Hmm. I wonder if you could “trip” such a virus with a drug that bound to the “legs”, especially at the “foot” or “knees”? My second thought was the same as the second article: a decoy (or muffler?) for the host cell recognizer.
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Hehe, I love your thought about aiming for its legs. 
Also a nice second thought.
OUR VIRAL DESCENT
Not only do we have more bacterial cells in our body than human cells. Turns out our genome is filled with virus fragments too. 8% of our genome has viral origin.
The article Are we viral from the beginning, tells a strange story about viral genes controlling when to switch on and off other genes, in our early beginning as embryos,
I just finished reading a fine small book A Planet of Viruses by Carl Zimmer. Each short chapter is a story about a virus and the history about how it got discovered. Here is one of my favorite passages:
“Breathe ten times, and one of those breaths comes to you courtesy of a virus.”
Zimmer explains that viruses are sharing borrowed genes, in this case photosythesis genes, with new hosts.
Want to know another reason why viruses are responsible for part of the oxygen in the air? Go listen to this podcast.
It’s a virus world and we just live on it
The book is praiseworthy understandable. I like how Zimmer closes it with blurring the traditional line between non-living and living matter.
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MP3 files written as DNA with storage density of 2.2 petabytes per gram
ARStechnica has an article on how some researchers encoded data into DNA. Some high-order bits: they used base 3 (to avoid runs of the same base), added parity info, and redundantly encoded information four times by using overlapping 25-base runs of 100-trits.
Supposedly, if kept cold and dark, DNA can safely store information for thousands of years.
Wow, JL. This is cool! A petabyte of data is crazy much. I had to look it up, as I had nothing to compare it too. WIKI gives some interesting examples.
Here is my favorite:
Neurology: It is estimated that the human brain’s ability to store memories is equivalent to about 2.5 petabytes of binary data.
I’m reading a classic on viruses, “Virus hunters” by Greer Williams from 1960. I got it recommended by the book "Virology - Molecular biology and pathogenesis. The discussion on whether viruses are alive or not is an old one. I found a rather cool section on viruses:
“While this midget microbe lacks the ordinary microbe’s capacity for independent life, most types of viruses are fantastically choosy about what living creatures they will infect - in fact, about what cells in these creatures they will persue their “borrowed life” in. Rabies, for instance is very nearly the only virus that will produce the same fatal disease in man, dog and a wide variety of animals, Even so, once inside the body, it will attack nerve cells only.” (page xii-xiii)
I also really like this quote from TWIV, where one of the hosts say, while they were discussing whether viruses are alive or not:
“We put these categories on life - and life didn’t get the memo.”
Hehe, love that!
From the TWIV episode 209 “When the virus hits the fans”.
VIRUS AS MEDICINE
Nascarnut found a really fine article about the potential of using viruses against cancer.
Genetically engineered virus kills liver cancer
I have been reading some history about virus discovery and read that bacteriophages - viruses that specifically kills bacteria had been used as medicin earlier. And there was some succes with it. But then came antibiotics, the new wonderdrug and people sort of forgot about it, as using antibiotics was easier.
The more I read and hear about virology, biochemistry and microbiology, the more I get conscious about that we owe a lot of our biotechnology tools and our knowledge about cells, to viruses. As they were the means that helped with the discovery. The article The next phage, is about healing infected wounds with viruses, when antibiotics is not working.
THE MACHINERY OF LIFE
EteRNA player DN8 introduced me to David Goodsell’s book “The Machinery of Life”. As he said: It’s full of hand drawn illustrations of the inside of a cell, with every part of it there, all at once. He showed me this picture.
I liked it very much, so I bought the book and have read it. It is just as good as DN8 promised. This is a very good place to start if you are all new to biochemistry and molecular biology. It is not on RNA alone, but on the whole machinery of the cell. It is a fascinating peek into a miniature world. It is easy to understand. It is also very concentrated, so it is best enjoyed in small bits. It’s sort of the poetry version of molecular biology books.
Here is one of my favorite passages:
Cells do almost all of their work with six types of atoms - carbon, oxygen, nitrogen, sulfur, phosphorus and hydrogen - adding more exotic atoms only when needed for special tasks. These atoms may be connected in only very limited ways, defined by the underlying chemistry of the atoms. Molecular machines must be constructed with these significant limitations. It is much like trying to build machines with Tinkertoys or Lego blocks: You may build a wide variety of different objects, but the final form is shaped and limited by the shapes and connections of the underlying units. (Page 10)
And things just got a lot easier to understand. Hereby the tip is passed on.
Edit by Starryjess
A VIRUS WITH AN IMMUNE SYSTEM
Here is a small video from DNews with an interesting angle on weather viruses are alive or not.
I later found an article by Carl Zimmer, that goes more into detail. It is beautiful written and full of surprises.
I heard a fun comment in TWIM (This Week in Microbiology) in an episode about spores. It was sort of a comment on the question if weather viruses are alive or not.
Vincent: Are they living, spores?
Jonathan: Yes, probably, but very very slowly.
Following is a link to a short video animation of “RNA interference (RNAi)" from Nature magazine online. It is very cool and only about 5 min long.
https://www.youtube.com/watch?v=cK-OGB…
“Nature” has a webpage that has slideshow which identifies the structures that were shown in the video:
http://www.nature.com/nrg/multimedia/…
Beautiful alien world! Thanks for sharing this video. It is the best looking animation I have seen of RNA and the cell.
BACTERIAS AS ELECTRICIANS
Chatout line from last month. Slightly edited down. Title in honor of one of MacClarc’s fine sayings.
Eli: I saw some very special bacterias recently. I have seen the electric cable bacteria. A danish mud scientist found a whole new type of bacterias living in the sea floor. About 2 cm long living electric wires.
starryjess: oh, “mud scientist”. Nice job title 
Eli Fisker: That was what he called himself
starryjess: that’s cool
Eli Fisker: We were allowed to take a look at the bacteria in the break. I could see it with my naked eye. No need for microscopes [Additional note: It wasn’t the cable bacterias themselves I could see when I was looking at them unaided. It was threads of them when the mud was stirred in water and the mud coloring the threads.]
starryjess: So you went to a lecture then
Eli Fisker: yep
Eli Fisker: Public lecture. I read about the bacteria earlier last year
Eli Fisker: And I just wanted to hear more
Eli Fisker: They also told about a microorganism that was able to eat whole trees, so the tree fell to the ground and left a whole big place of ground deforested.
Eli Fisker: Wish I remembered its name
starryjess: O.o
Eli Fisker: Very creepy and cool too. It had a special trick that I haven’t heard about any microorganism having.
starryjess: what trick?
Eli Fisker: It could move DNA packages through veins, just like blood cells flows through our veins. But normally DNA is encapsulated in a cell. But here they were flowing like small green packages through the veins system, like it was a bigger living organism
starryjess: O.o
Eli Fisker: They even had a rhythm to them. Almost like something out of a horror movie
mat747: hehe
Eli Fisker: It laid bare a huge area
Eli Fisker: But still it was really beautiful, when watched as a high speed video through microscope
Eli Fisker: We also heard about nanowires
starryjess: ah yes
Eli Fisker: Made by bacterias
Eli Fisker: They were electrical too
Eli Fisker: And thinner than the electric cable bacteria
Eli Fisker: The scientists found out, that when they starved a bacterial community of electrons, they connected up with nanowires to each other and made a system to help alleviate the problem
Eli Fisker: Here is a small video about these nanowires:
macclark52: That sounds pretty cool, Eli. Can you find out what the microorganism was?
Eli Fisker: Macclark, thx, was. The tree eating one I can’t. The others yes
macclark52: Was it taking down living trees or dead ones?
Eli Fisker: Living ones
Eli Fisker: The nanowires are in the video and the cable bacteria is in here:
macclark52: Which ones were the electricians?
Eli Fisker: Here is a link: Bacteria unite to form living electric cables that stretch for centimetres
Eli Fisker: Macclark, the nanowires and the cable one. The scientist that discovered the cable bacteria contacted the one who was working on the nanowires and they are working together now
macclark52: Wow, that is just astonishing!
Eli Fisker: Another cool thing is that they found out that the nanowire bacteria was not just talking with their own kind.
Eli Fisker: Do you know about the 3 domains of life?
macclark52: Yes.
macclark52: Archaea, Eubacteria, eukaryotes?
Eli Fisker: They found out that Archaea and Bacteria can connect with each other with these nanowires and communicate
macclark52: Holy moly.
macclark52: That is SO SF!
Eli Fisker: As the american scientist jokingly said, we still haven’t figured that out yet. When he traveled here, he needed an adapter for the current to his computer
macclark52: Haha!
Eli Fisker: Absolutely. One of the best lectures I been to ever
Eli Fisker: By the way, I forgot to tell that the cable bacteria could move and feel its way through. They looked funny in high speed. [Additional note: The movie they showed of the bacteria moving, the bacterias were fine transparent threads, moving towards the source of food and some of them were fighting with each other on how to get there.]
macclark52: Do you think they are talking about us behind our backs?
Eli Fisker: hehe, who knows.
Eli Fisker: They are probably seeing food
Eli Fisker: I mean smelling or sensing
Eli Fisker: As the one scientist said: Thinking like bacteria. Think small
Eli Fisker: I quickly changed that to, Thinking like RNA. Think folding
macclark52:
starryjess: 
Eli Fisker:
starryjess: how do you know bacteria think small? maybe they think they’re big 
Eli Fisker: hehe
Eli Fisker: good point
Eli Fisker: Compared to viruses they are
I also found a fine small podcast about the bacteria Shewanella which makes nanowires.
SPACE INVADER DNA
Have you heard about DNA parasites aka transposons? I learned something really fascinating today while I was reading in my molecular biology book. Not only do we have 10 times more bacterial cells than human cells and virus fragments takes up more space in our genome than our actual genes. Apparently we also have lots of traces of transposons in our genomes. Check out this description:
“These transposable DNA elements (transposons) are parasitic DNA sequences that colonize genomes and can spread within them. In the process, they often disrupt the function or alter the regulation of existing genes. On occasion, they can even create altogether novel genes through fusion between transposon sequences and segments of existing genes. Over long periods of evolutionary time, transposons have profoundly affected the structure of genomes. In fact, nearly half of the DNA in the human genome has recognizable sequence similarity with known transposon sequences, thereby indicating that these sequences are remnants of past transposition events. Even more of our genome is no doubt derived from transposition events that occurred so long ago (>10 lifted to 8 years) that the sequences can no longer be traced to transposons.” (Molecular Biology of THE CELL, fifth edition, page 247)
That last bit was what really surprised me. I knew we had some of these jumping genes in our DNA, but not this much.
I found a great article about the fascinating space invader DNA.
THE BIOGRAPHY OF E. COLI
An illustrator had fun imagining what a magazine would look like if its readers were E. coli.
Illustation by Velica, found here.
I recently got hold of a book about E. coli. The book is called Microcosm by Carl Zimmer. E. coli has been a main character in the unraveling of many of the secrets of life. It is great history telling about science discoveries.
Here is a note from the book jacket:
“In 1946, a twenty-year-old medical school student called Joshua Lederberg decided to find out whether microbes make love.”
See, that’s a very fine start on a story
Another amazing fact is that E. coli is living with several atmospheres pressure on its inside. Quote:
“If you prick us, we bleed, but if you prick E. coli, it blasts.”
Actually I love these special abbreviated names, like E. coli and C. elegans. I find them very poetic. (They stand for Escherichia Coli and Caenorhabditis Elegans). Starry added: “Elegans sounds elegant ;)”.
I also find this fascinating:
“E. coli needs iron to live, for example, but iron is exquisitely scarce. In a living host most iron is tucked away inside cells. What little there is outside the cells is usually bound up in other molecules, which will not surrender it easily. E. coli has to fight for iron by building iron-stealing molecules, called siderophores, and pumping them out into its surroundings. As the siderophores drift along, they sometimes bump into iron-bearing molecules. When they do, they pry away the iron atom and then slide back into E. coli. Once inside, the siderophores unfold to release their treasure.”
I recently heard a podcast from This Week in Microbiology, TWIM episode 8 about exactly this. From minute 27 and forward.
Iron Piracy - The microbial battle for Iron
Edit by Starryjess
Lroppy shared a fantastic article about our microbiome. I in particular liked this quote:
“Knight also found that the presence of a family dog tended to blend everyone’s skin communities, probably via licking and petting.”
Fascinating. I bet I got cat microbes all over my skin too.
Check the article out here:
I CAN DO PCR
I just found a way for us to get a little “hands on” experience with lab equipment. Since we are already science gamers, the answer is of cause a science game.
Universities around the world are now using the game to teach their students about the different processes going on in a lab. Right now it is free for everybody for a short period, later it will later cost money to access.
You can read more about Labster in the European Biotechnologist.
I have run a round of PCR. I think this will be a great help to demystify things a bit. Want to know more about what PCR and Next generation sequencing is? Want to play the lab game? Go make an account HERE. Choose this option furter down the page:
You can also become beta tester for them and get access to cool lab stuff.
Welcome in the virtual real lab!
Now available for free on www.coursera.org and on iTunesU is a course titled ‘Virology 101’ by one professor Vincent Racaniello of Columbia University. It’s a very interesting course and it touches on some of the viral RNA mechanics. You only need a fundamental understanding of biology to grasp the lectures effectively. I’ve listened to the whole thing, and it’s great material, well worth anyone’s time.
Oh, yeah! I can only recommend. Vincent Racaniello is the host of TWIV - This Week In Virology, which is a podcast on viruses - as their motto goes - The kind that makes you sick. I’m enjoying the podcast very much, it is brilliant and even fun.
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Thx for the tip, Paramodic!
Yeah, I listen to TWiV and TWiM regularly on my commute. Have you watched episode 200: ‘Threading the NEIDL’? Great stuff, that. Hey, they should have Rhiju on as a guest some time!