crAssphage – an ancient virus

_{David L. Hagen

July 25, 2014

Biology, Cell biology, Genomics, Intelligent Design}

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Are you what you eat? Or what’s eating you?
Novel virus discovered in half the world’s population

A new study led by researchers at San Diego State University has found that more than half the world’s population is host to a newly described virus, named crAssphage, which infects one of the most common types of gut bacteria, Bacteroidetes. This phylum of bacteria is thought to be connected with obesity, diabetes and other gut-related diseases. . . .It’s unknown how the virus is transmitted, but the fact that it was not found in very young infants’ fecal samples suggests that it is not passed along maternally, but acquired during childhood. The makeup of the viral DNA suggests that it’s circular in structure. Further laboratory work has confirmed that the viral DNA is a singular entity, but it’s proven difficult to isolate. . . .
Some of the proteins in crAssphage’s DNA are similar to those found in other well-described viruses. That allowed Edwards’ team to determine that their novel virus is one known as a bacteriophage, which infects and replicates inside bacteria—and using innovative bioinformatic techniques, they predicted that this particular bacteriophage proliferates by infecting a common phylum of gut bacteria known as Bacteriodetes.
Gut punch
Bacteriodetes bacteria live toward the end of the intestinal tract, and they are suspected to play a major role in the link between gut bacteria and obesity. What role crAssphage plays in this process will be a target of future research.. . .

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
Nature Communications 5, Article number: 4498 doi:10.1038/ncomms5498 Published 24 July 2014

Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ~97 kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases.

Or are you what you think?
Or were you were designed that way?

Comments

OT: So according to critics of the ENCODE study which found widespread functionality for 'junk' DNA, functionality does not determine if a sequence is actually functional, only 'conservation of sequence' determines what is functional??? DNA mostly 'junk?' Only 8.2 percent of human DNA is 'functional', study finds - July 24, 2014 Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution -- a clear indication that this DNA matters, it has some important function that needs to be retained. http://www.sciencedaily.com/releases/2014/07/140724141608.htm So basically, only if Darwinian evolution is assumed as true will Darwinists accept that a given sequence of 'junk' DNA may be functional! Do Scientists Accept the Results of the ENCODE Project? September 12, 2013 - By Dr. Fazale Rana Excerpt: In a recent article, Mattick and his coauthor, Marcel Dinger, argue, like me, that the criticisms of ENCODE are unwarranted technically and are motivated by non-scientific considerations. One of the chief criticisms leveled at ENCODE relates to its use of a causal definition of function to determine functionality within the human genome. That is, a sequence element in the genome possesses function if it performs an observationally or experimentally identified role. ENCODE skeptics argue that this definition is faulty; instead, the project should have relied on sequence conservation (the so-called selected effect definition) as a way to measure function. According to the selected effect definition, sequences in genomes can be deemed functional only if they evolved under evolutionary processes to perform a particular function.,, Hence, functional sequences are those under the effects of selection. And based on a selected effect definition of function, only 10 percent (not 80) of the human genome could be considered functional. Mattick and Dinger decry the weakness of the selected effect definition.,,, http://www.reasons.org/articles/do-scientists-accept-the-results-of-the-encode-projectbornagain77_{July 27, 2014
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Although it is commonly thought that viruses are harmful to humans, I was surprised to learn that the vast majority of viruses that 'infect' people are actually beneficial.
(Bacteriophage) Viruses in the gut protect from infection - 20 May 2013 Excerpt: Barr and his colleagues,, show that animal mucus — whether from humans, fish or corals — is loaded with bacteria-killing viruses called phages. These protect their hosts from infection by destroying incoming bacteria. In return, the phages are exposed to a steady torrent of microbes in which to reproduce. “It’s a unique form of symbiosis, between animals and viruses,” says Rotem Sorek, a microbial geneticist ,, “It’s groundbreaking,” adds Frederic Bushman, a microbiologist ,, “The idea that phage can be viewed as part of the innate immune system is original and exciting. http://www.nature.com/news/viruses-in-the-gut-protect-from-infection-1.13023
Viruses have even been harnessed for use against pathogenic bacteria:
Bacteriophage Excerpt: Bacteriophages are among the most common biological entities on Earth,,,They have been used for over 60 years as an alternative to antibiotics in the former Soviet Union and Eastern Europe.[5] They are seen as a possible therapy against multi drug resistant strains of many bacteria.,,,development of phage therapy was largely abandoned in the West, but continued throughout 1940s in the former Soviet Union for treating bacterial infections, with widespread use including the soldiers in the Red Army—much of the literature was published in Russian or Georgian, and unavailable for many years in the West. Their use has continued since the end of the Cold War in Georgia and elsewhere in Eastern Europe.,,,In August, 2006 the United States Food and Drug Administration (FDA) approved using bacteriophages on cheese to kill the Listeria monocytogenes bacteria, giving them GRAS status (Generally Recognized As Safe).[10] In July 2007, the same bacteriophages were approved for use on all food products.[11] Government agencies in the West have for several years been looking to Georgia and the Former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, e.g., Anthrax, Botulism. - per Wikipedia Viruses: A Pirate Phage Commandeers the Immune System of Bacteria - Feb. 27, 2013 Excerpt: The study provides the first evidence that this type of virus, the bacteriophage ("phage" for short), can acquire a wholly functional and adaptive immune system. The phage used the stolen immune system to disable -- and thus overcome -- the cholera bacteria's defense system against phages. Therefore, the phage can kill the cholera bacteria and multiply to produce more phage offspring, which can then kill more cholera bacteria. The study has dramatic implications for phage therapy,,, http://www.sciencedaily.com/releases/2013/02/130227134334.htm
Bur perhaps most surprising for me to learn about was how complex a bacteriophage is.
Virus (Bacteriophage) - Assembly Of A Nano-Machine - video https://www.youtube.com/watch?v=Ofd_lgEymto
Here is a short video of the Bacteriophage 'landing' on a bacterium:
Bacteriophage T4 - landing - video https://www.youtube.com/watch?v=kdz9VGH8dwY
The first thought I had when I first saw the bacteriophage virus is that it looks very similar to the lunar lander of the Apollo program. The comparison is not without merit considering some of the relative distances to be traveled and the virus must somehow possess, as of yet unelucidated, orientation, guidance, docking, unloading, loading, etc... mechanisms. And please remember this level of complexity exists in a world that is far too small to be seen with the naked eye. Also of note is how complex, and powerful, the DNA packing machine is:
Bacteriophage T4 DNA Packing - video https://www.youtube.com/watch?v=wNQQz0NGUNQ Phage Molecular Motor DNA Packaging Mechanism - 3D version - video http://www.youtube.com/watch?v=H0xdDaWcrdk Discovery of first motor with revolution motion in a virus-killing bacteria advances nanotechnology - March 20, 2013 Excerpt: Peixuan Guo and colleagues explain that two motors have been found in nature: A linear motor and a rotating motor. Now they report discovery of a third type, a revolving molecular motor.,,, The motor moves DNA with a revolving in the same motion as the Earth revolving around the sun. "The revolution without rotation model could resolve a big conundrum troubling the past 35 years of painstaking investigation of the mechanism of these viral DNA packaging motors," the report states. http://phys.org/news/2013-03-discovery-motor-revolution-motion-virus-killing.html Clockwork That Drives Powerful Virus Nanomotor Discovered Excerpt: Because of the motor's strength--to scale, twice that of an automobile--the new findings could inspire engineers designing sophisticated nanomachines. http://www.sciencedaily.com/releases/2008/12/081229200748.htm The physics of going viral: Researchers measure the rate of DNA transfer from viruses to bacteria - June 27, 2012 Excerpt: previous work has shown that the genetic material (in a bacteriophage virus) is under more pressure within its protein shell than champagne experiences in a corked bottle. After all, as Phillips says, "There are 16 microns [16,000 nanometers] of DNA in a tiny 50-nanometer-sized shell. It's like taking 500 meters of cable from the Golden Gate Bridge and putting it in the back of a FedEx truck." Phillips's group wanted to find out whether that pressure plays a dominant role in transferring the DNA. Instead, he says, "What we discovered is that the thing that mattered most was not the pressure in the bacteriophage, but how much DNA was in the bacterial cell.",,, The mean ejection time was about five minutes, though that time varied considerably. This was markedly different from what the group had seen previously when they ran a similar experiment in a test tube. In that earlier setup, they had essentially tricked the bacteriophages into ejecting their DNA into solution—a task that the phages completed in less than 10 seconds. But Phillips says, "What was true in the test tube is not true in the cell." E. coli cells contain roughly 3 million proteins within a box that is roughly one micron (1,000 nanometers) on each side. Less than 10 nanometers separate each protein from its neighbors. "There's no room for anything else," Phillips says. "These cells are really crowded." http://phys.org/news/2012-06-physics-viral-dna-viruses-bacteria.html
bornagain77_{July 27, 2014
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Really? It lives in the anus and they call it crAssphage?Jehu_{July 25, 2014
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crAssphage? Sounds like a bad joke to me.Mung_{July 25, 2014
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