viruses

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Fragile Viruses

Viruses are scary enough as small micro-organisms that we cannot see with the naked eye, but artist Luke Jerram takes these deadly microscopic agents, and blows them up, literally, as glass sculptures.

Instead of the usual cartoons found in textbooks, these viruses can be examined from various angles, to understand their structures better. Great detail is put into each piece, making the glass sculptures practically exact replicas. Aesthetically, the work is beautiful, and few would even know that what they are admiring are the structures of an HIV virus, E. coli or even Smallpox

The sculptures allow viewers to better understand, or at least to finally see for themselves, what attacks their immune (or other) systems, and especially what causes them to be sick. Of course, this does not mean that it will be easier to fight a virus if you know what it looks like, but for science, the sculptures are a great learning tool to understand the virus’ structures, and possibly even to recognize them better when looking under a microscope.

-Anna Paluch

Viruses can spread through the air in two ways: inside large droplets that fall quickly to the ground (red), or inside tiny droplets that float in the air (gray). In the first route, called droplet transmission, the virus can spread only about 3 to 6 feet from an infected person. In the second route, called airborne transmission, the virus can travel 30 feet or more.

Ebola In The Air: What Science Says About How The Virus Spreads

Illustration credit: Adam Cole/NPR

Huge Viruses Are Shaking Up The Tree of Life

Pandoraviruses are challenging some long-held biological beliefs. These newly-discovered beasts are larger, in size and in genetic complexity, than any other virus that we know of (details on the graphic are below). They are not as doom-worthy as their name implies, but they may have opened a box full of new biological forms that will challenge what we think of when we say “alive” or “virus”. For the scientific low-down on pandoraviruses, check out this great article by Carl Zimmer.

Giant viruses of all kinds seem to be more common than we’ve ever imagined. It makes sense, in a way. Just like there is not a clear transition point between any two species, the complexity of life should also exist on a continuum from the small (bacterial viruses) to the complex (us). So maybe these little guys aren’t so surprising after all?

I drew up a little graphic (above) to show just how large and complex pandoraviruses are compared to other life forms. 

  • Pandoraviruses are huge. A human egg cell is about 100 millionths of a meter across. An E. coli is about 50 times smaller. But pandoraviruses (which dwarf flu viruses) are nearly as big as the bacterium! 
  • The area of the circles show how many genes each type of cell contains. The human genome has about 20,000 genes, while E. coli has about 4,500. Compared to a measly 13 genes in the flu virus, pandoraviruses have about 2,500!, almost none of which seem to be related to known genes.
  • The size of the genome, in bases, is where it gets weird. The human egg’s genome, at 3 billion bases, dwarfs them all. E. coli and pandoraviruses have around 4 and 2 million, respectively. And there’s a tiny little single pixel in there representing the 13,588 letters of the influenza genome.

I can’t wait to see what other kinds of life/not life we find inside this Pandora’s box.

Viruses Reconsidered

"The discovery of more and more viruses of record-breaking size calls for a reclassification of life on Earth."

The theory of evolution was first proposed based on visual observations of animals and plants. Then, in the latter half of the 19th century, the invention of the modern optical microscope helped scientists begin to systematically explore the vast world of previously invisible organisms, dubbed “microbes” by the late, great Louis Pasteur, and led to a rethinking of the classification of living things.

In the mid-1970s, based on the analysis of the ribosomal genes of these organisms, Carl Woese and others proposed a classification that divided living organisms into three domains: eukaryotes, bacteria, and archaea. (See “Discovering Archaea, 1977,” The Scientist, March 2014) Even though viruses were by that time visible using electron microscopes, they were left off the tree of life because they did not possess the ribosomal genes typically used in phylogenetic analyses. And viruses are still largely considered to be nonliving biomolecules—a characterization spurred, in part, by the work of 1946 Nobel laureate Wendell Meredith Stanley, who in 1935 succeeded in crystallizing the tobacco mosaic virus. Even after crystallization, the virus maintained its biological properties, such as its ability to infect cells, suggesting to Stanley that the virus could not be truly alive.

Recently, however, the discovery of numerous giant virus species—with dimensions and genome sizes that rival those of many microbes—has challenged these views. In 2003, my colleagues and I announced the discovery of Mimivirus, a parasite of amoebae that researchers had for years considered a bacterium. With a diameter of 0.4 micrometers (μm) and a 1.2-megabase-pair DNA genome, the virus defied the predominant notion that viruses could never exceed 0.2 μm. Since then, a number of other startlingly large viruses have been discovered, most recently two Pandoraviruses in July 2013, also inside amoebas. Those viruses harbor genomes of 1.9 million and 2.5 million bases, and for more than 15 years had been considered parasitic eukaryotes that infected amoebas.

Now, with the advent of whole-genome sequencing, researchers are beginning to realize that most organisms are in fact chimeras containing genes from many different sources—eukaryotic, prokaryotic, and viral alike—leading us to rethink evolution, especially the extent of gene flow between the visible and microscopic worlds. Genomic analysis has, for example, suggested that eukaryotes are the result of ancient interactions between bacteria and archaea. In this context, viruses are becoming more widely recognized as shuttles of genetic material, with metagenomic studies suggesting that the billions of viruses on Earth harbor more genetic information than the rest of the living world combined. These studies point to viruses being at least as critical in the evolution of life as all the other organisms on Earth.

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Mystery surrounding millions of sea star deaths on B.C. coast solved

Scientists have cracked the mystery of what has killed millions of sea stars in waters off the Pacific coast, from British Columbia to Mexico.

Microbiology Prof. Ian Hewson of Cornell University in Ithaca, N.Y., said the culprit is densovirus, commonly found in invertebrates.

He said the virus literally made what are commonly called star fish dissolve within two to 10 days after infection, leaving them in a pile of goo on the ocean floor.

Hewson is the lead author of a study along with Ben Miner of Western Washington University that was published Monday in the Proceedings of the National Academy of Sciences.

He said the wasting disease hit about 18 months ago, at a time when the number of sea stars inexplicably exploded.

Most viruses in nature are common and help keep dominant species in check, but he said divers reported seeing mountains of sea stars in the ocean around the time mass mortalities started occurring.

"This very high number of sea stars in the Pacific Northwest leading up to this disease epidemic probably is what exacerbated the virus and made the switch between something relatively benign into something that was totally virulent," Hewson said.

Continue Reading.

Is This the Future of Flu Vaccines?

See that picture up above? You’re looking at one of the most advanced weapons (to fight a microscopic enemy) the human race has ever created. It’s a nanoparticle (in gray) coated with synthetically produced coat proteins (HA, to be precise) from the influenza virus. Normally, flu mashes its coat proteins together like so:

The nanoparticles may be a major step toward a universal vaccine, which, of course, would be an awesome thing to have, save millions of lives, help us prevent a mass pandemic, etc.

Because flu viruses mutate, shuffle and swap their genes so frequently, the precise shape of the proteins that make up their spiky suit of armor is constantly being tweaked. It’s like how, from afar, a Sarahan sand dune might appear the same shape and height from day to day, but when you look closely, the precise contours of its windswept dimpled have been changed ever so slightly by erosion. On and on it changes, never the same twice.

Our immune system relies on sentry proteins called antibodies in order to recognize foreign invaders like flu based on their binding to those precise contours and shapes, like tiny chinks in the armor. The exact set of antibodies that killed last year’s flu are stored in your immune system’s memory, ready to keep you safe from that infection in the future. Because the flu virus shuffles and tweaks its shape from  year to year, we are constantly playing catch-up, reacting to new armor every year. It’s like going home to find the lock changed, every day having to cut a new key.

If we could just make antibodies that bind to an unchanging part of the viral protein, like the trunks of those blue protein trees up there, we might be able to defend ourselves from future mutants with a single vaccination. But the virus keeps those parts hidden just enough to keep otherwise universal antibodies from attacking it. 

That’s where this new research from Gary Nabel and his group might come in handy. By attaching the HA coat protein (again, the blue thing) from influenza to nanoparticles, their Achilles Heel is exposed and strong, universal antibodies are amplified and stored in your body’s defense bank. They built this nanoparticle vaccine from a 1999 strain’s HA protein, and it protected animals from a half-century’s worth of H1N1 viruses! It’s as close to universal as I’ve ever heard.

Point: humans. But, these are tricky bugs, and we shouldn’t get cocky, especially without human trials (yet). But we have brains, and they don’t. That’s really our best weapon, no? 

Ed Yong has more at Nature News, and you can check out the original research in Nature.

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This is what happened when I searched “nightmare” on Facebook after an anonymous tip

This is what happened when I searched the word “nightmare” under “places” on Facebook after an anonymous tip. As of now, I’m guessing that this is just a mass emailing virus. Still, it’s pretty creepy. If any of you have had similar emails, or messages, please let me know.

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Your daily dose of Myoviridae TEM images:

Here’s a nice picture of some Myoviridae phage which infect Salmonella. Generally in the phage world, there are three more common families although others have been found:

  • Siphoviridae with long flexible tails. (P2 above)
  • Myoviridae with long contractile tails (T4 above)
  • Podoviridae with short non-contractile tails. (P22 above)

Phage are first classified based on their morphologies, but bioinformatic information shows the relationships between the families. Typically families of phage are grouped on their appearance as a large amount of the phage genome goes into making the structural proteins.

Myoviridae are quite interesting in the sense that when they bind their host, there are large visible structural changes in the tail region. The tail sheath contracts and the DNA is transported from the head into the bacterium. Other less visible mechanisms are present in the other two morphology types too.

Sam