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Dude96
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A biology question
#8448772 - 05/26/08 09:57 PM (15 years, 11 months ago) |
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Completely random if theres any biology geeks out therelike myself... the other day my prof posed a question to the class asking the following.
If theres a bacteria residing within one's stomach which is responsible for causing stomach ulcers and you were hired to create a bacteria that could kill it, from a simple, harmless streptococcus bacteria, its species is unimportant. What mutations would you force this bacteria to undergo?
I'm just interested in your thoughts, i'll post mine if anyones actually interested...I just thought it was kinda neat due to the differnt ideas people came up with.
(no, taking an antibiotic is not an option =P)
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zouden
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Re: A biology question [Re: Dude96]
#8449702 - 05/27/08 06:22 AM (15 years, 11 months ago) |
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I'm not sure I fully understand the question. But I won't let that stop me posting 
I'm thinking it's a two-part problem.
1. It would need to survive in the stomach long enough to kill the ulcer-causing bacteria but I don't think we'd really want it to thrive, or even reproduce in the stomach. Hmm. How long can streptococcus survive at low pH? How do you increase that survival? Maybe it's not necessary?
2. Secrete an antibiotic. That shouldn't be too hard giving that most antibiotics come from streptococcus species. Or is that streptomycetes?
The first option could be done randomly (aka directed evolution), the second could be done with recombinant DNA. Bah, my answer is hopeless. What's yours?
-------------------- I know... that just the smallest part of the world belongs to me You know... I'm not a blind man but truth is the hardest thing to see
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Seuss
Error: divide byzero



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Re: A biology question [Re: Dude96]
#8450290 - 05/27/08 11:40 AM (15 years, 11 months ago) |
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I'd start with a bacteriophage... they are some of the most simple 'organisms' to work with and seem well suited for the task at hand.
-------------------- Just another spore in the wind.
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Dude96
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Re: A biology question [Re: Seuss]
#8450997 - 05/27/08 03:22 PM (15 years, 11 months ago) |
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=O people actually are interested, or at least bored enough to post! =D woot!
Well what you say is completely correct, biggest problem with most peoples answer was they assumed it would be able to survive in the stomach with ease. Another problem was many people said remove acidophile DNA from an archaebacteria and through transformation allow your bacteria to gain these traits...but to my knowledge bacteria are restricted from exchanging dna with archaebacteria due to biochemical differences? So you'd just need a bacteria that can survive in these conditions, through transformation give its acidic survivability to your test/to be mutated bacteria.
I had then said, as transformation is generally easiest to get the results you desire to use it again to imbed several recessive 'weaknesses' which inhibit the bacteria from surviving at all in even moderate pH, however due to the dominant acidophile trait they would survive. Yet when conjugating and randomly transferring information with the bacteria in your stomach, over time the recessive traits would be implanted in the bad bacteria, killing them.
And yea, it was pretty much assumed we had something at least similar to a bacteriophage to bend to our purpose..otherwise i'd have prolly responded along the lines of "Arguuh...durp?"
-------------------- "We cross our bridges when we come to them and burn them behind us, with nothing to show for our progress except a memory of the smell of smoke, and a presumption that our eyes once watered." -Tom Stoppard "He who makes a beast out of himself gets rid of the pain of being a man." -Samuel Johnson I will be a cancer upon you, ravaging all that you love and sundering your beliefs. Then, and only then, once you have fallen so far and are but a shell of that which you once were, I will grant you your every dream. Only to crush them all before your eyes. You doubted my willpower, you abused my generosity, and now you will recognize my cruelty. -Anonymous
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johnm214



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Re: A biology question [Re: Dude96]
#8451286 - 05/27/08 04:47 PM (15 years, 11 months ago) |
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Quote:
Dude96 said: =O people actually are interested, or at least bored enough to post! =D woot!
Well what you say is completely correct, biggest problem with most peoples answer was they assumed it would be able to survive in the stomach with ease. Another problem was many people said remove acidophile DNA from an archaebacteria and through transformation allow your bacteria to gain these traits...but to my knowledge bacteria are restricted from exchanging dna with archaebacteria due to biochemical differences? So you'd just need a bacteria that can survive in these conditions, through transformation give its acidic survivability to your test/to be mutated bacteria.
I had then said, as transformation is generally easiest to get the results you desire to use it again to imbed several recessive 'weaknesses' which inhibit the bacteria from surviving at all in even moderate pH, however due to the dominant acidophile trait they would survive. Yet when conjugating and randomly transferring information with the bacteria in your stomach, over time the recessive traits would be implanted in the bad bacteria, killing them.
And yea, it was pretty much assumed we had something at least similar to a bacteriophage to bend to our purpose..otherwise i'd have prolly responded along the lines of "Arguuh...durp?"
So that was it? Just pH? Seems like a kinda silly question I guess. Their was no discussion about how to make something that would target the specific species of interest? That's kinda the problem I envisioned, how to make it selective. I wonder why he didn't just ask how to get an acidotolerant strain?
But I gues the question was vague enough that you didn't know what you were targeting, even though I'm only aware of one species that frequents ulcers.
Those kinda question kinda irritate me sometimes.
Profs ask a question that is very broad with a specific answer in mind. And you can spend a shitload of time on answering the broad question and when you get the test back you find that the correct answer was 1/10 of what you wrote and based on all sorts of presupositions not noted in the question :/ This is bilogy profs all the time, especially w/ complicated regulatory functions.
And yeah, I don't know how easy it is to clone acidophillic traits, like you mention. I presume their are a ton of problems w/ that since so much of the genome must be modified to survive at low pH's like the plasma membrane-bound structures that control pH and many if not all of the proteins. You're probably correct that it may be easier to just breed a strain rather than try to find all the neccesary genes to clone and transfer, though I wonder how easy it is to get a common bacterium able to tolerate pH's that low?
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zouden
Neuroscientist



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Re: A biology question [Re: johnm214]
#8451306 - 05/27/08 04:51 PM (15 years, 11 months ago) |
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Quote:
though I wonder how easy it is to get a common bacterium able to tolerate pH's that low?
Mmm... here's something I hadn't thought of: Helicobacter pylori is not an archaea
-------------------- I know... that just the smallest part of the world belongs to me You know... I'm not a blind man but truth is the hardest thing to see
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Dude96
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Re: A biology question [Re: zouden]
#8451458 - 05/27/08 05:27 PM (15 years, 11 months ago) |
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Yea, it was relatively broad, I don't have the test on me..once I get it back i'll go into more specific detail, the ulcer causing bacteria was a pseduomonus (sp?) variant, and what we were given was something which grew in a streptococcus type colony.
And yea...that bacterium modification thing is interesting, I imagine if you took just normal bacteria, subjected it to slight acidity..like 3.5 or so, then 3, then 2.5 etc, over time you could probably create bacteria with acid resistance. And yea, zouden, I wasn't sure of a specific strain but I knew there had to be some non-archae bacteria with acidophilic traits.
This is completely random, but with relation to mushrooms, I was considering making something of a clone mushroom garden from the species which grow son my lawn in this little built up garden type spot I have in my backyard but havn't used in years...would they thrive or die? It'd be pretty much just natural outdoor cultivation with the advantage of constant nutritious material to decompose (Interested in seeing how long it would take an apple placed in the center of this mushroom garden (I'm envisioning hundreds of closely clustered mushrooms here xD) to decompose, vs if it was left on mere dirt.
Any thoughts?
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heilfire
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Re: A biology question [Re: Dude96]
#8452257 - 05/27/08 08:21 PM (15 years, 11 months ago) |
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i would rather make a bacteriophage. no idea about original question.
-------------------- You swallow propaganda like a birth control pill, Sellin' your soul to the eye on the back of the dollar bill
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wisp

Registered: 04/13/08
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Re: A biology question [Re: heilfire]
#8454035 - 05/28/08 05:48 AM (15 years, 11 months ago) |
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I believe that many of the "primitive" bateria are thermacidophiles right? So working with those to begin with was seems like a logical step. Or even working with other bacteria that inhabit the stomachs of other animals. Then as it has already been said, genetically modify it to express your desired traits.
Your mushroom garden sounds like it would need a bit of planning.
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Dude96
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Re: A biology question [Re: wisp]
#8455712 - 05/28/08 03:04 PM (15 years, 11 months ago) |
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Yea, i'm just not really sure what to do with it...completely new to the entire mushroom thing, any off hand thoughts or tips?
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