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.

Continue reading “How Scientists Discovered 85,000 Viral Species in Leftover Data” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

Coming to News Stands Near You / Tell Me What You Want, What You Really Really Want

[A statue of Charles Darwin. CGP Grey/Flickr (CC BY 2.0)]

First things first: This August you’ll be able to buy a piece of my writing (on real paper) at a bookstore or newsstand near you! 

I have a front-of-book story about bacterial biofilms and how we can attack them with sugar-cutting enzymes out in the August issue of Scientific American.

You could read it online OR you could do me and all other emerging science writers a solid by buying an actual copy of one of our flagship magazines. 

Or you could do us a digital solid by purchasing a digital subscription to an outlet that pays us. (If you’re curious about why I’m so adamant about outlets that pay me making bank, read Bethany Brookshire’s excellent spiel on the subject.)

Also, over at Lateral, we have a new history & philosophy article out about why “Darwin Didn’t Delay” by the awesome Andrew Katsis. It’s part of Lateral’s SLOW issue and the first history & philosophy piece to debut with me as editor, so I hope you check it out!

But onward into the future! A few days ago, I internet-stumbled across a post by journalist Jennifer Brandel. Her company, Hearken, helps news outlets reach out to audience members and ask for story ideas! And not in a “Please-take-this-five-minute-survey way. As in, audience members can submit questions, participate in reporting, and give feedback to the journalists who are writing the story. 

Immediately, I realized that’s the sort of process I want to incorporate on this blog. 

Continue reading “Coming to News Stands Near You / Tell Me What You Want, What You Really Really Want” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

Vetting the Spleen: Is it a blood filter or something more?

[Ultrasound of a spleen by Nevit Dilmen via Wikimedia Commons & CC 2.0] 

Blood moves fast.  It only takes about 20 seconds for a red blood cell  to make a full circuit through your entire body, and your blood makes that journey thousands of times each day.

The speed of the blood stream is a challenge for scientists who study how the body copes with invading bacteria. Normally, the bloodstream is devoid of microbial interlopers, but when bacteria do break into the blood stream, they can be extremely dangerous. Sepsis, for example, occurs when the immune system tries to fight off a large number of blood-invading bacteria. And sepsis kills up to half of the people who develop it, according to the NIH

So when bacteria find their way into blood, your body wants to take them out ASAP.  Blood-filtering organs like the liver, the kidneys, and the spleen have dedicated local immune cell task forces that help kill microbes, and of course, blood itself has loads of white blood cells on patrol.

But platelets–the globs of gunk that form scabs on wounds–also trap bacteria. When the bacteria are whizzing through the bloodstream, sometimes they collide with a platelet and get stuck to it. But according to a recent study in Cell Host and Microbe,  getting stuck to a platelet doesn’t kill the bacteria. 

Instead, the platelets carry their trapped bacteria through the bloodstream until they wash up at the spleen, says the study’s senior co-author Admar Verschoor from University of Lubeck in Germany.

Continue reading “Vetting the Spleen: Is it a blood filter or something more?” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

Best Shortform Science Writing April-June 2016

(A Highly Subjective Round-up of Standout Science News)

The online science news ecosystem teems with blog posts and videos about animals doing interesting things. And why not? Animals are fascinating, adorable, and beloved by the science nerds who frequent science news websites. Many of those stories are well-written. So when you’re sitting down to choose “standout” shortform science writing, how do you choose between them?

News judgement”–the journalese terms for “ability to spot impactful stories”– was the subject of a lively Google Hangout debate amongst the Best Shortform Science Writing editors: Did we want to highlight the articles with the cutest and cleverest turns of phrase? Did we want to focus on the stories with the most potential to change readers’ minds? Or feature the ones that explain new developments with the most accuracy and nuance?

The hangout included returning editors Sarah Lewin (staff writer at Space.com) and Jennifer Caitlin Welsh (editor-in-chief of Wonderhowto.com), new recruit Amanda Alvarez (writer at RIKEN Brain Science Institute in Japan), and me (freelancer for hire). Collectively–along with fellow editors Shahla Farzan (UC Davis PhD student and reporter at KBBI Public Radio in Alaska) and Christine Scaduto (PhD student at Brown)–we’d gone over almost 200 short science stories from around the internet and were trying to narrow down a dense pack of “news-length” honorable mentions down to a select few.

“So this CRISPR mushroom story,” Jen began. “Does it really make you feel that the story’s important?”

“Hmm…Well, I’ve got a soft spot for fungi,” I said. And besides, gene editing policy is important.

However, covering an interesting topic isn’t the same as showing–rather than telling, or worse, assuming–the story’s impact, Jen countered. At the same time, judging based on practical impact crowds out a lot of well-written stories about studies that are just, y’know, interesting.

In the end, we decided to prioritize impactful stories–especially for the News, Investigations, and Opinion sections. But since Best Shortform Science Writing is a crowd-sourced project, our audience will ultimately drive the evolution of these round-ups. Send us the sorts of stories you want to see recognized via this submission form!  

Also, if you’re interested in joining the project as an editor, email me at diana@dianacrowscience.com.

Enjoy our picks from April, May, and June:

Continue reading “Best Shortform Science Writing April-June 2016” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

Why You Can Blame Your Metabolism on Liver Proteomics Instead of Your Genes

Blaming things on genetics–everything from lateness to diet quirks–is wildly popular these days. However, DNA’s role in your body’s overall destiny has been greatly exaggerated. Sure, DNA is the “master blueprint”, but any one gene from that blueprint can contain instructions for making hundreds or thousands of tiny cell parts. And even so, there are plenty of cell parts that defy the master template.

Proteins–tiny biological machines made from proteins that you eat– are key players in pretty much every biological process that happens. Yet, their behavior remains almost impossible to decipher. Scientists have gotten pretty good at decoding genes and RNA snippets, and tracking a single type of protein is pretty doable. Also, since RNA snippets are templates for building proteins, scientists often use RNA diet to estimate the total number of proteins. But there are thousands of different protein forms in every cell; tracking all of them at once remains basically impossible.

However, variations in those proteins can make an enormous difference in processes like weight gain. And according to a new study, our most-used method for estimating protein numbers–counting the RNAs–only works about 30% of the time. 

As in, according to science’s latest numbers, at least 2/3rds of all “genetic bad luck” happens outside of genes. 

Continue reading “Why You Can Blame Your Metabolism on Liver Proteomics Instead of Your Genes” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

How to Ace an Interview with a Science Journalist [Part 2]

[Illustration by Fredik Walloe via Flickr & CC 2.0] 

A few days ago, I posted Part 1 of an informal guide to rocking interviews with journalists about your science. That post covers what to do before an interview; this post focuses on the During and the After.

Step 5: Invite Co-Authors Along.

8725703891_d0216cd42a_o

[Photo via UBC Learning Commons on Flickr & CC 2.0] 

Science writers know that grad students and post-docs carry out most of the experiments, not lab leaders–aka “Primary Investigators” aka “The Profs Who Do the Paperwork, Presenting, and Mentoring” aka “Boss Scientists”.

If you are a lab leader, looping in key co-authors is not just good manners; it shows that you’re giving credit where credit is due.

Not to mention that the post-docs and grad students who carry out the bulk of the experiments may have some cool stories of their own to share.

Step 6: Be a Good Listener.

8672736002_42eff5ece0_o

[Photo by Britt Reints via Flickr & CC 2.0] 

Scientist-journalist interviews start off like any other conversation, with a quick “Hi! How are you?” and confirmation that you’ve got the right person on the phone.  A journalistic interview is just a conversation, except for the fact that both parties have very specific goals.

Continue reading “How to Ace an Interview with a Science Journalist [Part 2]” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

How to Ace an Interview with a Science Journalist [Part 1]

[A woman interviewing a Lego Sculpture. Photo by Matt Brown via Flickr & Creative Commons 2.0] 

Let’s say you’re a young lab leader or grad student and you’ve just gotten an email from a journalist asking if you can speak to them about your upcoming paper.  You haven’t heard of this reporter before. You ‘re not sure which outlet they’re writing for, and you’re concerned that a badly botched piece about your research might harm your standing in your field.

At the same time, a well-researched and well-written piece can actually help your research become more visible.  A piece that highlights your research in Nature News & Comment might actually be something you want to (humbly) mention when up for faculty gigs. Plus, links to news articles for general audiences liven up your lab’s home page.

You may ask yourself, “How do I work this?How do I make sure this interview goes as well as possible? How do I make sure that the reporters don’t take my comments out of context?  Which reporters are worth talking to in the first place?!

As a young journalist, I can’t pretend not to have a horse in the race: I’m in favor of scientists taking time to talk to journalists, even (and maybe especially) those of us who are just starting out. There are a lot of resources out there on “media training” for scientists, which focus on telling scientists how to best “sell” yourself and your research, and I’ll link to several resources at the end of the article.

My perspective is that of a young journalist, not a seasoned media training expert. But I have interviewed enough scientists to recognize some behavior patterns. Here are some of the habits that good scientist sources* share and etiquette tips for responding to journalist behavior. 

*[“source” = journalese for person or entity giving a journalist information]

Before the Interview

Step 0: Don’t Panic.

8300870890_534ed795ca_o

[Photo by Ruth Hartnup via Flickr & Creative Commons 2.0]

Continue reading “How to Ace an Interview with a Science Journalist [Part 1]” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

Why DNA is like a phone cable (Recap of a Talk by Prof. Jacqueline Barton)

[Computer rendering of DNA. Via Caroline Davis2010 on Flickr & CC 2.0] 

The Talk:

“DNA-mediated Signaling with Metalloproteins”

In Plain English:

DNA can conduct electricity–like metal wire–and that helps the cell life

The Speaker:

Jacqueline Barton of Caltech

The Sponsor:

MIT Inorganic Chemistry (invited by the grad students)

What It Covered:

When Jacqueline Barton’s lab began publishing papers claiming that DNA can conduct electricity, many of her colleagues didn’t believe them. But in experiment after experiment, they kept finding that they could send small amounts of electricity–much lower than the amount that flows through your charger cord–from an electrode on one end of a DNA strand through to the other.

The exceptions were stretches of DNA with “missense mutations“, hiccups in the genetic code that violated the rule of “G” aligns with “C” and “A” aligns with “T”.

A,T, G, and C are biologists’ shorthand for four small molecular structures– adenine, thymine, guanine, and cytosine– that repeat over and over again along DNA’s backbone. It just so happens that a G-C pair takes up exactly the same amount of space and adds exactly the same amount of twist as an A-T pair.  Anything else–a misplaced guanine, a broken cytosine, or a chemical tag on thymine– throws the DNA’s twist out of whack. And apparently,  the missense mutations also blocked electrical currents’ flow through a tiny gap in the center of the DNA.  Mismatched base pairs or base pairs that were even slightly damaged blocked the electrons’ path. Continue reading “Why DNA is like a phone cable (Recap of a Talk by Prof. Jacqueline Barton)” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

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” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone

New Gig: Acting Editor of Science Philosophy & History at Lateral Mag!

[A screenshot of the webzine Lateral’s home page. The theme of June is Sport.]

I am super-psyched to announce that I’m taking on a new part-time gig as editing stories on the history & philosophy of science at an up-and-coming webzine called Lateral.

It’s based out of Australia, has monthly themes like Nautilus, and is largely written and edited by grad students who are considering or transitioning into science writing careers. (And if, I’m not mistaken, that’s a large chunk of the audience here on this blog.)

I’ll still be posting original blog posts on this site every Thursday(ish)*and pitching stories as a freelancer. The good news is that if you’ve ever thought, “Hmm…I wish I could get Diana to edit some of my science writing,”  now you can, by pitching me stories and essay ideas for Lateral. 

Continue reading “New Gig: Acting Editor of Science Philosophy & History at Lateral Mag!” »

Share on FacebookTweet about this on TwitterShare on Google+Share on LinkedInShare on TumblrShare on StumbleUponDigg thisEmail this to someone