Tag Archives: viruses

How Scientists Discovered 85,000 Viral Species in Leftover Data

[Phage viruses attempt to infect a cell. Image via Wikimedia Commons.]

In 2015, the largest database of genetic information in the world– the National Center for Biotechnology Information (NCBI)–had complete genomes for 45,000 species of bacteria–but only 2,200 genomes from viruses.

Viruses outnumber bacteria in every habitat researchers have sampled. In fact, they outnumber stars in the universe and grains of sand on planet Earth.  Scientists tend to zero in on the handful of viruses that threaten human lives, but we know nothing about the vast majority of our invisible, arguably non-living neighbors. 

Last week, a paper in Nature announced that scientists had identified 85,000 previously undiscovered viral species by combing through leftover data from environmental DNA samples. Many of those viruses appear to infect bacteria and microbes that we’ve never seen come down with an infection before.

No spiffy new virus capturing techniques were required; the researchers, led by Nikos Kyrpides and David Paez-Espino, simply used existing data collected by previous scientific projects. Scientists gather environmental samples all the time. When microbiologists want to  see if a bacterial species lives in people’s mouths, they do a cheek swab. When marine biologists track the spread of algae-killing viruses, they scoop up samples of ocean water. But human mouths and open oceans are both home to complex microbial ecosystems. When scientists sequence the DNA from their organism of interest, they often end up sequencing the DNA from many of the other microbes in their sample, too. 

Most of the time that data about off-target species isn’t used in the original study, but sometimes scientists add their raw environmental DNA data–aka “metagenomic data”–to publicly available databases.

Kyrpides and Paez-Espino, who both work at the Department of Energy’s Joint Genome Institute in Walnut Creek, California, had access to a vast database.  “The largest amount of data was in metageonomic sequences,” said Kyrpides. “We were very interested in mining all of this information.”

The range of habitats in the data they used spanned from deep sea hydrothermal vents to human guts, from forest soil to synthetic environments like petri dishes, and everywhere in between. Freshwater lakes, saltwater lakes,  human mouths, open oceans, sewage, swamps, termite guts, and more were all represented in the data they crunched.

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The Case of the Sugars that “Strike Back” Against HIV

[Electromicrograph of an HIV-infected T-cell via NIAID & CC2.0] 

“Pitch Imperfect” is a series of blog posts where I highlight stories that I pitched but didn’t quite sell and discuss why it was tough to sell them. The goal is to share both interesting research stories and some of the obstacles in getting them into the news cycle.

Proposed Headline:

Sugar signals force HIV out of hiding

Proposed Dek:

And the same sugar signalling pathway “poisons the virus on the way out”

The Pitch:

Anti-retroviral therapies can block HIV’s attempts to infect new cells in patients but do nothing to get rid of HIV sleeper cells that are already in the patient’s blood stream. The immune system can’t spot infected cells unless the HIV is actively building viruses.

However, a paper in PLOS Pathogens may have revealed an unexpected ally in the fight against HIV–the sugar coatings on immune cells. Having sugars on the surface of a cell isn’t unusual; surface-sugars serve as ID-badges that allow immune cells to tell self from not-self. But they’re usually thought of as relatively passive in cell-to-cell communications. This study indicates that yanking on a certain class of surface sugar can start a chain reaction that forces HIV into the open.

“Even though it seems kind of counter-intuitive to wake up the HIV, it really boils down to: the infected cells will die if we wake them up,” says the study’s senior co-author Satish Pillai of the Blood Systems Research Institute in San Francisco.

The paper came out on Thursday, but a Google News search turned up zero hits.

Sugars, in general, are relatively underused in next-gen medicine strategies–while genes, proteins, and RNAs hog all the glory–but they may have been potential allies ambushing HIV, hiding in plain sight.

Continue reading “The Case of the Sugars that “Strike Back” Against HIV” »

Viruses can shut down our anti-viral proteins – Recap of talk by Dr. Ileana Cristea

The Talk:

Host Defense and Viral Immune Evasion: A Proteomics Perspective

In Plain English:

Human cells and viruses are locked in a protein-based arms race for global domination: Will the cell’s defensive proteins successfully recognize viral DNA and alert the immune system? Or will the virus counter with proteins that stop the defensive proteins in their tracks? The answer is that both of these processes are happening all the time.

The Speaker:

Ileana Cristea of Princeton University’s Molecular Biology Department

The Location:

Harvard Medical School’s Microbiology & Immunobiology department

What it covered:

Full disclosure: I got to the talk about 10 minutes late after being stopped by a security guard (who wasn’t sure how to react to a 22-year-old with a backpack who could speak proteomics-babble but couldn’t produce a student ID). So I missed the first few slides of the talk, but when I arrived, Dr. Cristea was introducing the HMS research crowd to Gamma-Interferon-Inducible Protein 16 (IFI-16) and its role in the innate immune system. Continue reading “Viruses can shut down our anti-viral proteins – Recap of talk by Dr. Ileana Cristea” »