Fanghur

OK; I don't think you guys are understanding my question. Let's use quinolones as an example; quinolones kill by covalently binding to DNA Gyrase and Topoisomerase IV, and inhibiting their ability to re-ligate the DNA strands after they nick them. Now, let's say a bunch of quinolones get inside of a persister cell and bind to gyrase and topo IV. While the cell is dormant, the antibiotic is useless. But when the cell becomes active again, wouldn't those quinolones still be bound to DNA gyrase and topo IV? And if not, why not?

I understand that part, CharonY. What I don't understand is why the antibiotics which had previously bound to the cells while they were in the persister state don't kill the persisters when they (the cells) become active again. Do antibiotics degrade rapidly once they enter the cells? In other words, how does the 'sleeper' (persister cell) untie (unbind/destroy) his shoelaces (the bound antibiotic) while he is sleeping (dormant) so that he doesn't trip (get killed) when he tries to walk (protein synthesis, DNA replication, or whatever the antibiotic targets). I understand that persister 'awaken' once the danger has past, so to speak, but what about the antibiotics/radicals that have already gotten inside them? What happens to them?

I'm currently writing a paper on persister cells and their role in biofilm tolerance to all known antibiotics for one of my classes, and I've read several articles about persisters, but there is something I don't understand. The accepted explanation (or at least one of them) of how persisters are unaffected by antibiotics is that they are completely dormant, that is, nothing inside them is active; no cell wall synthesis, protein translation, enzymes, etc, all turned off. This means that even though the antibiotics do successfully bind their targets, it has no effect since their targets are effectively inanimate, and thus cannot be corrupted by the antibiotic. This I understand. But what I don't understand is that persisters eventually do become active again, as they have to in order to regrow the biofilm, and indeed this is the case. But wouldn't the antibiotics still be bound to their targets when the persisters 'awaken'? And if so, why don't they carry out their intended function once the persisters activate? An analogy; let's say that shoelaces are the antibiotic, and your friend jokingly ties your laces together while you are sleeping so that you'll trip when you wake up. While you are asleep, you are analogous to a persister cell in this situation; the 'antibiotic' (ie tied laces) is on you, but since you aren't moving, it doesn't affect you - you can't trip if you aren't walking. But once you wake up and try to get out of bed you'll still trip, because your laces are still knotted together. Can someone explain to me why this isn't the case for actual persister/antibiotic relations?

But Charon; that's exactly my point. Why would NASA have published when they did, in a way which even I admit makes the evidence seem circumstantial at best, when they could have easily proved it beyond questionable doubt using mass spectroscopy? Probably in less than a day, I might add? They must have known that a claim this groundbreaking would be highly controversial, and yet they didn't have the sense that an undergrad has to verify it first? The only explanations I can think of off-hand are; either they're idiots, or they were up to something. The fact that they hailed this as a breakthrough in the field of Astrobiology and peaked the whole planet's interest tends to suggest the latter.

OK, I'm pretty sure many of you have heard about the bacteria discovered by NASA which is allegedly able to incorporate arsenic into its DNA in place of phosphorous. I cannot for the life of me understand why this claim is proving so difficult to prove or disprove. I mean I've got a Biotechnology diploma from college and am currently working on my Undergrad in Microbiology at the University of Guelph, so I know about various DNA-probing techniques. However it strikes me that the easiest method to definitively prove (or disprove) that the bacterium incorporates arsenic into its DNA would be to grow a sample of the bacterium in an environment starved of phosphorous and rich in arsenic; and also another sample of the bacterium in ordinary phosphorous-rich medium with no arsenic as a control. Then isolate and purify the DNA of both samples, and then run both of them through a mass spec to see whether its DNA has a peak corresponding to arsenic. Any college or university lab could run this experiment, so why the heck is there so much controversy over this bacterium? Am I overlooking some fundamental problem here?

Swansont, what you just said was implicit in how I worded my question, what I need is why? Why are hollow bones more resistant to torsional strain than solid bones would be? Why would it be easier to twist a solid bone than it would be to twist a hollow bone?

Let's say we have two rods/bones/whatever, that are the same length and mass. And let's say that one of the rods is solid and the other one is hollow. Can someone explain to me why it is that it's easier to twist (i.e. shear forces) the solid rod than it is the hollow one? That seems completely counter-intuitive. And also, just correct me if I am mistaken here; since the solid one is easier to twist, that would also mean that its angle of shear (i.e. θ) would be greater than the θ of the hollow rod, right? This concept is driving me mad, someone please help me.

Does anyone know whether or not the skulls of predators such as lions or bears are much thicker than those of humans? For example; could a lion or a bear survive a well-placed blow to the head from an aluminum baseball bat? I know such a bat could crush a human skull like a watermelon, but would the same apply to most predators? Assuming you could avoid the claws, could you kill or at least incapacitate a lion or grizzly with a bat?

I'm just curious; am I the only one who finds the World Trade Center bombing more than a little suspicious? Now I'm not some crazy conspiracy nut job, but I've always thought that the whole situation with 9/11 was suspicious to the extreme. First of all, the fact that in this day and age nobody realized what was going on with the planes until it was too late; even though the flight paths of every airplane are supposed to be carefully monitored, seems to be highly unlikely. Second, as I understand it, the planes hit the towers near the top, which means that the fire was "mostly" localized to the upper floors (and let's not forget that the sprinkler system in BOTH building just conveniently malfunctioned). And finally; how is it possible for not just one, but both buildings to collapse in the manner that they did just from having a plane crash into them? I mean the videos clearly showed both buildings collapsing within minutes of each other, they plummeted straight down at terminal velocity, there were supposedly explosions heard immediately before they collapsed, and most suspicious of all (if this is true) is that there were supposedly sections of of liquefied steel beams that were found; there's no way in hell ordinary fire could liquefy steel, maybe weaken it, but not liquefy it. Now admittedly I'm no expert in building fires, but if I'm not mistaken, there have been instances of skyscrapers being completely engulfed in flames from bottom to top, and they didn't collapse. And then of course, some of the so-called terrorists behind the "attack" were supposedly found to be alive and well, being just ordinary citizens, wondering what the hell the US was talking about tagging them as suicide bombers. Believe me guys, I'm not a conspiracy theorist; I'm an educated university student. Does no one else even find it remotely suspicious?

I've always wondered how any person could bear to breathe oxygenated perfluorocarbons. I mean sure, as long as the liquid oxygenates the lungs it would keep you alive, but I would think it is an extremely traumatic experience for whoever does it; both physically and mentally. But besides the fact that I very much doubt that a person could acclimatise as quickly as in the movie "The Abyss", how would they keep from swallowing the liquid? Swallowing is an unconscious action for the most part; are perfluorocarbons safe to swallow? And I'm just curious; has anyone other than deep sea divers breathed this stuff before? Dan Brown's new book "The Lost Symbol" claims that there are facilities which allow people to experience this, basically like a sensory-deprivation tank; is this true? Or is it strictly a navy technology at this point?

I've taken several courses on microscopy and I was just wondering why it is that nobody has tried to make a microscope that uses gamma rays? If I'm not mistaken such a microscope would theoretically give much higher resolution and magnification than even an electron microscope, because the wavelength of an electron dwarfs the wavelength of a gamma ray (ie. gamma rays have much shorter wavelengths than electrons do). I mean I know you wouldn't be able to use it to study living organisms, but in principle why couldn't we build one?

I was just wondering if it would be a good idea to autoclave a bottle of ether; I need it sterile for a Virology experiment. Would it work or would the autoclave cause the ether to evaporate since it is volatile? I need to know soon because I don't want to autoclave the bottle of ether only to come back and find that it all evaporated; of course I could just have the lid on tightly to prevent evaporation. Can someone give me advice on how I should proceed?

I've got a friend who has a sonicator/de-gasser, whatever you want to call it in his house. He told me that he would like to see what would happen if he sonicated an un-opened bottle of champagne; I need to know if that would be dangerous? I mean it would obviously make a huge mess, but would there be any actual danger in doing that?

Does anybody know what the host range is for filoviruses (i.e. Ebola and Marburg)? I mean I known that they can infect most if not all types of mammals as well as several species of birds, but I can't find the actual host range anywhere. Any help here would be appreciated.

Who's to say that it can't happen? Just because it doesn't happen on Earth doesn't mean that it is impossible.

Does anyone know whether or not the levitating boulders on Pandora is realistic? I mean I know that at the very least the science behind it is sound; superconducting material levitating in the presence of strong electromagnetic fields is a well known phenomenon called the Meissner effect. So since "Unobtainium" is both a room-temperature superconductor and gives off strong magnetic fields, theoretically it would levitate; but could the Meissner effect really cause whole boulders to levitate like that?

OK, it seems I must be more direct; could a great white shark survive being bitten full in the face by a 23 foot saltwater crocodile? That's all I want to know.

Thank you Mokele; that tirade was very enlightening, but you didn't answer my question. And for your information saltwater crocodiles have been seen in the ocean and even with shark remains in their stomachs.

I was recently watching an episode of Animal Face-off involving a saltwater crocodile vs a great white shark; now I'm not a PhD zoologist, but can someone tell me whether or not this fight is at all realistic? I mean I know that great whites are very skilled hunters, as are saltwater crocodiles, but would these two animals even dare go after each other in the wild? I always thought that unless they are defending their young, predators usually avoid attacking other predators that are the same size as they are. And if they did, is there anyway that the shark would even survive that final bite from the crocodile (the two go straight at each other and the croc bites the shark with all its strength straight between the shark's top jaw; ie the crocodile's lower jaw was pressed to the inside of the sharks upper jaw, and the crocodile's upper jaw was pressed against the outside of the shark's upper jaw). Or want to continue the fight after having its fin torn off by the crocodile? This is an entertaining show, but I can't believe that a shark would possibly want to continue fighting after taking the beating that it did; not to mention the fact that with only one fin the shark would have a hard time swimming straightly. Any thoughts? Merry christmas.

Oh I think I get it now; the reason that you run both a transformation control with both the phosphatased and unphosphatased vector is so that you will be able to tell whether or not the transformation worked the way it was supposed to when you do the actual transformation of the vector plus your insert. Assuming that no self-ligation occurred, then the number of colonies for the (let's call it the unknown, for lack of a better term) should be roughly the same as the control where the vector was treated with alkaline phosphatase, in which case you'll know if the cloning procedure worked properly. On the other hand, if there was self-ligating, then the unknown would have the same (roughly) number of colonies as the control that was not treated with alkaline phosphatase, which would indicate that the cloning procedure was not very efficient. Am I at least on the right track? Merged post follows: Consecutive posts mergedAnd just to take that logic a bit further, that's also why the uncut plasmid would have the most colonies of the three controls; because it would essentially be the same as the self-ligated plasmids in terms of size. So it would have more colonies than the unphosphatased (control b) because b would be a mixture of both self-ligated and inserted plasmids; so since the transformation rate is lower for the plasmids with the insert, there wouldn't be as many colonies in control b as in control a.

But wouldn't the number of colonies be greater in the unphosphatased vector? Since it is the selectable marker, not the insert that makes the plasmid ampicillin resistant, I would think that if anything, unphosphatased vector would stand a better chance of making it inside the cells because the vectors which self-ligated would not contain the insert and would therefore be smaller than the ones that did. If I'm overlooking something obvious it's only because when we actually did this experiment the only control we actually used was the uncut plasmid; I didn't even know what alkaline phosphatase was until some time after the experiment was finished. I'm not being lazy, CharonY. We just haven't been taught this stuff before; or if we have it wasn't in any great detail.

I guess the purpose of dephosphorylation is to ensure that the DNA ligase only ligates the foreign DNA inserts into the cut vectors rather than simply undoing the actions of the restriction enzymes by re-ligating the two ends of the cut vectors together; since the inserts would still have their phosphates attached, but the cut ends of the vectors wouldn't. But I'm still drawing a blank as to what the point of the b control is.

Well I know that the phosphatase removes the 5' phosphates from the strands to prevent them from self-ligating to themselves; but wouldn't that also prevent the insert from being ligated into the plasmid at a later time? As for b, the only thing I can think of is that it would be used to check the frequency of self-ligation; but I don't see what good that would do. Merged post follows: Consecutive posts mergedAnd I meant to say "transformation frequency" not efficiency; since we could use the number of transformants to determine what percent of the total number of cells plated took in the plasmid (only they could survive on the antibiotic media).

I really need help with this question; my teacher told us that he is not going to be collecting these questions but that they might show up on the final exam next week; and I was not in class when we took it up due to my previous class (which was an Immunology lab where we were doing an ELISA assay, so it wasn't my fault) running late. The question is this; What is the purpose of the following transformation controls in the construction of Recombinant plasmids? a) Uncut plasmid b) Ligation of cut vector that hasn’t been phosphatased. c) Ligation of cut, phosphatased vector. I'm pretty sure that the uncut plasmid is used so that we can calculate the efficiency of transformation, but the other two have me stumped. Any help would be greatly appreciated. And like I said; this is just exam review, not an assignment

I just finished reading a book where one of the characters was born without any eyes; no lids, sockets, etc. It got me wondering what it would be like to not have any eyes. What would that person "see" (for complete lack of a better term)? Normally a blind person would just see blackness, but if you actually didn't have eyes at all, you couldn't even see darkness; you couldn't even "see" nothing. This is probably something that only someone in that situation would know.