube, no matter which organism they came from,” he says. “The output is a mélange of different genes from bacteria, viruses, fungi, plants and humans.  The data is fascinating but the analysis is daunting.” Read more

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