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A Virus Has Ribosomes?

January 3, 2016


Sorry for the long absence, thanks to writing my NSF grant –the one that keeps my lab in business. (If you drill down you’ll find my current award “Kenyon 1” in Ohio.) I had thought I could put it off for a year–but my group has grown to 20+, with three major projects (E. coli on aspirin,  bacterial neurotransmitters, high pH evolution) plus my Antarctic metagenomes, so besides completing Evolving Science 4E (almost) the grant had to get in. I won’t say what I proposed to NSF, except we already have a clinical lab inquiry for our early data, but that’s a story for another day.

My New Year’s resolution is to complete at least one blog story per week, plus make progress on Blood Star before all the science comes true already (see plant virus gene therapy).
Today’s post is perhaps last year’s biggest story you never heard, the giant Mollivirus recovered from 30,000 years-old tundra in Siberia.

Thirty thousand years, remember? Woolly mammoths, saber-tooth tigers, and three species of humans still roamed the Earth. And amebas full of viruses. Some ameba froze to death, still infected by a giant virus called Mollivirus which remained infective.  French students at the lab of Chantal Abergel and Jean-Michel Claverie incubated the tundra sample with live amebas (and a bunch of antibiotics to get rid of bacteria), then looked for where the amebas died. Previously, similar frozen samples have released Pandoravirus and Pithovirus. Can smallpox and 1918 influenza be far behind?

The new virus shows remarkable complexity in its reproduction cycle. First the ameba has to engulf the virus (by phagocytosis) which is large enough to resemble a tasty bacterium. That’s the selective pressure for ameba-host viruses to be giant: If too small,  the ameba won’t engulf them. Once engulfed, the virus escapes the phagosome and invades the ameba’s nucleus where it sets up a virus factory. The factory starts churning out new virions. But interestingly, each virion packs unidentified fibrous material (see above). Maybe like packing peanuts? To make the whole package bigger and more attractive to the next predatory host?

Beyond that, the most intriguing point: Possibly for the first time, we have a virus that packs ribosomal proteins. Transfer RNA (tRNA to carry amino acids to the ribosome) has been found before, even specified by viral genes–Mollivirus has those genes too. But never the protein components of ribosomes. If a virus actually made working ribosomes, that would pretty much tip the scale to say, This “virus” is an honest-to-goodness cell. So far, we don’t know if (1) the Mollivirus-packed ribosomal proteins form ribosomes (probably not); (2) the ribosomal proteins “moonlight” serving other tasks for the virus, similar to how lysine tRNA serves as a reverse-transcriptase primer for HIV (AIDS virus); or (3) they’re just more packing peanuts to plump the virion.

Stay tuned for the French group’s next ancient virus discovery.

Water Flows on Mars

September 29, 2015

After years of hints, NASA finally calls it: Water flows on Mars. Not anything like Niagra Falls, but enough to see signs of channels forming. In the past, evidence had accumulated for water channels a billion years ago. But now, we see signs of water “days” ago.

The time-lapse animation of Palikir Crater, above, shows streaks that lengthen during the Martian summer. The streaks fade as it gets colder; presumably the water sublimes or freezes.

Where does the water come from? Calculation show that it can’t come from the Martian atmosphere, which is too thin to precipitate more than a few microns deep. Does it come out of the ground?

If water does come up and flow, even brine (salty water), would it contain life?
We already have evidence that life existed on Mars three billion years ago, more or less. The fossil mats that Nora Noffke analyzed look just as convincing as similar fossils on Earth. Unless some catastrophe sterilized the entire planet, one would think living descendants remain today.



Bacterial Sharers

September 20, 2015


The last place we’d expect to find life forms sharing their resources without a clear payoff is the human gut. Of course, there must be a payoff, but the relationships amongst gut bacteria are so complex that we cannot yet see them. What we see is something Tyrrell Conway in Microbe Magazine calls the “restaurant hypothesis.” Certain biofilms of mixed species (such as Bacteroides species) feed off complex sugar chains that others such as E. coli cannot break down. Within the gut lining, different patches of biofilm digest sugar chains into different kinds of sugars–which then E. coli can feed upon. So E. coli bacteria can visit different “restaurants” to consume different meals.

How does Bacteroides get paid for the meal? Hard to say, although I might wildly speculate that because Bacteroides are anaerobes (poisoned by too much oxygen) they benefit from E. coli sucking up the oxygen as it chows down on sweets.

Be that as it may, the Harvard research team of Laurie Comstock  has devoted countless research hours to figuring out the various restaurant management teams. The result (from Current Biology 24:40) is a chart like this:


If I may venture to decipher what’s going on here, based on the paper, this is what I come up with:

Bo = Bacteroides ovatus. A super chef, B. ovatus offers a long menu with all kinds of fresh ingredients: inulin (most plants), pectin (from fruits), levans (from onions), xylan (plants and algae). B. ovatus actually provides the enzymes (called hydrolases) needed to break down these ingredients, to the sous-chefs: Bv (B. vulgatus), Pd (P. distatonis) and sometimes Bc (B. caccae).  These sous-chefs then break the stuff down further to a mix of simple sugars that end up on E. coli‘s plate.

Bt = Bacillus thetaiotaomicron. (Somebody liked Greek letters.) B. thetaiotaomicron doesn’t service xylan, but it provides enzymes to break down levan for lots more kinds of bacteria.  And so forth.

How do the chef bacteria provide the hydrolase enzymes? They wrap them up in packages of outer membrane, called outer membrane vesicles, then share them within the restaurant biofilm.

That’s about as much as my brain can digest for tonight.




Insect Visitor

September 9, 2015


Sorry I’ve been busy starting new students at Bacteria Lab Kenyon.
For the moment: Today my office PC received an unexpected visitor.
No, it’s not a leaf.
How it got here, up on third floor of a building with sealed windows, we have no idea.

Can anyone identify this amazing insect?

Join the Antarctic Fire Dept

August 19, 2015


At a fan’s request, I’m sharing more about my brief stint with the Antarctic Fire Department. Yes, there is a fire department in McMurdo–you can see above, the Antarctic medallion on the truck, and Ob Hill in the background. The Christmas tree ornament on the pole was cute–it was December after all.

Intrigued, I asked the fire fighters to see more of the equipment on the trucks, and how they dig through the snow. Little did I know how I’d end up(!)

The trucks of course carry long spools of hose. Some of the trucks have those triangular tractor wheels to get through any snow or mud. That time of year, mud was what you mainly saw in McMurdo.


And of course they have stretchers, with extra padding for warmth, to rescue people out of the snow.


And worse–out of an icy crevasse!


This triangular stand with pulleys is designed ingeniously to lift a trapped hiker out of a narrow crack in the ice. The pulleys distribute the force so that anyone with minimal muscle strength can pull the victim up. Even me!


That went so well, the next thing I knew–I was drafted into the fire training program! With a room upstairs “burning” and a body to rescue, there was no time to waste.


The suit weighed a ton, especially with that oxygen tank. It made those Antarctic red coats (upper right) feel like nothing. That black thing in back is the motion sensor–you have to “dance the Macarena” the whole time, or an alarm goes off in case you passed out.


There’s my partner. She and I had to climb up the stairs through “smoke” –I was just scared I would fall over, with all the weight. We crawled along the floor, without stopping lest the sensor go off. I found the “body” under a bed (apparently kids do that) and she dragged it out. We did so well, they told us there are always job openings in the department. Who knows where I’d be now, if I didn’t have my seat out on the Herc scheduled the next day.



A Day at London’s Natural History Museum

August 3, 2015

1_NHMThe most amazing experience I had in London was visiting the Natural History Museum. Built in 1881–just a few years after Darwin’s Origin of Species–this extraordinary building (by Alfred Waterhouse) intended to represent a “cathedral of nature.” The columns of this ornate building purposely differ in style, representing the diversity of natural life. Animals of all different species perch upon the windows.


The animals exhibit “natural” behaviors–the lion (above, center) is entwined by a python. Inside the vast edifice (below) amid zig-zagging stairs out of Hogwarts, monkeys climb the arch.


Above all the exhibits and thousands of visitors, the cathedral ceiling represents the most important of life forms: all different kinds of plants.


Darwin gets his statue, which visitors crowd to share his photograph.


Darwin also gives his name to the Darwin Centre, the super modern laboratory (2009) next door. This laboratory actually faces the visitors’ gallery, where the public can watch live action in three floors of labs, like the scene in Jurassic Park.


So what goes on in these labs? Anne Jungblut, Antarctic microbial explorer, gave me a tour. I had met Anne in Antarctica during my adventure there in November. Anne writes a blog about cyanobacteria, on which she is a world-class authority, as well as the school-children’s Microverse project. In Antarctica, we were sampling cold-adapted cyanobacteria. Here, Anne shows some of her samples, which she cultures to study their photosynthesis and phylogeny.


Today, phylogeny means DNA. Below, Anne and her student study DNA of cyanobacteria, which she obtains from all parts of the world, from the Dry Valley Lakes to Lake Biwa, Japan.

But beyond our modern samples–What about the museum’s 80 million samples collected since the mid nineteenth century?


Insects, plants, and animal pelts abound. Some find homes in modern collection boxes; other remain shelved in towering wooden cabinets, even cardboard boxes. Historic expeditions left samples–even William Colbeck’s famous mission to rescue Scott’s ship from Antarctica brought back cyanobacteria, now stored in boxes in the museum.

And all these old dried samples have DNA.


These dried plants, “Flora of the British Isles,” include (middle) Primula veris, the common cowslip, from 1942. How do these cowslips relate to plants of modern Britain? Are they the same species, or different? Can we map how species distributions change over time–and climate change? And what about their microbes? We now know those plants harbor a treasure trove of microbes in their veins, and in the soil trapped in their dried roots.
All we need is hands to explore them. I hope to send a Kenyon student there on an Oden fellowship, next summer, to help unearth this treasure.

Antarctic Crab Farms Hair

July 7, 2015

This Antarctic crab gets my vote for the most bizarre summer lifestyle. The crab grows in hydrothermal vents, part of the ocean floor where volcanic heat drives hydrogen-rich molecules up through a super-heated spring. Hydrogen sulfide, methane etc. Bacteria can oxidize these molecules for food; such bacteria inhabit the guts of tube worms and giant clams that have evolved to support them, and can eat nothing else.

But the crabs have a different twist–they farm the vent bacteria on the hairs of their claws. Their claws look furry from all the bacteria-covered hair; and the crab scarfs off the bacteria.

According to the journal, the bacteria actually fix CO2 like plants do. Instead of photosynthesis, the bacteria oxidize reduce molecules such as methane. There is plenty of oxygen at the ocean floor, from phototrophs at the ocean surface; the water is so productive that excess oxygen reaches the floor. That won’t always be true though, as human-made “dead zones” are expanding throughout the ocean.

In order to survive, the crab needs to stay within a narrow range of habitat between the vent (400 degrees C) and the near-freezing water at the bottom. So the crabs crowd together, jockeying for the best spot. An epic survival story, for sure.


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