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Author Topic:   Genetic variability in a bacteria species
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 8 of 36 (580163)
09-07-2010 11:58 PM
Reply to: Message 7 by ICANT
09-07-2010 11:56 PM


Re: Bacteria
Anybody game to clear my misconceptions up?
I've done so in the other thread.

This message is a reply to:
 Message 7 by ICANT, posted 09-07-2010 11:56 PM ICANT has replied

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 Message 10 by ICANT, posted 09-08-2010 12:40 AM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 11 of 36 (580174)
09-08-2010 1:07 AM
Reply to: Message 10 by ICANT
09-08-2010 12:40 AM


Re: Bacteria
The experiment was started with a lot of bacteria in the beginning.
Yes. All clones of a single individual, called the "founding individual."
Then the colonies were stamped and stamped on a plate with penicillin on it.
Right, that's "replica plating." A sterilized piece of velveteen acts as a huge "paintbrush", picking up individuals from each colony on the plate and then stamping them down in the exact same relative position on the replica plate.
That enables a researcher to positively identify replica colonies with their original culture.
The immunity had to exist in their DNA and was not acquired during the experiment.
The antibiotic resistance was acquired during the initial culture - the step you describe as "they were allowed to grow into several different colonies." We know that this is true because of the proportion of colonies that survived vs. those that died. If no colonies survived then we would have known that none of the bacteria had developed any resistance. If the bacteria had an inherent resistance they inherited from the founding individual then all colonies would have survived on both plates, because the vast majority of organisms would have been resistance-positive.
We observed neither of those. We observed that some colonies replicated and some did not - thus proving that resistance was an acquired trait, acquired during the "log phase" of the experiment (the initial culture, when bacterial growth is exponential) by a mechanism other than inheritance, which is so unlikely that across tens of billions of individuals only 20-30 actually developed the trait.
This proves that random mutation was the source of the acquired resistance. The mutation in question occurred during the initial culture of the original plate, as proven by the fact that the same colonies on both plates are resistant.
Edited by crashfrog, : No reason given.

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 Message 10 by ICANT, posted 09-08-2010 12:40 AM ICANT has replied

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 Message 17 by ICANT, posted 09-08-2010 4:20 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 20 of 36 (580336)
09-08-2010 6:15 PM
Reply to: Message 17 by ICANT
09-08-2010 4:20 PM


Re: Bacteria
Where does the statement found Here say what you said?
You understand that this is just a summary of the Lederberg's experiment, right? That this doesn't even begin to describe their actual techniques or results? That the images are cartoons, not actual science data?
This is a summary that would be appropriate for 8th graders, roughly, so naturally it's not a complete description of their actual experiment. If you want to know what they actually did you need to go to the actual paper the Lederberg's wrote, which is this:
Just a moment...
It's no mark against you that you didn't go out looking for other sources - the one you found is a good place to start - but a lot of these questions you have can be addressed by going to the primary source, which is going to be the scientific literature that the Lederbergs had published. (It's an interesting and very accessible paper - I hadn't realized the Lederbergs invented replica plating.)
To answer your question - I know that's what they did because that's the standard technique for setting up culture - you quadrant streak an agar plate to produce isolated colonies:
Do you see the isolated colonies up at the top? By the pattern we know that those colonies each formed from an individual cell. If you take a sample of one of those colonies and transfer to liquid media, you have a soup of bacteria that are clones of each other. That soup is what the Lederbergs used, highly diluted, to inoculate their original plates.
I don't think that 1. means 1 bacteria.
Each colony is the result of a single bacterium. That's how they grow. If they produced a plate with 30 colonies on it, they added 30 cells.
That's so reliable that it's an established way to find out how many bacteria are in a liquid culture - take a sample, dilute it about a hundred-thousand-fold, spread it on a plate, and count how many colonies you get after a day of incubation. Each visible colony indicates the presence of a single cell; multiply it by the dilution factor and that's how many cells are in your original sample.
It nowhere says all these bacteria was from a single bacteria.
It's a summary of the experiment. It's not going to say everything. You need to read the original paper.
Since the so called single individual that is your founding individual was not exposed to penecilin you have no way of knowing whether that individual had an immunity to penecilin.
Certainly the single individual was exposed to the streptomycin (what they actually used), as were all its descendants. If the individual was resistant to the antibiotic then all of its clonal descendents would have been.
Remember bacteria don't breed like people; there's nothing that "skips a generation." They don't obey the Mendelian genetics you may have learned in school because they have only a single chromosome, and therefore only a single allele per trait.
Yes that is obvious as all did not survive when exposed to penecilin.
Thus proving that antibiotic resistance was the acquired trait.
Well no there has been no proof that the trait was acquired during the "log phase".
The experiment is the proof, ICANT.
Either the original single individuall bacteria as you put forth had to have no immunity and some of its offspring gained immunity or the original single individual bacteria posessed immunity and then some of the offspring lost that immunity and their offspring did not have the immunity.
If resistance was the widespread trait and loss of resistance the new thing, then each colony would have been primarily comprised of individuals who had retained the resistance, and therefore every single colony would have replicated on antibiotic media.
That's not what happened. That proves that lack of resistance was the widespread trait and that resistance to the antibiotic was the new, acquired trait - acquired by random mutation.
The proof of this is that some colonies replicated on antibiotic media and some did not, and that the same colonies died when exposed to antibiotic on the original plate.
My question then is if the immunity was not in the DNA how did any bacteria survive until today?
They survived by not living somewhere where they were exposed to streptomycin. Quite simple, actually. Esterichia coli lives primarily in the gut of animals - see, that's what "coli" in the name means, "colon" - which is a place where Streptomyces griseus, the bacterium in which streptomycin originally evolved, does not generally reside.
The other possibility is that the original individual had immunity and some of the offspring and their offspring did not receive that immunity due to a bad mutation.
Any particular mutation is very rare, so if the population had been originally resistance and susceptibility was the acquired trait, only a very small number of individuals would have lost the resistance to the antibiotic and resistant individuals would have dominated every single colony, which means that we would observe that every colony successfully replicated to antibiotic media.
But they didn't. Some did and others did not. That proves that antibiotic resistance was the acquired trait, not the reverse. Like I've told you three times, now.

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 24 of 36 (580524)
09-09-2010 4:34 PM
Reply to: Message 22 by ICANT
09-09-2010 1:56 PM


Re: Bacteria
Where does this paper mention the experiment that I referenced from Berkeley?
The paper is the experiment you referenced from Berkeley. Are you asking why a paper written in 1952 doesn't reference a website you're looking at in 2010? I trust even you can solve that conundrum.
How many different mutations are possible in bacteria?
There's no way to count, really; the E. coli genome is comprised of 4.6 million base pairs and 4300 genes. Any one of those base pairs could be deleted, duplicated, or substituted, or any number of base pairs could be added at any position on the chromosome. Any one of those genes could be mutated. It's a bit like asking "how many different ways could you insert a typo into Moby Dick."
Because if there is one mutation in 10 billion that survive why would that one mutation be a trait of immunity?
Nobody said that "only one mutation in 10 billion survive". But only one mutation in 10 billion might provide resistance to antibiotic, which is why that bacterium survived and others did not - natural selection.
If mutations are truly random as proposed isn't it possible that there are hundreds of mutations that could arise rather than a mutation of immunity to penecilin?
Yes, absolutely; those mutations probably did arise, but the environment selected for antibiotic resistance not nylon digestion, so the nylon digestive bacteria died when antibiotic was introduced to the plate.
There are people who have immunities that are not active in their offspring but is active in later descendants. Why could that not be possible in bacteria?
People are diploid and bacteria are not. Human beings have two copies each of 23 different chromosomes. Bacteria have only one copy of a single chromosome.
If something's in their DNA, it gets expressed. There's no "skipping a generation" in bacteria, it's not physically possible for that to happen. As I've repeatedly told you bacteria don't follow Mendelian genetics.

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 Message 22 by ICANT, posted 09-09-2010 1:56 PM ICANT has not replied

Replies to this message:
 Message 27 by barbara, posted 09-11-2010 1:54 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 28 of 36 (580844)
09-11-2010 5:27 PM
Reply to: Message 27 by barbara
09-11-2010 1:54 PM


Re: Bacteria
they don't skip generations is confusing to me.
It shouldn't be. Bacteria are haploid organisms - one copy of one chromosome. You're a diploid organism, you have two copies of 23 chromosomes, half from each parent. That's why you're not a clone of either of your parents, you merely share traits with both of them.
But bacteria reproduce clonally, by cell division. There's not really a notion of "generations" in bacteria because they're constantly dividing and doubling, and when a single bacterium undergoes fission, what you have is two completely identical individuals where one used to be. Which one was the "first" and which one is of the "next generation"? It's impossible to say. Both of those bacteria are going to continue to double themselves at the same rate.
So we don't really talk about "generations" of bacteria, we talk about how long it takes for a population to double in size. In something like E. coli that can be about 20-40 minutes.
Isn't each row replicated considered another generation of bacteria?
No. There's not really anything that can be considered a "generation" of bacteria because bacteria can go on doubling and doubling until they run out of a nutrient.

This message is a reply to:
 Message 27 by barbara, posted 09-11-2010 1:54 PM barbara has replied

Replies to this message:
 Message 29 by barbara, posted 09-11-2010 9:17 PM crashfrog has replied
 Message 31 by Minnemooseus, posted 09-11-2010 9:52 PM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 30 of 36 (580866)
09-11-2010 9:27 PM
Reply to: Message 29 by barbara
09-11-2010 9:17 PM


Re: Bacteria
I understand that during the lag phase that the cell is actively metabolizing for cell division but it also does this again in the stationary phase.
No, that's exactly wrong. The bacteria metabolize for growth during the log phase, when their population expands at an exponential rate (and can therefore be logarithmically modeled.) During lag phase the bacteria are upregulating and downregulating appropriate metabolic pathways in response to the conditions of their new environments; it lasts about 20 minutes because that's how long protein translation takes, start to finish.
In stationary phase the bacteria have exhausted some nutrient and are no longer growing exponentially; they're engaging in enough cell division to replace individuals who die, and they're also expressing secondary metabolic activity (that's not really relevant to what we're talking about, but it's in stationary phase that bacteria produce their own antibiotics and other secondary metabolites.)
What stage must be completed before samples are taken to determine antibiotic resistance?
To determine resistance, bacteria are incubated on antibiotic-positive media. If colonies are present, that indicates resistance. If colonies are absent then log phase never even occurred - the bacteria didn't live long enough.
The presence of colonies means that the bacteria underwent a log phase. Otherwise there wouldn't be enough individuals to have colonies.

This message is a reply to:
 Message 29 by barbara, posted 09-11-2010 9:17 PM barbara has replied

Replies to this message:
 Message 33 by barbara, posted 09-12-2010 3:20 AM crashfrog has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 32 of 36 (580870)
09-11-2010 10:01 PM
Reply to: Message 31 by Minnemooseus
09-11-2010 9:52 PM


Re: What is a bacteria generation?
Would the population doubling period be what is called a generation?
You could probably say that. It wouldn't be any less accurate than applying the term "species" to bacteria. (How do you define a "reproductive community" in an asexual species?)

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 Message 31 by Minnemooseus, posted 09-11-2010 9:52 PM Minnemooseus has seen this message but not replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 34 of 36 (580929)
09-12-2010 12:43 PM
Reply to: Message 33 by barbara
09-12-2010 3:20 AM


Re: Bacteria
Ok, so what was your question?

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