I love reading bioephemera; Jessica always has interesting things to say about biology and art (and her artwork is amazing). I was impressed at the insight in her latest post. It taught me a thing or two about detachment and human nature. Don't take my word for it, get over there and read it.
Jessica Palmer
Bee and Echinacea
watercolor on Strathmore paper
2007
Fraenkel-Conrat H. and Williams R.C. (1955). Reconstitution of active tobacco mosaic virus from its inactive protein and nucleic acid components. PNAS USA 41: 690-698.
This week's citation classic is probably the coolest experiment you've never heard of. Fraenkel-Conrat and Williams literally took a virus apart, separated its components, then put it back together again. Granted TMV is a relatively simple virus, consisting of 2130 molecules of coat protein and one molecule of genomic RNA 6390 bases long. Nonetheless, this experiment caused quite a buzz in the scientific world.
Gunther Stent wrote to Sidney Brenner, "Frankel-Conrat seems to have done the biggest thing with TMV since Stanley crystalized it. He can add soluble TMV protein to soluble TMV RNA, aggregate the whole mess into rods of which 0.1% are infective!!! Naturally, you don't believe it--nor did I or anyone else, but unless he has made up the whole thing it seems that it must be true. You can't beat that for laughs, can you buddy?"
It was true.
First Fraenkel-Conrat and Williams treated TMV with a mild acid. This treatment eliminated the charges that held the virus together. Then they separated and purified the protein. In parallel, they treated TMV with a detergent to strip away the protein, and recovered the RNA. After these steps, the viruses were no longer infective. Then they mixed the whole mess together again, and lo and behold! Reconstituted viruses!
The following year, Fraenkel-Conrat hybridized the viruses by mixing protein from one strain with RNA from another. Not only did he get viable viruses, he also was able to show that progeny viruses always had the same type of protein coats as the parent strain that donated the RNA. Thus proof that RNA was the genetic material for these viruses.
Photo of Tobacco Mosaic Virus from NIH.
From David Ng: I'd like to suggest a meme, where the premise is that you will attempt to find 5 statements, which if you were to type into google (preferably google.com, but we'll take the other country specific ones if need be), you'll find that you are returned with your blog as the number one hit.
Looks like I've cornered the market in all things Evilutionary.
Was I the first to ask "What has phage done for you?"
How is it that I'm not the number one John Dennehy?
Admittedly bacteriophage art is kind of an exotic interest.
Is there anything bacteriophages cannot do? I dunno. You tell me.
Hat tip Larry Moran
Hmm my virus traps work seems to be generating quite a bit of interest. I originally thought it was kind of a neat idea, but just a special case of a broader research program I've been involved in: bacteriophage growth in environments containing multiple host types.
However the virus trap idea seems to have captured the popular imagination. First, Carl Zimmer wrote about virus traps for the NY Science Times. Then the we the German public broadcaster ARD contacted my former PI about including a segment about virus traps in a series of documentary films about viruses. (No word yet whether they will go thru with it; as the director mentions, it might be difficult to "find a 'visual' way to explain your work"). Finally, Janet Ginsburg wrote about virus traps for New Scientist. (Unfortunately it is not open access so go buy a copy at your newsstand or get 4 issues for $4.95 if you purchase online). Janet promises to write about it for her excellent blog as well. I, for one, am eagerly waiting the article.
In the meantime, I've copied a quote from the article.
"Tackling the issue from a different perspective is ecologist Paul Turner of Yale University. To him, a virus trap is an example of an 'ecological trap' - a habitat that looks fertile but is actually a blind alley. The classic example is mayflies mistaking asphalt for water and laying their eggs on it. In nature, ecological traps can cause local populations to decline, or even die out if they outnumber fertile habitats. Turner wanted to know under what conditions artificial virus traps could do the same, so he created a mini-ecosystem made up of the bacterium Pseudomonas syringae and a virus called phi 6, which preys on it (Ecology Letters, vol 10, p 230).
He chose this system because it is easy to introduce a trap. To attack Pseudomonas, phi 6 first latches onto telescopic appendages called pili, which the bacterium uses to invade plants. When the pili are retracted, the virus is pulled inside. However, there is a mutant 'superpiliated' strain of Pseudomonas which has more pili than normal but cannot retract them, meaning phi 6 can bind to but cannot enter and infect the bacterium. This is the strain used to trap would-be invaders.
To test its effectiveness, Turner prepared test tubes of the bacterium with varying levels of trap, then introduced the virus. 'We set up a game playing by the simplest rules possible,' he explains. He judged success or failure by viral survival and growth rates. If the trap works, virus levels should decline - which is exactly what happened. A 50:50 mix of traps and normal bacteria vanquished phi 6 completely.
Turner's team is now looking to turn experiment into therapy, removing red blood cells and adding decoy attachment sites for viruses. Their focus right now is HIV. 'All of our drugs against HIV are effective because they keep immune cell counts up,' says Turner. 'That's a very expensive venture that a lot of people can't afford. If you could find a way to protect those cells through a sheer onslaught of traps, that might be another way to achieve the same thing.'"
Photo of HIV budding from a CD4 cell from NIH.
Previously I posted on aging in bacteria. One question I posed was "is, given an initial population that supposedly contains both old and young cells, are the differences in growth rate between cells sufficient to produce large differences in microcolony sizes when microcolonies are initiated on agar?" If true, this finding would have considerable bearing on the biology of an organism I am interested, the bacteriophage. Eric Stewart, author of the original manuscript I wrote about, responded to my question. Turns out there is not much reason to expect large differences in microcolony size due to cell age. However, other factors, such as whether the cell recently divided or not, could affect microcolony size. Here is what Dr. Stewart had to say:
I did not record the size variation of the microcolonies, but even a two-fold difference is completely expected, based on the fact that some cells should arrive on the agar just after division, and some just before (a two-fold difference in starting biomass). Elio noted little variance in his colony sizes, and you wondered if old and new cells were different enough in growth rate to cause visible size differences in microcolonies. In fact, the very mechanism of how cells age (and rejuvenate) makes this almost impossible. Even a very old cell, as long as it can divide once, will produce one young cell in addition to its even older self. That young cell will have a nearly maximal growth rate, and should divide again relatively quickly, producing one more young cell, in addition to its now slightly older self. This means that as long as one division occurs, the colony is once again quickly populated with young cells, and eventually, at large enough population sizes, the entire 'standard' distribution of ages is recapitulated in every colony.
While the explanation above reduces the microcolony size difference due to the age of the starting cell, there are other factors at play as well. First, the difference in growth rates is something like 2% per old pole cell division, so if the cells are not extremely different in age, it will be very hard to detect, given the already two-fold variation in microcolony size due to the cell cycle timing of the first cell. Second, old cells are exponentially decreasing in frequency, by the very nature of the division that produces them. Young (first division) cells make up half of any E. coli population, due to the fact that one is produced in every division. The exact same process means that one half of the population is at least one division old, one quarter is at least two divisions old, 1/8th is at least three divisions old, etc. This means that in order to find one arbitrarily old cell, you must examine 2^X cells, where X is the division age you are seeking. As this doubles with each additional division, you can see that truly huge numbers must be examined to find really old cells. For example, examining about one thousand colonies will, on average, reveal one that arose from a ten division old cell; this would then need to be detected in the distribution of nine, eight, seven, etc. division old cells, taking into account the fact that the very first division produces a young cell, as noted above. Finally, there is a large amount of noise; that 2% difference is an average of very many cells. The distribution is quite
large.
For those reasons, it is quite difficult to detect senescence in bacteria. We accomplished it by examining very large numbers of cells, and measuring their actual individual growth rates (exponential fit to the increase in length over time). It was the automation that allowed us to achieve this; others had come very close in the past, but were limited by the need to measure and record all of the data by hand e.g. Powell EO and Errington FP. 1963. Generation times of individual bacteria: Some corroborative measurements. J Gen Microbiol 31: 315–327.
Dr. Stewart also responded to questions regarding the number of cells dying during the course of the experiments.
Elio Schaechter wrote that he spread Salmonella cells on nutrient agar on a slide, and counted how many didn't form colonies. This type of experiment was also performed by others (e.g. Gallant, J., and Palmer, L. (1979) Error propagation in viable cells. Mech. Ageing Dev. 10: 27-38), as well as repeated by myself before the timelapse experiments in the paper. Counting 17,000 microcolonies, I found a 'failure to grow' rate of about 1 in 400 for E. coli, which agreed with the Gallant and Palmer results as well. I suspect that there may be a 'plating shock' that results in such relatively high levels of non-growth, compared with the different measurement of non-growth during timelapse, which came out at about 1 in 2000. Therefore, this rate probably doesn't indicate much about senescence, but some other cause of 'death' (non-growth).
So there you have it. Cells age. But you have to check quite a few cells before you notice much of an effect.
Photo of Bacillius subtilis by Dr. Leendert Hamoen, Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne.
This Week's Citation Classic comes from the venerable W. D. Hamilton. 1967. Extraordinary Sex Ratios. Science 156: 477-488.
Here's a test. Read pgs. 142-143 of R.A. Fisher's Genetical Theory of Natural Selection. Then read the first paragraph of Hamilton's Extraordinary Sex Ratios. Both explain why the sexes usually come in equal numbers. Which is easier to understand? I suggest the latter.
Perhaps now you will understand why so many evilutionary biologists hold Bill Hamilton in such high esteem. I still recall my initial reading of the paper during my first semester of graduate school. My advisor said to me one day, "mumble mumble dominance... mumble mumble sex ratios... mumble mumble foraging....mumble sex ratio... mumble have more males...." In his defense, he was probably speaking clearly. I was just so cowed that I had trouble concentrating. I left his office thinking, "I better read up on sex ratios". I look up "Sex Ratios" in ISI Web of Knowledge. Wow... 8,549 results! OK, sort by times cited. Hmmm... Extraordinary Sex Ratios 1,406 citations. OK, I'll start with that one.
My reaction on reading the first page: WHOA! So that's why the number of males and females are equal. Sex ratio is one of those things that seems obvious until you start to think about it. Darwin himself thought the problem of sex ratios was too difficult to tackle, and left it for future generations (Descent of Man, p. 399). Fisher first figured it out as I mentioned above.
Much of Extraordinary Sex Ratios deals with exceptions from balanced sex ratios, usually cases where females outnumber males, and gives excellent examples of these. One example in particular totally blew my mind: the Pyemotidae. Take Acarophenax tribolii for example. These mites usually occur in broods biased 15-1 in favor of females, and they are quite naughty. The single male will mate with and fertilize all of his sisters. Hang on. Before you get too excited, all this happens in full view of the mother. Are you slackjawed yet? Is your jaw slack? This will make your jaw hit the floor. All this takes place in the mother's womb! That's right. The enormously swollen, gravid, female A. tribolii has~16 full-grown adult mites having a great, big, incestuous orgy in her womb! Eventually these ungrateful offspring burst her open, killing her. Actually not all of them. The poor male completes his life cycle and dies before he is born. At least he isn't a virgin.
The reason the sex ratio is so biased in Pyemotidae is because they engage in incest exclusively (or nearly so). So why make lots of males? One can fertilize all his sisters; a second would be a total waste of energy and effort. The Pyemotidae have evolved further to protect this male as much as possible by having the mating take place within the womb because, if he dies, the females evolutionary life is over. Moreover, you keep all the actors in close proximity, ensuring all offspring are fertilized.
Stephen Jay Gould writes about the Pyemotidae in Ch. 6 of The Panda's Thumb. Olivia Judson also mentions them in her book, Dr Tatiana's Sex Advice to All Creation.
Bill Hamilton died on 7 March 2000 from complications of malaria. A page is dedicated to his memory.
The drawing above is Fig. 53 Progenesis in the mite Siteroptes graminum. A sexually mature female with one male and four females growing within her body. (From Rack, 1972.)
Tara posted a down-right scary article today at at Aetiology. I don't mean Halloween spooky goblins and ghosts scary; I mean scary as in getting sent to PMITA prison scary.
"...a University of Pittsburgh geneticist, Robert Ferrell, plead guilty to charges of failing to follow proper [Material Transfer Agreement] procedures in mailing [microbiological] samples, after being investigated initially for charges related to bioterrorism that were dropped... and another professor awaits trial.... Ferrell violated this [Material Transfer Agreement] agreement by sharing [Bacillus subtilis and Serratia marcescens] strains with Kurtz. Normally, this would be an issue handled between Ferrell (and his university) and ATCC; however, under the broad definitions of mail and wire fraud under the Patriot Act, the government stepped in and charged Kurtz and Ferrell with mail and wire fraud--felonies that, since they're being charged under the Patriot Act, could carry a possible 20-year sentence."
Has the government no sense of decency at long last?
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