No big deal. Just some big viruses.

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Searching PubMed for the keyword "giant virus" always provides some fun results. That's not what I did today - though I do recommend trying it sometime - as the recent reports about oversized viruses have been spreading like some kind of very small causative agent of infectious disease.

Here's the first one: the isolation of a Mimivirus from a patient with pneumonia. The particular viral isolate is more than 550 nanometers wide and has a 1.23 megabase genome. For reference, that's huge. For a better reference, that's about the width of an average E. coli cell and a genome in the same size range as many of the more genetically streamlined bacteria (it's more than twice as large as the tiny Mycoplasma genitalium genome, though that's about as minimal as known bacterial genomes get). Most viruses we know of aren't quite this massive, though Mimiviruses and other record-holders for viral size share the characteristic of infecting Acanthamoeba polyphaga amoebae. So if this new mimivirus infects amoebae, is it pathogenic to humans as well? The authors of this paper seem to think so. As always, further viral isolates will be necessary. (The actual paper is right on the other side of this concrete paywall.) 

If you thought that mimivirus was big and/or had a silly name, check out the Pandoraviruses. These viral isolates average more than 700 nanometers in diameter and bear genomes of, in at least one case, more than 2 megabases. They were found in sediments and mud where amoebae are plentiful. There are some hyperbolic news reports out there about these new viruses already so I'll just pick some interesting bits out of the paper itself:
Unlike eukaryotic DNA viruses and phages, which first synthesize and then fill their capsids, the tegument and internal compartment of the Pandoravirus particles are synthesized simultaneously, in a manner suggestive of knitting, until the particles are fully formed and closed.
Knitting viruses. Don't tell Pinterest. Not yet.

The high percentage (93%) of CDSs without recognizable homolog (ORFans), the alien morphological features displayed by P. salinus, and its atypical replication process raised the concern that the translation of its genes into proteins might not obey the standard genetic code, hence obscuring potential sequence similarities.
The authors are trying to say that these viruses are almost suspiciously strange. It's not uncommon to see large chunks of viral genome sequences that don't look like any known sequence, but when you're talking about genomes larger than many bacterial ones then this becomes a sizable reservoir of new, uncharacterized genes and proteins. They may be more familiar than we can initially tell.

...their DNA polymerase does cluster with those of other giant DNA viruses, suggesting the controversial existence of a fourth domain of life ... The absence of Pandoravirus-like sequences from the rapidly growing environmental metagenomic databases suggests either that they are rare or that their ecological niche has never been prospected. However, the screening of the literature on Acanthamoeba parasites does reveal that Pandoravirus-like particles had been observed 13 years ago ... although not interpreted as viruses. 
So these viruses aren't totally alien. They've been around for at least 13 years! Probably even longer,* though exactly how much longer may determine how controversial that claim about the "fourth domain of life" becomes.

Citations follow.

Saadi, H., Pagnier, I., Colson, P., Cherif, J. K., Beji, M., Boughalmi, M., … Raoult, D. (2013). First Isolation of Mimivirus in a Patient With Pneumonia. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. doi:10.1093/cid/cit354.

Philippe, N., Legendre, M., Doutre, G., Coute, Y., Poirot, O., Lescot, M., … Abergel, C. (2013). Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes. Science, 341(6143), 281–286. doi:10.1126/science.1239181.


* Some varieties of amoebae may have been around as long ago as the Neoproterozoic Era, or between 1,000 and 541 million years ago. If there were amoebae then viruses with amoebic hosts may have also been present.

New job, same as the old job

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I'm finding this report on the growth of temporary work in the US quite interesting. It's at least partially because I've worked temp jobs before, even immediately after finishing the undergraduate stages of my ongoing academic career. The unnerving thing about each job wasn't the uncertainty, the mediocre pay or the lack of decent benefits. Rather, it was the sense that you could serve as a critical element of a larger whole yet retain absolutely no role in your long-term fate with the company. Anyway, here are some bits from the report I found especially damning:
Every year, a tenth of all U.S. workers finds a job at a staffing agency.
That's both temporary and contract workers. The American Staffing Association states that staffing agencies employ more than 2.9 million people in the US every day. That time factor is the critical element here -- these may not be the same 2.9 million employees from one day to the next.
“We’re seeing just more and more industries using business models that attempt to change the employment relationship or obscure the employment relationship,” said Mary Beth Maxwell, a top official in the Labor Department’s Wage and Hour Division. 
Obscuring the employment relationship doesn't initially seem like an ideal goal but it certainly looks like an effective way to turn formerly long-term employment into a more commitment-free model.

“I think our industry has been good for North America, as far as keeping people working,” said Randall Hatcher, president of MAU Workforce Solutions, which supplies temps to BMW. “I get laid off by Employer A and go over here to Employer B, and maybe they have a job for me. People get a lot of different experiences. An employee can work at four to five different companies and then maybe decide this is what I want to do.”
This kind of attitude reminds me of the whole "self-deportation" idea. Nothing with that much uncertainty can be a solid long-term solution. There will always be enough work for everyone but not at the same time. Traditionally, this problem was alleviated by unions, though clearly they come with their own issues. Aren't they worth a try for temp workers?
A 2004 order by the National Labor Relations Board barred temp workers from joining with permanent workers for collective bargaining unless both the temp agency and the host company agree to the arrangement.
Oops, maybe not.
Only 8 percent get health insurance from their employers, compared with 56 percent of permanent workers. What employers don’t provide, workers get from the social safety net, i.e., taxpayers.
And don’t look for Obamacare to fix it. Under the law, employers must provide health coverage only to employees who average 30 hours a week or more. After pressure from the temp industry and others, the IRS ruled that companies have up to a year to determine if workers qualify. 
Health care, or the lack thereof, may be the most worrisome element of the growth of temp work. If most of the temp job growth is in industrial jobs, more people will continue to be at risk of experiencing injuries they will never be able to afford. Many of them may not even work for a single employer more than a year, or when they do, they still won't be able to afford the plans the employers offer (in my experience, the plan wasn't exactly cost-competitive).

This whole problem is genuinely worrisome from numerous perspectives. It's yet another economic maelstrom waiting to happen, with the added stench of Industrial Age exploitation swirling throughout.




Time to BRCA the habit

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The US Supreme Court has ruled that human genes cannot be patented. That's great news until we stop to consider what a human gene includes. The ruling bars patents on original human DNA, presumably in any variation of its sequence. That is, I couldn't file a patent for the sequence of my favorite human gene or of any of its alleles. The ruling does specifically permit any implementation or subsequent product made using that sequence, up to and including synthesis of cDNA. By means of awkward simile, that's like prohibiting patents on maple trees (or, at least, the concept and structure of a maple tree) but permitting patents on maples grown in a tree farm. There's still plenty of room for perfectly legitimate patents to be granted and for new products to be protected. I'm just concerned that this ruling stops well short of actually resolving the issue of what kinds of biological material can or can't be patented.

We've reached the point at which the whole "natural" vs. "artificial" dichotomy just doesn't pass muster anymore. Advancements in synthetic biology promise to blur a line that wasn't especially crisp to begin with, especially when discussing raw DNA sequences. The SCOTUS ruling states "cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments...creation of a cDNA sequence from mRNA results in an exons-only molecule that is not naturally occurring." The issue here really shouldn't be whether cDNA of a patented sequence could be found in a human (that is, without influence by outside factors like viruses), but rather that the cDNA still bears exactly the same protein-coding message as the RNA transcript does, just in an edited format.

We can, of course, get more philosophical about the issue and debate what constitutes a "human" gene. At least eight percent of the sequenced human genome is made up of retroviral sequences. Some of them even code for things in active use. There have also been suspected instances of bacterial sequences jumping into the genome of their human host. I suppose each of these issues will create their own legal issues when the time comes, i.e. the next time a biomedical company gets overzealous about their intellectual property. In the meantime, this new ruling will have to suffice.

Update: I like the 2010 district court ruling. It went farther than today's SCOTUS ruling.

Golden eggs

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I just got back from visiting my lovely lady counterpart in Germany. In lieu of describing the whole trip, here is a photo of a gold-plated silver chicken.
Click here and see if you can find this guy. Hint: he's smaller than the average rooster.

Many, many more photos, presented with no context at all, are present here.  Nope, that link is no longer operational. Photos available upon request.