Comments for Microbial Population Biology http://micropopbio.org Open access blog network of courses focused on the population biology of bacteria and viruses Tue, 06 Jan 2009 10:58:16 +0000 http://wordpress.org/?v=2.5.1 Comment on Summary of your presentations on community interactions in space and/or time by Vaughn http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-30 Vaughn Fri, 25 Apr 2008 18:03:13 +0000 http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-30 Sam -- really good addition and an important point. VC Sam — really good addition and an important point.

VC

]]> Comment on Summary of your presentations on community interactions in space and/or time by samantha http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-29 samantha Tue, 22 Apr 2008 05:10:43 +0000 http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-29 Just a small additive to the blurb Vaughn wrote: There is the "frozen state" Quasi-equilibrium that he mentions, but there is also a Hyperimmunity Quasi-equilibrium. Basically in this situation the patches (cubes of the grid) survive long enough to collect more toxin + immunity genes by mutation which leads to multiple toxicity. Once there is an accumulation of these toxin + immunity genes the loss of toxin-producing genes and the maitanence of the resistance becames advantagous due to a lower metabolic cost. Just a small additive to the blurb Vaughn wrote:

There is the “frozen state” Quasi-equilibrium that he mentions, but there is also a Hyperimmunity Quasi-equilibrium. Basically in this situation the patches (cubes of the grid) survive long enough to collect more toxin + immunity genes by mutation which leads to multiple toxicity. Once there is an accumulation of these toxin + immunity genes the loss of toxin-producing genes and the maitanence of the resistance becames advantagous due to a lower metabolic cost.

]]> Comment on Summary of your presentations on community interactions in space and/or time by Vaughn http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-28 Vaughn Tue, 22 Apr 2008 02:58:03 +0000 http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-28 Thanks Laura for a clear summary, and I agree with the problems of re-seeding populations to maintain diversity. Sometimes models must be forced to maintain ecology and disallow evolution. Thanks Laura for a clear summary, and I agree with the problems of re-seeding populations to maintain diversity. Sometimes models must be forced to maintain ecology and disallow evolution.

]]> Comment on Summary of your presentations on community interactions in space and/or time by laura http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-27 laura Mon, 21 Apr 2008 04:39:12 +0000 http://micropopbio.org/blog/2008/04/17/summary-of-your-presentations-on-community-interactions-in-space-andor-time/#comment-27 “The Evolution of Restraint in Bacterial Biofilms Under Nontransitive Competition” Notes In this paper, the authors investigate evolution within toxic bacterial biofilms using a computer simulation representing a nontransitive (rock-paper-scissors) community of 3 E. coli populations (colecin producer, colecin sensitive, colecin resistor) Using their simulations, they explore how factors known to vary among isolates (such as cost of resistance and level of toxicity) evolve in space. They also explored cases where the level of toxicity is a function of the cost of it. These investigations were done to shed light on how evolutionary changes in the nature of these interactions influenced the behavior of the bacterial community. Simulation -Virtual bacteria ‘embedded’ in a square lattice of L x L nodes, individually assigned a state (S:sensitive, P:producer, R:resistant, E:Empty node) -Randomly nodes were selected and its state changed due to probability (neighborhood is a key factor in this probability) -Neighborhood: the set of nodes around the focal node (one being changed) that influences the probability of change -Small neighborhood=natal dispersal, competition for space, toxicity effects spatially restricted -Large neighborhood=same interactions over greater distances -Local neighborhood=8 lattice points surrounding focal node, structured community Findings: -There is restraint in the average death rate of R guys in structured communities with all three phenotypes present, death rate does not evolve to its minimum, resistant population evolves competitive restraint *My complaint here is that they ‘re-seeded’ the populations to keep all three strains, otherwise 1 or 2 were quickly lost. This is kind of stacking the deck to get the outcome they want -They also found that significantly restrained growth rate evolves in the complete structured community only. -“In a structured environment, toxicity has the effect of “clearing” sensitive cells and allowing (P cells)…prime access to the cleared real estate.” Again, they re-seeded. R cells in this instance evolved toxicity to a high level, but not their maximum value this = restraint TAKE HOME MESSAGE: -In structured communities with all three strains present, in a nontransitive dynamic, the strains don’t evolve the best competitive strategy. They are restrained. -They argue that selection favors “survival of the weaker.” The weakest die early and the strongest “improve themselves to death.” Restraint allows the middle guy to live longer and is an evolutionary stable strategy. “The Evolution of Restraint in Bacterial Biofilms Under Nontransitive Competition”
Notes
In this paper, the authors investigate evolution within toxic bacterial biofilms using a computer simulation representing a nontransitive (rock-paper-scissors) community of 3 E. coli populations (colecin producer, colecin sensitive, colecin resistor)

Using their simulations, they explore how factors known to vary among isolates (such as cost of resistance and level of toxicity) evolve in space. They also explored cases where the level of toxicity is a function of the cost of it. These investigations were done to shed light on how evolutionary changes in the nature of these interactions influenced the behavior of the bacterial community.

Simulation
-Virtual bacteria ‘embedded’ in a square lattice of L x L nodes, individually assigned a state (S:sensitive, P:producer, R:resistant, E:Empty node)
-Randomly nodes were selected and its state changed due to probability (neighborhood is a key factor in this probability)
-Neighborhood: the set of nodes around the focal node (one being changed) that influences the probability of change
-Small neighborhood=natal dispersal, competition for space, toxicity effects spatially restricted
-Large neighborhood=same interactions over greater distances
-Local neighborhood=8 lattice points surrounding focal node, structured community

Findings:
-There is restraint in the average death rate of R guys in structured communities with all three phenotypes present, death rate does not evolve to its minimum, resistant population evolves competitive restraint
*My complaint here is that they ‘re-seeded’ the populations to keep all three strains, otherwise 1 or 2 were quickly lost. This is kind of stacking the deck to get the outcome they want
-They also found that significantly restrained growth rate evolves in the complete structured community only.
-“In a structured environment, toxicity has the effect of “clearing” sensitive cells and allowing (P cells)…prime access to the cleared real estate.” Again, they re-seeded. R cells in this instance evolved toxicity to a high level, but not their maximum value
this = restraint

TAKE HOME MESSAGE:
-In structured communities with all three strains present, in a nontransitive dynamic, the strains don’t evolve the best competitive strategy. They are restrained.
-They argue that selection favors “survival of the weaker.” The weakest die early and the strongest “improve themselves to death.”
Restraint allows the middle guy to live longer and is an evolutionary stable strategy.

]]> Comment on Brucella ecology and host specificity by brucellosis http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-26 brucellosis Fri, 14 Mar 2008 22:11:14 +0000 http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-26 [...] ...State takes over wolf management in two weeks Jackson Hole Star-Tribunewww.casperstartribune.netBrucella ecology and host specificityBrucella ecology and host specificity Posted by Vaughn on February 29, 2008 Hope you all enjoyed the [...] [...] …State takes over wolf management in two weeks Jackson Hole Star-Tribunewww.casperstartribune.netBrucella ecology and host specificityBrucella ecology and host specificity Posted by Vaughn on February 29, 2008 Hope you all enjoyed the [...]

]]> Comment on Brucella ecology and host specificity by samantha http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-25 samantha Thu, 06 Mar 2008 05:23:00 +0000 http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-25 I thought the presentation was really interesting too. At times I had trouble hearing her. She would kind of trail off at the end of sentences, but I posted something on my blog so check it out. I thought the presentation was really interesting too. At times I had trouble hearing her. She would kind of trail off at the end of sentences, but I posted something on my blog so check it out.

]]> Comment on Brucella ecology and host specificity by david http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-24 david Thu, 06 Mar 2008 03:58:40 +0000 http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-24 The presentation had a lot of very fascinating information. I agree with Laura that it would have been good if she had gone into less detail on brucella in general. It was interesting, but it meant she had less time to talk about the relation to marine species. That said, I am very happy to know it has been virtually wiped out in cows in the United States. The marine species were very interesting. At first I thought it was strange that it was not harmful to the vast majority of seals, yet it was very damaging to other sea life like dolphins. I can't think of any great examples about bacteria right now, but the HIV virus is horrible in humans, but SIV in monkeys is not. http://news.nationalgeographic.com/news/2003/06/0612_030612_hivvirusjump.html I also thought the possible connection to the worm was interesting. On a side note I am also very glad it does not infect people easily. The presentation had a lot of very fascinating information. I agree with Laura that it would have been good if she had gone into less detail on brucella in general. It was interesting, but it meant she had less time to talk about the relation to marine species. That said, I am very happy to know it has been virtually wiped out in cows in the United States.
The marine species were very interesting. At first I thought it was strange that it was not harmful to the vast majority of seals, yet it was very damaging to other sea life like dolphins. I can’t think of any great examples about bacteria right now, but the HIV virus is horrible in humans, but SIV in monkeys is not.
http://news.nationalgeographic.com/news/2003/06/0612_030612_hivvirusjump.html
I also thought the possible connection to the worm was interesting.
On a side note I am also very glad it does not infect people easily.

]]> Comment on Brucella ecology and host specificity by laura http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-23 laura Mon, 03 Mar 2008 23:01:50 +0000 http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-23 I thought the presentation was interesting; definitely relevant to our species question debates, since marine Brucella species names are still being debated. I wished the presenter would get down to the nitty gritty instead of going into so much intro about Brucella in general. I thought the presentation was interesting; definitely relevant to our species question debates, since marine Brucella species names are still being debated. I wished the presenter would get down to the nitty gritty instead of going into so much intro about Brucella in general.

]]> Comment on Brucella ecology and host specificity by dan http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-22 dan Mon, 03 Mar 2008 18:38:37 +0000 http://micropopbio.org/blog/2008/02/29/brucella-ecology-and-host-specificity/#comment-22 I definitely thought the seminar was intriguing. It struck me as quite appropriate when Inga mentioned the thin veil barely separating Brucella species. I'm glad the bacterium doesn't infect humans nearly as easily as livestock. <i>B. abortus</i> seems quite scary. Poor cows. I definitely thought the seminar was intriguing. It struck me as quite appropriate when Inga mentioned the thin veil barely separating Brucella species.

I’m glad the bacterium doesn’t infect humans nearly as easily as livestock. B. abortus seems quite scary. Poor cows.

]]> Comment on Check out “The Loom” blog site by sanjuro http://micropopbio.org/blog/2008/02/11/check-out-the-loom-blog-site/#comment-21 sanjuro Tue, 19 Feb 2008 03:50:15 +0000 http://micropopbio.org/blog/2008/02/11/check-out-the-loom-blog-site/#comment-21 Forget about the tree, check out the science tatoos! Forget about the tree, check out the science tatoos!

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