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A couple little "Sputnik" viruses seen as green blobs infect part of the bigger mamavirus, which is the big red blob.  (Source: La Scola, B. et al. Nature doi:10.1038/nature07218 (2008)

Big viruses may be an integral, and perhaps living, part of the ocean plankton ecosystem which impacts both the entire ocean and the global climate.   (Source: J. SCHMALTZ/NASA)
Looks like viruses can catch colds just like the rest of us

One of the fundamental questions in science is "what is life?", a question particularly pertinent of late with the search for signs of life on Mars and the advances in developing synthetic life in a lab.  Scientists have devised many complex answers to the question, but basically most scientists would agree that a "living" creature must be able to produce a variety of useful structural units (proteins), carry a genetic code (DNA), and reproduce.

Following this definition of life, viruses typically met the latter two tests, but failed the first as they only produced a few structural or protective proteins to encase themselves.  This was a primary justification in classing them as nonliving.  However, recent discoveries have troubled this comfortable notion of the solid boundary between life and nonlife.  First, a variety of parasitic bacteria have been discovered, many of which lack the key protein enzymes needed to survive outside their host -- another bacteria.

Also, giant viruses have been discovered, which in addition to infection related proteins, make a variety of other proteins which help it carry out other processes.  On a level of complexity they can surpass the microbacteria, but they're clearly related to other much smaller viruses.

Now a new piece of evidence supporting that viruses may be somewhat "alive" has been added -- viruses can catch a virus. 

The discovery began more than a decade prior when researchers found a massive parasite in an amoeba from a cooling tower in Bradford, UK.  The little creature was frozen, as it was thought to be run-of-the-mill parasitic bacteria.  However, upon closer inspection, years later the scientists recognized it as a virus, with a gigantic genome, capable of encoding over 900 proteins.  The virus was named Acanthamoeba polyphaga mimivirus (for mimicking microbe).  It was over three times bigger than any previous virus. 

The discovery brought great excitement to some nontraditional biologists who had long believed viruses to be living.  Says Eugene Koonin of the National Center for Biotechnology Information in Bethesda, Maryland, "It was the cause of great excitement in virology.  It crossed the imaginary boundary between viruses and cellular organisms."

Now Professor Koonin, Jean-Michel Claverie, a virologist at the CNRS UPR laboratories and Didier Raoult at CNRS UMR, made an even more shocking discovery.  The team in 2003 discovered an even bigger virus.  They named this one mamavirus.

The shocker came when they found that a smaller virus with just 21 genes was associated with the new mega-virus and was infecting it.  While the main virus infected the amoeba, hijacking the amoeba's enzymes and structure to make a protein factory, the tiny virus, which researchers named "Sputnik" set to work hijacking this factory and making copies of itself.

The result was the mamavirus got more than just a bad cold -- it produced fewer and deformed mamaviruses, effectively making it less infective.  This relationship of a viral parasite sickening a host is one only expected by something living, further evidence that the big viruses might be "alive".

Says Jean-Michel Claverie on the mamavirus, "There’s no doubt this is a living organism.  The fact that it can get sick makes it more alive."

Mr. Koonin adds, "It infects this factory like a phage infects a bacterium.  It’s doing what every parasite can — exploiting its host for its own replication."

Intriguingly the little virus has genes similar to those used by the mamavirus and mimiviruses for reproduction.  This leads some researchers to speculate the virus could have been created by a failed reproduction by the big viruses.  This also supports the idea of the big viruses as being alive, as a prevalent theory for the origin of viruses was that they came from misreplicated bacterial DNA.  Further the little virus can transform genes between big viruses, similar to horizontal-gene-transfer in bacteria.

The new finding may have a big impact on global biology.  In plankton blooms genetic sequences have been found similar to those in the big viruses.  These blooms may be teaming with big viruses, which would likely have been destroyed by sample collectors' bacterial filters.  By impacting the life and death of plankton the big viruses could impact not only ocean nutrient cycles, but the global climate itself. 

Curtis Suttle, an expert in marine viruses at the University of British Columbia in Vancouver states, "These viruses could be major players in global systems.  I think ultimately we will find a huge number of novel viruses in the ocean and other places.  It emphasizes how little is known about these organisms — and I use that term deliberately."

The full study on the topic of large plankton viruses can be viewed here, while the study on the mamavirus can be viewed here.

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RE: Future Job
By Chemical Chris on 8/7/2008 11:17:03 AM , Rating: 5
Gene Programmer: Like a computer programmer, but instead of working with bits or qubits (for the future computer programmers), you work with genes. Recode a virus to infect AIDS, cancers, meningitis, and whatever else you want.

Actually, yes, thats exactly what the future holds. Currently, there is some gene therapy being done with virus's (the virus has a beneficial/repaired gene added to its genome, so when it infects, sometimes the beneficial gene will be added to the host genome, curing the disease caused by a deformed gene copy). This is very very expensive and time consuming, and doesnt work as well as hoped (it works, sometimes, but often kills the patient afterward by causing some rare forms of cancer; ie, more work is needed before gene therapy becomes a good reality). Also, functional genes must be isolated from another host. We currently have the tech to produce 'custom' pieces of dna (one nucleotide at a time, up to ~100 nucleotides long, max). So, not big enough to do anything useful (used to make primers for PCR currently).
But in the future, one could design a piece of DNA to give novell function to a virus, build this DNA (or RNA, as it quite often goes), then splice it into the virus much more accurately then at present, and voila, a 'custom' virus. This could be used to cure all kinds of diseases and genetic defects (ie, make a virus that infects malaria and prevents it from multiplying, curing the condition, or make a virus that can only integrate itself into a region of DNA that is different in cancer cells vs healthy cells, inject a cancer patient, and destroy the cancer cells (as simply as initiating the cell death response, or inhibit cellular replication, whatever)
While more work is yet to be done to make this a reality, it is coming, and I hope to help develop it during the course of my career (almost completed my Biochem degree)
If you want to help make it a reality in a non-professional capacity, just run folding!
Chem C

RE: Future Job
By William Gaatjes on 8/7/2008 2:42:00 PM , Rating: 2
As long as we do not have a full understanding about every detail of what atoms, protons, elektrons, quarks, blah really are this will always be repetitive guess work. I think quantum leaps will be made on every field of science when we truly understand physics. Because that is what it all comes down too.

Nature has found numerous ways of using specific characteristics of elements and combinations of elements. It is amazing to see what proteins are capable of. For example : Proteins used as chemical switches. Or as springloaded contraptions that fire when exited by a single atom or ion from a specific element. Proteins that can strip a complex molecule made of different elements apart and use the stripped ions to start another chemical reaction. This reaction can be for instance be the start of a new protein.

I can only say it is wonderfull and keeps amazing everytime.
But it still all comes down to physics. If we crack that code, every other science field will be a whole lot easier to understand because you have a solid base to start from.

"The whole principle [of censorship] is wrong. It's like demanding that grown men live on skim milk because the baby can't have steak." -- Robert Heinlein
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