Category Archives: Science No Chaser

The (Mostly) Untold Story of the Oxygen Revolution

[Cyanobacteria–green, brown, and orange streaks–grow in hot spring at Yellowstone National Park. Photo by Harvey Barrison via Flickr & Creative Commons 2.0] 

The troublemakers were hardly new to the neighborhood. For 300 million years, they had lived in the water column, floating in the sunlight near the surface, sending tiny plumes of toxic gas into the air. That was how they ate: sunlight in, poison out. But it was nothing the ecosystem couldn’t handle. The atmosphere was vast, and the troublemakers were microscopic. The poison diffused. Life went on.  

Until something changed. For some reason, there were more of the green troublemakers. Quadrillions more. So many more that their poison became the air itself. An entire world’s atmosphere transformed. Those that could tolerate the miasma grew and spread. Others survived in pockets of the planet where the new air couldn’t reach them. Uncountable numbers died.

The sunlight-eating oxygen-makers inherited the Earth.

In other words, 2.3 billion years ago, photosynthesis caused a mass extinction.

Continue reading “The (Mostly) Untold Story of the Oxygen Revolution” »

NIH scientists identify a genetic disorder that may affect 1 in 20

[Mast cells from a sinus stained in blue. Image via Wikimedia Commons & CC 2.0] 

On July 10, 2010, a DC restauranteur came down with what seemed to be food poisoning. He had no energy and no appetite. Rashes flared up. He could barely get out of bed. First hours and then days dragged by without any relief from the symptoms.

The restauranteur’s family sought out doctor after doctor, until finally they were referred to a lab at the NIH (National Institutes of Health) that studies how allergies pass down through families. 

His symptoms fit a diagnosis of Mast Cell Activation Syndrome, (MCAS)  a disorder where a type of immune cells called mast cells release chemicals that send other immune cells into a destructive frenzy. Ideally, mast cells detect infection and spur other immune cells into action. However, some people’s mast cells have a hair trigger. When mast cells release their chemical contents too often, immune cells end up attacking healthy tissue, causing allergies, stomach issues, and heart palpitations. 

[Above: An NIH-produced video about MCAS and Milner’s research into mast cell activation genetics.] 

Unfortunately, most treatments for MCAS aim at the symptoms, not the root cause.  But the NIH team delved deeper into the genetics and found a pattern:  many MCAS-related symptoms run in families.

And oddly enough, hyperflexible joints, dysautonomia, and baby teeth that fail to fall out also ran in many of those families.  [Correction 6/15: A commenter has pointed out that “hyperflexible” and “hypermobile” are not interchangeable terms. The term “hypermobile” refers to joints that can move outside the typical range of motion due to laxness in ligaments. “Hypermobility” is also sometimes called “double-jointedness.”]  Many of these symptoms skipped generations, only showing up occasionally in individuals, but genetic sequencing revealed the correlation wasn’t coincidence.

In October, NIH scientist Joshua Milner and his team described the  genetic disorder in a paper in Nature Genetics. According to the team’s paper, 4-6% of the U.S. population has the genes that predispose them to this syndrome–which has been tentatively named alpha-tryptasemia or “alpha-T”.

The symptoms can be cryptic and unrelenting: Dizziness, chronic pain, irritable bowels, and fainting. For many patients with these conditions, there’s no explanation and no treatment. “These [symptoms] are really all triggers to get an eyeroll from a doctor,” said Milner. But for a sizeable portion of population, these seemingly unrelated problems might be part of the previously undiscovered genetic disorder.

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Cachexia: How Cancer Sabotages Patients’ Metabolism

[A cancer patient rests in a hospital bed. Photo by Christine Gleason via Creative Commons 2.0 & Flickr

Tumors are master manipulators. They have to be in order to escape human immune systems. Scientists have found evidence that tumors hide by wearing biochemical disguises and some tumors can even recruit turncoat immune cells to their cause.

And now scientists have found evidence that some tumors alter the whole body’s metabolism by “reprogramming” the liver,  according to a study in the journal Cell Metabolism. [Full disclosure: I have an accepted an internship position at Cell Press’s media relations office, but I don’t start until January. I conducted the interviews this post is based on prior to accepting the internship.] The consequences of that reprogramming are often deadly. 

It’s no secret that many cancer patients waste away. They lose weight, including lean muscle mass.  Many lose their appetites, too. Food doesn’t seem to nourish them anymore. They grow weaker.  Breathing gets harder.  And, too often, they die.

This wasting syndrome is called cachexia.  

“The wasting can get so severe in so many patients that it’s estimated to account for 30% of all deaths due to cancer,” explains study co-author Thomas Flint of University of Cambridge. “Lots of people are saying [the cause of death] is the metastasis; it’s this and that, but about 30% of the deaths don’t seem to be directly explained by the tumor.”  Continue reading “Cachexia: How Cancer Sabotages Patients’ Metabolism” »

7 Things To Know About Mitochondria: 2016 edition

Mitochondria: To most people, they’re little more than a ghostly memory fragment from middle school biology. However, these tiny “powerhouse(s) of the cell” are much more than they seem.

They’re actually the shape-shifting descendants of ancient bacteria that were eaten by a larger archaebacterium billions of years ago. . (If you want to know more about that theory, check out my recent Lateral magazine piece on the scientist who developed that theory.)  Mitochondria have complex relationships with other organelles, swim around in our neurons, and make up 1/3rd of the mass of heart cells.  In the past year, scientists have learned how to add and remove them with cellular surgeries and how to manipulate them directly.

Mitochondria live in every cell in your body and are essential for human life. As University of California post doc Samantha Lewis pointed out to me: “There’s mitochondrial involvement in almost every disease.” 

Yet, we rarely hear of or think about our cells’ powerhouses.

Here are seven facts you probably haven’t heard about mitochondria:

1:  Mitochondria are interconnected shape-shifters.

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[A bone cancer cell with stringy mitochondria highlighted in yellow. Photo by NICHD via Flickr & CC 2.0 License.] 

We say “Mitochondria is the powerhouse of the cell” as if mitochondria is a singular word, but actually it’s plural. (The singular of mitochondria is mitochondrion.)  However, in most cells mitochondria act as a collective, passing electrons and genetic information from mitochondrion to mitochondrion.

“They’re [descended from] bacteria that divide in a binary fashion,” explained UC Davis cell biologist and mitochondria specialist Jodi Nunnari. “During the course of evolution [the mitochondrial] genome has been greatly reduced. As a consequence of that and the fact that they were reproducing in a new environment, a few of those do mitochondrial fusion.” Mitochondria’s habit of merging sets them apart from all known bacteria. “Bacteria divide, but they don’t fuse,” Nunnari added.

In fact, mitochondria are so tightly connected that many scientists think of them as a membrane network rather than a series of jelly-bean shaped organelles.

Continue reading “7 Things To Know About Mitochondria: 2016 edition” »

How 600 Citizens Helped to Document an Underwater Epidemic

[A Sunflower Sea Star with several arms missing. Photo by Jerry Kirkhart via Flickr & CC 2.0 License.] 

In 2013,  something strange started happening to the starfish, or sea stars, that live along North America’s Pacific Coast. Casual observers began reporting starfish that were “dissolving” or “melting”.

What you first see is they start getting spots on them,” explains marine veterinarian Joseph “Joe” Gaydos of University of California Davis. “They [the sea stars]  start shrinking, and then legs start falling off…Legs will fall off and then crawl around, so it really is like something out of a horror show.”

In 2014,  researchers were able to identify a viral culprit as the immediate cause of the disintegrating sea stars, but we still know very little about how it spreads or which starfish species are most affected by it.

The dying sea stars that were easiest to spot were the ones that live close to shore.  But no one knew what the mysterious Sea Star Wasting Disease (SSWD) was doing to the sea stars deep underwater and in the open ocean. 

“When the sea star wasting disease hit in the Salish Sea in 2013, my first thought was, ‘Gosh, we have 29 species of sea stars. Who’s going to get hurt?’”  Gaydos told me over the phone. 

Luckily, the Salish Sea, an area which includes Puget Sound in Washington State and the Gulf Islands in British Columbia, Canada,  is home to an organization called REEF. Since 2006, REEF has been training amateur divers to count the organisms they see, and over 8,000 of those dives have included sea star counts. 

Gaydos and his colleagues, led by Diego Montecino-Latorre, analyzed the data from REEF’s dives. They also supplemented the REEF data by systematically criss-crossing the Salish Sea’s basins, counting the starfish they saw.

And the data tell a story of devastation. At least, for some of the sea stars.  Continue reading “How 600 Citizens Helped to Document an Underwater Epidemic” »

What Lake Beds Know (Interview with Janice Brahney of USU)

[Photo by Jake Eberhardt via Flickr & CC 2.0 License] 

Lakes make excellent witnesses, says Utah State University assistant professor Janice Brahney The sediment at the bottom of lakes can hold clues about life in the lake thousands of years ago, preserving everything from fossils to traces of rainfall.

I wanted to be a detective growing up, solving puzzles and looking at trace evidence to piece together what happened,” she said. “Lakes are just really excellent recorders.”

Brahney focuses on glacial lakes, which form when giant ice sheets melt. Specifically, she’s been studying the glacial lakes high in the mountains of British Columbia.  Her research could help predict how our planet will handle melting glaciers.

Most of the lakes are so remote they don’t even have names.  For example, one basin has  five lakes that are collectively called Coven Lakes, but the individual Coven lakes are anonymous. 

Continue reading “What Lake Beds Know (Interview with Janice Brahney of USU)” »

The Slow Poisoning of the UK’s Bees (and What to Do About It)

[Photo by David Short via Flickr & Creative Commons 2.0]

“By Request” is a series of posts where I track down studies that answer questions asked by you, my blog’s readers. 

High School Friend Elna asked: Impending extinction of bees- what can prevent?”

That’s a tough question to answer, because some bee populations are at much higher risk than others. Domesticated honey bee numbers are actually growing, largely due to the large scale industrialized pollination companies, which  bring giant swarms to farmers whose crops rely on bees.

Bees are an enormously diverse group that includes over 20,000 species, spread over 6 continents. (As far as we know, there are no bees in Antarctica.)  Like other animals, bees can be vulnerable to habitat loss, changing temperatures, and pollution.  However, bees do have one persistent problem that stands out: they keep getting caught in the line of fire when humans spray insecticides.

Well, bees are insects, after all.

However, bees are not equally vulnerable to all pesticides.

For example, when Ben Woodcock and his colleagues at the UK’s Natural Environmental Research Council’s Centre for Ecology and Hydrology published a study which analyzed 18 years’ worth of data on 62 species of British bees, they found that some bee species’ populations are holding steady in the face of insecticides, while others aren’t.

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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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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.

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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” »