Talk:CH391L/S13/CleanGenomes - Revision history

Kevin Baldridge: /* Multicopy Genes */

Kevin Baldridge — Mon, 18 Feb 2013 20:12:36 GMT

Multicopy Genes

←Older revision		Revision as of 20:12, 18 February 2013
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	'''[[User:Kevin Baldridge\|Kevin Baldridge]] 14:05, 14 February 2013 (EST)''':One of the things mentioned in the introduction is duplicate genes being superfluous. I wonder what the cutoff for minimal repetition of a gene, for example ribosomal RNA genes. If you only had one copy, I find it surprising that the cell would be able to be viable/healthy given the large amount of ribosomal RNA that is produced in exponential phase for cell growth.		'''[[User:Kevin Baldridge\|Kevin Baldridge]] 14:05, 14 February 2013 (EST)''':One of the things mentioned in the introduction is duplicate genes being superfluous. I wonder what the cutoff for minimal repetition of a gene, for example ribosomal RNA genes. If you only had one copy, I find it surprising that the cell would be able to be viable/healthy given the large amount of ribosomal RNA that is produced in exponential phase for cell growth.
	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:07, 17 February 2013 (EST)''':''E. coli'' can survive pretty well with [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC93859/ just one ribosomal RNA copy]. You're right that at some point it becomes limiting and there is an [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29826/ overall trend that microbes with greater growth rates have more rrn copies]. One thing we don't usually think about is that there are multiple copies of most genes during exponential growth due to overlapping rounds of genome replication before segregation of daughter cells.		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:07, 17 February 2013 (EST)''':''E. coli'' can survive pretty well with [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC93859/ just one ribosomal RNA copy]. You're right that at some point it becomes limiting and there is an [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29826/ overall trend that microbes with greater growth rates have more rrn copies]. One thing we don't usually think about is that there are multiple copies of most genes during exponential growth due to overlapping rounds of genome replication before segregation of daughter cells.
		+	**'''[[User:Kevin Baldridge\|Kevin Baldridge]] 15:12, 18 February 2013 (EST)''':Along the lines of producing genes as cell division occurs, there was a cool paper that did high throughput screens of phenotypes in multiple gene knockout cells, they did a pretty good analysis of how chromosomal location corresponds with the essentiality of a given gene [http://www.sciencedirect.com/science/article/pii/S0092867410013747 Phenotypic Landscape of a Bacterial Cell]

	== Blattner Group ==		== Blattner Group ==

Evan J. Weaver at 17:16, 18 February 2013

Evan J. Weaver — Mon, 18 Feb 2013 17:16:24 GMT

←Older revision		Revision as of 17:16, 18 February 2013
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	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?
	**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.		**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.
-	*'''[[User:Evan J WeaverIEvan Weaver]] 11:13, 18 February 2013 (EST)''':I was unaware that Blattner had more recent papers on reduced cells. I was referring to the paper that was published in 2002. I ~~was referring to new recombination techniques that~~ have ~~been used in other papers~~.	+	***'''[[User:Evan J WeaverIEvan Weaver]] 11:13, 18 February 2013 (EST)''':I was unaware that Blattner had more recent papers on reduced cells. I was referring to the paper that was published in 2002. I must not have seen his name.

	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:01, 17 February 2013 (EST)''':I think that it is a valid observation that the state of the art has not progressed much since the Blattner genome and Venter's work. Why is that? Have all the cool things been done? I'd say that MDS42 actually is a useful resource, particularly with the refinements that Neil mentions, but I don't really see any papers switching to using this strain. It's a lot easier to keep working with what you know.		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:01, 17 February 2013 (EST)''':I think that it is a valid observation that the state of the art has not progressed much since the Blattner genome and Venter's work. Why is that? Have all the cool things been done? I'd say that MDS42 actually is a useful resource, particularly with the refinements that Neil mentions, but I don't really see any papers switching to using this strain. It's a lot easier to keep working with what you know.

Evan J. Weaver at 17:15, 18 February 2013

Evan J. Weaver — Mon, 18 Feb 2013 17:15:23 GMT

←Older revision		Revision as of 17:15, 18 February 2013
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	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?
	**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.		**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.
		+	*'''[[User:Evan J WeaverIEvan Weaver]] 11:13, 18 February 2013 (EST)''':I was unaware that Blattner had more recent papers on reduced cells. I was referring to the paper that was published in 2002. I was referring to new recombination techniques that have been used in other papers.

	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:01, 17 February 2013 (EST)''':I think that it is a valid observation that the state of the art has not progressed much since the Blattner genome and Venter's work. Why is that? Have all the cool things been done? I'd say that MDS42 actually is a useful resource, particularly with the refinements that Neil mentions, but I don't really see any papers switching to using this strain. It's a lot easier to keep working with what you know.		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:01, 17 February 2013 (EST)''':I think that it is a valid observation that the state of the art has not progressed much since the Blattner genome and Venter's work. Why is that? Have all the cool things been done? I'd say that MDS42 actually is a useful resource, particularly with the refinements that Neil mentions, but I don't really see any papers switching to using this strain. It's a lot easier to keep working with what you know.

Evan J. Weaver at 17:02, 18 February 2013

Evan J. Weaver — Mon, 18 Feb 2013 17:02:45 GMT

←Older revision		Revision as of 17:02, 18 February 2013
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	'''[[User:Max E. Rubinson\|Max E. Rubinson]] 10:34, 14 February 2013 (EST)''': Shouldn't a "clean" or "minimal" genome refer to the minimum set of genes that an organism needs to survive and reproduce ''in a defined environment''?		'''[[User:Max E. Rubinson\|Max E. Rubinson]] 10:34, 14 February 2013 (EST)''': Shouldn't a "clean" or "minimal" genome refer to the minimum set of genes that an organism needs to survive and reproduce ''in a defined environment''?
-	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I'm sorry that I didn't fix this sooner. I've been Internet deprived for the last 1.5 days and I'm just reading everyone's comments. I'm typing this through an iPAD, since the place I'm staying at doesn't have Internet access, so if I make any mistakes let me know. Thanks for bringing this up, totally forgot about it.	+	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': Fixed it.
	*'''[[User:Thomas Wall\|Thomas Wall]] 19:05, 14 February 2013 (EST)''': I believe that is what it is. But in the world of biocatalysts/metabolic engineering you are constantly changing the environment.		*'''[[User:Thomas Wall\|Thomas Wall]] 19:05, 14 February 2013 (EST)''': I believe that is what it is. But in the world of biocatalysts/metabolic engineering you are constantly changing the environment.
	*'''''[[User:Marco Howard \| Marco Howard]] 19:05, 14 February 2013 (EST)''': When working with biocatalysts, do we know the rate constant? If so, we should be able to predict how the environment will change over time. Perhaps we could use Neil's iterative approach to design bacteria that can tolerate these conditions.		*'''''[[User:Marco Howard \| Marco Howard]] 19:05, 14 February 2013 (EST)''': When working with biocatalysts, do we know the rate constant? If so, we should be able to predict how the environment will change over time. Perhaps we could use Neil's iterative approach to design bacteria that can tolerate these conditions.
	'''[[User:Yunle Huang\|Yunle Huang]] 20:20, 14 February 2013 (EST)''': What are some advantages and disadvantages of each of the genome reduction methods?		'''[[User:Yunle Huang\|Yunle Huang]] 20:20, 14 February 2013 (EST)''': What are some advantages and disadvantages of each of the genome reduction methods?
-	*'''[[User:Evan J WeaverIEvan Weaver]] 18:36, 14 February 2013 (CST)''': ~~Oh, advantages are important.~~ The papers I'd read had not listed any advantages compared to other methods, they just said their own methods and then about the cool reduced cell they created. Here's some stuff I thought of. Comparative genomics would find things that gene disruption wouldn't because gene disruption may disrupt a conserved essential gene. All of the 3 first techniques are a roadmap for genome reduction: without them reduction would take longer and be much more expensive.	+	*'''[[User:Evan J WeaverIEvan Weaver]] 18:36, 14 February 2013 (CST)''': The papers I'd read had not listed any advantages compared to other methods, they just said their own methods and then about the cool reduced cell they created. Here's some stuff I thought of. Comparative genomics would find things that gene disruption wouldn't because gene disruption may disrupt a conserved essential gene. All of the 3 first techniques are a roadmap for genome reduction: without them reduction would take longer and be much more expensive.

	==Core and Accessory Genes, Pan-genomes==		==Core and Accessory Genes, Pan-genomes==
Line 33:		Line 33:
	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?
	**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.		**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.
		+
	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:01, 17 February 2013 (EST)''':I think that it is a valid observation that the state of the art has not progressed much since the Blattner genome and Venter's work. Why is that? Have all the cool things been done? I'd say that MDS42 actually is a useful resource, particularly with the refinements that Neil mentions, but I don't really see any papers switching to using this strain. It's a lot easier to keep working with what you know.		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:01, 17 February 2013 (EST)''':I think that it is a valid observation that the state of the art has not progressed much since the Blattner genome and Venter's work. Why is that? Have all the cool things been done? I'd say that MDS42 actually is a useful resource, particularly with the refinements that Neil mentions, but I don't really see any papers switching to using this strain. It's a lot easier to keep working with what you know.

Jeffrey E. Barrick at 16:54, 17 February 2013

Jeffrey E. Barrick — Sun, 17 Feb 2013 16:54:35 GMT

←Older revision		Revision as of 16:54, 17 February 2013
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	*'''[[User:Thomas Wall\|Thomas Wall]] 19:00, 14 February 2013 (EST)''': At this point in biology knowledge that a bottom up approach will be much longer. Figuring out what is causing your problem in a native genome is much easier then trying to figure out what you took out needed to be there (if its truly minimal). I think getting rid of non coding DNA might not be as big of a problem.		*'''[[User:Thomas Wall\|Thomas Wall]] 19:00, 14 February 2013 (EST)''': At this point in biology knowledge that a bottom up approach will be much longer. Figuring out what is causing your problem in a native genome is much easier then trying to figure out what you took out needed to be there (if its truly minimal). I think getting rid of non coding DNA might not be as big of a problem.
	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:10, 17 February 2013 (EST)''':I agree that it's much harder to build something than to selectively lose parts to get adaptation. Should we be thinking about building a '''maximal genome'''? As long as it survived with a ton of new genes, then it would be far more likely to have the potential to evolve useful functions.		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:10, 17 February 2013 (EST)''':I agree that it's much harder to build something than to selectively lose parts to get adaptation. Should we be thinking about building a '''maximal genome'''? As long as it survived with a ton of new genes, then it would be far more likely to have the potential to evolve useful functions.
		+
		+	'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 21:15, 14 February 2013 (EST)''':Given that the fitness effects of a gene can only be stated in the context of a particular genome, isn't the genome reduction method extremely haphazard? Many genes likely fall into families where the removal of one produces no change in viability, but prevent the removal or alteration of other genes.

	==Environmental Dependence ==		==Environmental Dependence ==
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	'''[[User:Yunle Huang\|Yunle Huang]] 20:20, 14 February 2013 (EST)''': What are some advantages and disadvantages of each of the genome reduction methods?		'''[[User:Yunle Huang\|Yunle Huang]] 20:20, 14 February 2013 (EST)''': What are some advantages and disadvantages of each of the genome reduction methods?
	*'''[[User:Evan J WeaverIEvan Weaver]] 18:36, 14 February 2013 (CST)''': Oh, advantages are important. The papers I'd read had not listed any advantages compared to other methods, they just said their own methods and then about the cool reduced cell they created. Here's some stuff I thought of. Comparative genomics would find things that gene disruption wouldn't because gene disruption may disrupt a conserved essential gene. All of the 3 first techniques are a roadmap for genome reduction: without them reduction would take longer and be much more expensive.		*'''[[User:Evan J WeaverIEvan Weaver]] 18:36, 14 February 2013 (CST)''': Oh, advantages are important. The papers I'd read had not listed any advantages compared to other methods, they just said their own methods and then about the cool reduced cell they created. Here's some stuff I thought of. Comparative genomics would find things that gene disruption wouldn't because gene disruption may disrupt a conserved essential gene. All of the 3 first techniques are a roadmap for genome reduction: without them reduction would take longer and be much more expensive.
		+
		+	==Core and Accessory Genes, Pan-genomes==

	'''[[User:Thomas Wall\|Thomas Wall]] 19:16, 14 February 2013 (EST)''': This is a cool paper I found talking about genome reduction that people might like (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002651)		'''[[User:Thomas Wall\|Thomas Wall]] 19:16, 14 February 2013 (EST)''': This is a cool paper I found talking about genome reduction that people might like (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002651)
	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': Yeah, this is the paper I mentioned in class. Thanks So much for linking it. It looks like it has a cool graphic as well that I may add.		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': Yeah, this is the paper I mentioned in class. Thanks So much for linking it. It looks like it has a cool graphic as well that I may add.
-		+	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:54, 17 February 2013 (EST)''':That paper brings up accessory genes as being even more easily lost (because they are genetically unstable). The opposite of an accessory gene is a core gene. This field of defining these two things has advanced a lot since the Blattner comparative genomics. For example, [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974192/ comparing 61 E. coli genomes].
-	'''[[User:~~Aurko Dasgupta~~\|~~Aurko Dasgupta~~]] 21:15, 14 February 2013 (EST)''':~~Given that the fitness effects~~ of a gene ~~can only be stated in the context~~ of a ~~particular genome, isn't~~ the ~~genome reduction method extremely haphazard? Many genes likely fall into families where the removal of one produces no change in viability~~, ~~but prevent the removal or alteration of other genes~~.	+

	==Multicopy Genes ==		==Multicopy Genes ==

Jeffrey E. Barrick at 16:10, 17 February 2013

Jeffrey E. Barrick — Sun, 17 Feb 2013 16:10:11 GMT

←Older revision		Revision as of 16:10, 17 February 2013
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		+	== Bottom-Up vs. Top-Down ==
		+
	'''[[User:Gabriel Wu\|Gabriel Wu]] 03:42, 13 February 2013 (EST)''': In principle, a minimal genome that has just enough genes for a cell to grow and divide sounds good. I wonder how reliable and stable this chassis might actually be though. What if removing all the "redundant" pathways results in a fragile cell where the addition of new genes results in cell non-viability? For example, biofuel products are notoriously toxic to the cell. If a bottom up approach is taken by starting with a minimal genome and then inserting ethanol genes, the minimal genome cell will likely never grow up due to alcohol toxicity. If engineering is an iterative process, it may be difficult to optimize no growth. Sometimes it's easier to start with a cell that can tolerate small amounts and then knock in or out whichever genes are needed to improve tolerance.		'''[[User:Gabriel Wu\|Gabriel Wu]] 03:42, 13 February 2013 (EST)''': In principle, a minimal genome that has just enough genes for a cell to grow and divide sounds good. I wonder how reliable and stable this chassis might actually be though. What if removing all the "redundant" pathways results in a fragile cell where the addition of new genes results in cell non-viability? For example, biofuel products are notoriously toxic to the cell. If a bottom up approach is taken by starting with a minimal genome and then inserting ethanol genes, the minimal genome cell will likely never grow up due to alcohol toxicity. If engineering is an iterative process, it may be difficult to optimize no growth. Sometimes it's easier to start with a cell that can tolerate small amounts and then knock in or out whichever genes are needed to improve tolerance.
	*'''[[User:Neil R Gottel\|Neil R Gottel]] 15:55, 13 February 2013 (EST)''':An iterative approach: start with a low-expression version of your ethanol production construct that reduces growth, but doesn't kill the cell. Then, start adding in ethanol tolerance genes, looking for increases in the growth rate. Then bump up the expression of the ethanol gene again, and tweak the ethanol resistance again. Question is: will the end result of this be better than starting with a non-minimized, ethanol resistant cell? And how long would each approach take?		*'''[[User:Neil R Gottel\|Neil R Gottel]] 15:55, 13 February 2013 (EST)''':An iterative approach: start with a low-expression version of your ethanol production construct that reduces growth, but doesn't kill the cell. Then, start adding in ethanol tolerance genes, looking for increases in the growth rate. Then bump up the expression of the ethanol gene again, and tweak the ethanol resistance again. Question is: will the end result of this be better than starting with a non-minimized, ethanol resistant cell? And how long would each approach take?
	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:45, 14 February 2013 (EST)''': I would be surprised if the bottom-up approach would be faster than top down. Also, if we knew all the interactions among ethanol tolerance genes, we might not need the bottom up approach to begin with. Also, are ability to "bump up" expression levels is less than well understood.		**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:45, 14 February 2013 (EST)''': I would be surprised if the bottom-up approach would be faster than top down. Also, if we knew all the interactions among ethanol tolerance genes, we might not need the bottom up approach to begin with. Also, are ability to "bump up" expression levels is less than well understood.
-	~~the end result of this be better than starting with a non-minimized, ethanol resistant cell? And how long would each approach take?~~
	*'''[[User:Thomas Wall\|Thomas Wall]] 19:00, 14 February 2013 (EST)''': At this point in biology knowledge that a bottom up approach will be much longer. Figuring out what is causing your problem in a native genome is much easier then trying to figure out what you took out needed to be there (if its truly minimal). I think getting rid of non coding DNA might not be as big of a problem.		*'''[[User:Thomas Wall\|Thomas Wall]] 19:00, 14 February 2013 (EST)''': At this point in biology knowledge that a bottom up approach will be much longer. Figuring out what is causing your problem in a native genome is much easier then trying to figure out what you took out needed to be there (if its truly minimal). I think getting rid of non coding DNA might not be as big of a problem.
		+	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:10, 17 February 2013 (EST)''':I agree that it's much harder to build something than to selectively lose parts to get adaptation. Should we be thinking about building a '''maximal genome'''? As long as it survived with a ton of new genes, then it would be far more likely to have the potential to evolve useful functions.
		+
		+	==Environmental Dependence ==
		+
	'''[[User:Max E. Rubinson\|Max E. Rubinson]] 10:34, 14 February 2013 (EST)''': Shouldn't a "clean" or "minimal" genome refer to the minimum set of genes that an organism needs to survive and reproduce ''in a defined environment''?		'''[[User:Max E. Rubinson\|Max E. Rubinson]] 10:34, 14 February 2013 (EST)''': Shouldn't a "clean" or "minimal" genome refer to the minimum set of genes that an organism needs to survive and reproduce ''in a defined environment''?
	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I'm sorry that I didn't fix this sooner. I've been Internet deprived for the last 1.5 days and I'm just reading everyone's comments. I'm typing this through an iPAD, since the place I'm staying at doesn't have Internet access, so if I make any mistakes let me know. Thanks for bringing this up, totally forgot about it.		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I'm sorry that I didn't fix this sooner. I've been Internet deprived for the last 1.5 days and I'm just reading everyone's comments. I'm typing this through an iPAD, since the place I'm staying at doesn't have Internet access, so if I make any mistakes let me know. Thanks for bringing this up, totally forgot about it.

Jeffrey E. Barrick at 16:07, 17 February 2013

Jeffrey E. Barrick — Sun, 17 Feb 2013 16:07:23 GMT

←Older revision		Revision as of 16:07, 17 February 2013
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	'''[[User:Thomas Wall\|Thomas Wall]] 19:16, 14 February 2013 (EST)''': This is a cool paper I found talking about genome reduction that people might like (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002651)		'''[[User:Thomas Wall\|Thomas Wall]] 19:16, 14 February 2013 (EST)''': This is a cool paper I found talking about genome reduction that people might like (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002651)
	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': Yeah, this is the paper I mentioned in class. Thanks So much for linking it. It looks like it has a cool graphic as well that I may add.		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': Yeah, this is the paper I mentioned in class. Thanks So much for linking it. It looks like it has a cool graphic as well that I may add.
-	'''[[User:Kevin Baldridge\|Kevin Baldridge]] 14:05, 14 February 2013 (EST)''':One of the things mentioned in the introduction is duplicate genes being superfluous. I wonder what the cutoff for minimal repetition of a gene, for example ribosomal RNA genes. If you only had one copy, I find it surprising that the cell would be able to be viable/healthy given the large amount of ribosomal RNA that is produced in exponential phase for cell growth.

	'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 21:15, 14 February 2013 (EST)''':Given that the fitness effects of a gene can only be stated in the context of a particular genome, isn't the genome reduction method extremely haphazard? Many genes likely fall into families where the removal of one produces no change in viability, but prevent the removal or alteration of other genes.		'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 21:15, 14 February 2013 (EST)''':Given that the fitness effects of a gene can only be stated in the context of a particular genome, isn't the genome reduction method extremely haphazard? Many genes likely fall into families where the removal of one produces no change in viability, but prevent the removal or alteration of other genes.
		+
		+	==Multicopy Genes ==
		+	'''[[User:Kevin Baldridge\|Kevin Baldridge]] 14:05, 14 February 2013 (EST)''':One of the things mentioned in the introduction is duplicate genes being superfluous. I wonder what the cutoff for minimal repetition of a gene, for example ribosomal RNA genes. If you only had one copy, I find it surprising that the cell would be able to be viable/healthy given the large amount of ribosomal RNA that is produced in exponential phase for cell growth.
		+	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:07, 17 February 2013 (EST)''':''E. coli'' can survive pretty well with [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC93859/ just one ribosomal RNA copy]. You're right that at some point it becomes limiting and there is an [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC29826/ overall trend that microbes with greater growth rates have more rrn copies]. One thing we don't usually think about is that there are multiple copies of most genes during exponential growth due to overlapping rounds of genome replication before segregation of daughter cells.

	== Blattner Group ==		== Blattner Group ==

Jeffrey E. Barrick: /* Blattner Group */

Jeffrey E. Barrick — Sun, 17 Feb 2013 16:01:12 GMT

Blattner Group

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	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?
	**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.		**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.
		+	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:01, 17 February 2013 (EST)''':I think that it is a valid observation that the state of the art has not progressed much since the Blattner genome and Venter's work. Why is that? Have all the cool things been done? I'd say that MDS42 actually is a useful resource, particularly with the refinements that Neil mentions, but I don't really see any papers switching to using this strain. It's a lot easier to keep working with what you know.

	== Readability ==		== Readability ==

Neil R Gottel: /* Blattner Group */

Neil R Gottel — Sat, 16 Feb 2013 22:41:29 GMT

Blattner Group

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	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 12:51, 14 February 2013 (EST)''':Since it's publicly posted on a poster on the Scarab Genomics website, I think we can also post that figure.		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 12:51, 14 February 2013 (EST)''':Since it's publicly posted on a poster on the Scarab Genomics website, I think we can also post that figure.
	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': This is pretty cool. I didn't know he was selling these. While I do agree that his work was very important, I'd be sceptical about calling it state-of-the-art since his reduction was done over 10 years ago. Wouldn't a newer source of reduced strains be more reduced, genetically stable, or contain less genetic scarring?
		+	**'''[[User:Neil R Gottel\|Neil R Gottel]] 17:41, 16 February 2013 (EST)''':10 years ago? The Science article describing MDS42 is from 2006 (although the project was started in 2002, if that's what you mean). They've also continued to improve on MDS42, [http://www.microbialcellfactories.com/content/11/1/11 such as this 2012 paper] in which three DNA polymerases that are induced by the SOS response were removed. The new strain has a mutation rate 50% lower than MDS42. With regards to scarring, they used lambda red recombination for in-frame deletions, which just leaves behind a FRT site.

	== Readability ==		== Readability ==

Marco D Howard at 04:06, 15 February 2013

Marco D Howard — Fri, 15 Feb 2013 04:06:38 GMT

←Older revision		Revision as of 04:06, 15 February 2013
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	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I'm sorry that I didn't fix this sooner. I've been Internet deprived for the last 1.5 days and I'm just reading everyone's comments. I'm typing this through an iPAD, since the place I'm staying at doesn't have Internet access, so if I make any mistakes let me know. Thanks for bringing this up, totally forgot about it.		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I'm sorry that I didn't fix this sooner. I've been Internet deprived for the last 1.5 days and I'm just reading everyone's comments. I'm typing this through an iPAD, since the place I'm staying at doesn't have Internet access, so if I make any mistakes let me know. Thanks for bringing this up, totally forgot about it.
	*'''[[User:Thomas Wall\|Thomas Wall]] 19:05, 14 February 2013 (EST)''': I believe that is what it is. But in the world of biocatalysts/metabolic engineering you are constantly changing the environment.		*'''[[User:Thomas Wall\|Thomas Wall]] 19:05, 14 February 2013 (EST)''': I believe that is what it is. But in the world of biocatalysts/metabolic engineering you are constantly changing the environment.
-	*'''''[[User:Marco Howard \| Marco Howard]] 19:05, 14 February 2013 (EST)''': When working with biocatalysts, do we know the rate constant? If so, we should be able to predict how the environment will change over time. Perhaps we could use Neil's iterative approach.	+	*'''''[[User:Marco Howard \| Marco Howard]] 19:05, 14 February 2013 (EST)''': When working with biocatalysts, do we know the rate constant? If so, we should be able to predict how the environment will change over time. Perhaps we could use Neil's iterative approach to design bacteria that can tolerate these conditions.
	'''[[User:Yunle Huang\|Yunle Huang]] 20:20, 14 February 2013 (EST)''': What are some advantages and disadvantages of each of the genome reduction methods?		'''[[User:Yunle Huang\|Yunle Huang]] 20:20, 14 February 2013 (EST)''': What are some advantages and disadvantages of each of the genome reduction methods?
	*'''[[User:Evan J WeaverIEvan Weaver]] 18:36, 14 February 2013 (CST)''': Oh, advantages are important. The papers I'd read had not listed any advantages compared to other methods, they just said their own methods and then about the cool reduced cell they created. Here's some stuff I thought of. Comparative genomics would find things that gene disruption wouldn't because gene disruption may disrupt a conserved essential gene. All of the 3 first techniques are a roadmap for genome reduction: without them reduction would take longer and be much more expensive.		*'''[[User:Evan J WeaverIEvan Weaver]] 18:36, 14 February 2013 (CST)''': Oh, advantages are important. The papers I'd read had not listed any advantages compared to other methods, they just said their own methods and then about the cool reduced cell they created. Here's some stuff I thought of. Comparative genomics would find things that gene disruption wouldn't because gene disruption may disrupt a conserved essential gene. All of the 3 first techniques are a roadmap for genome reduction: without them reduction would take longer and be much more expensive.

←Older revision		Revision as of 16:10, 17 February 2013
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		+	== Bottom-Up vs. Top-Down ==
		+
	'''[[User:Gabriel Wu\|Gabriel Wu]] 03:42, 13 February 2013 (EST)''': In principle, a minimal genome that has just enough genes for a cell to grow and divide sounds good. I wonder how reliable and stable this chassis might actually be though. What if removing all the "redundant" pathways results in a fragile cell where the addition of new genes results in cell non-viability? For example, biofuel products are notoriously toxic to the cell. If a bottom up approach is taken by starting with a minimal genome and then inserting ethanol genes, the minimal genome cell will likely never grow up due to alcohol toxicity. If engineering is an iterative process, it may be difficult to optimize no growth. Sometimes it's easier to start with a cell that can tolerate small amounts and then knock in or out whichever genes are needed to improve tolerance.		'''[[User:Gabriel Wu\|Gabriel Wu]] 03:42, 13 February 2013 (EST)''': In principle, a minimal genome that has just enough genes for a cell to grow and divide sounds good. I wonder how reliable and stable this chassis might actually be though. What if removing all the "redundant" pathways results in a fragile cell where the addition of new genes results in cell non-viability? For example, biofuel products are notoriously toxic to the cell. If a bottom up approach is taken by starting with a minimal genome and then inserting ethanol genes, the minimal genome cell will likely never grow up due to alcohol toxicity. If engineering is an iterative process, it may be difficult to optimize no growth. Sometimes it's easier to start with a cell that can tolerate small amounts and then knock in or out whichever genes are needed to improve tolerance.
	*'''[[User:Neil R Gottel\|Neil R Gottel]] 15:55, 13 February 2013 (EST)''':An iterative approach: start with a low-expression version of your ethanol production construct that reduces growth, but doesn't kill the cell. Then, start adding in ethanol tolerance genes, looking for increases in the growth rate. Then bump up the expression of the ethanol gene again, and tweak the ethanol resistance again. Question is: will the end result of this be better than starting with a non-minimized, ethanol resistant cell? And how long would each approach take?		*'''[[User:Neil R Gottel\|Neil R Gottel]] 15:55, 13 February 2013 (EST)''':An iterative approach: start with a low-expression version of your ethanol production construct that reduces growth, but doesn't kill the cell. Then, start adding in ethanol tolerance genes, looking for increases in the growth rate. Then bump up the expression of the ethanol gene again, and tweak the ethanol resistance again. Question is: will the end result of this be better than starting with a non-minimized, ethanol resistant cell? And how long would each approach take?
	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:45, 14 February 2013 (EST)''': I would be surprised if the bottom-up approach would be faster than top down. Also, if we knew all the interactions among ethanol tolerance genes, we might not need the bottom up approach to begin with. Also, are ability to "bump up" expression levels is less than well understood.		**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:45, 14 February 2013 (EST)''': I would be surprised if the bottom-up approach would be faster than top down. Also, if we knew all the interactions among ethanol tolerance genes, we might not need the bottom up approach to begin with. Also, are ability to "bump up" expression levels is less than well understood.
-	~~the end result of this be better than starting with a non-minimized, ethanol resistant cell? And how long would each approach take?~~
	*'''[[User:Thomas Wall\|Thomas Wall]] 19:00, 14 February 2013 (EST)''': At this point in biology knowledge that a bottom up approach will be much longer. Figuring out what is causing your problem in a native genome is much easier then trying to figure out what you took out needed to be there (if its truly minimal). I think getting rid of non coding DNA might not be as big of a problem.		*'''[[User:Thomas Wall\|Thomas Wall]] 19:00, 14 February 2013 (EST)''': At this point in biology knowledge that a bottom up approach will be much longer. Figuring out what is causing your problem in a native genome is much easier then trying to figure out what you took out needed to be there (if its truly minimal). I think getting rid of non coding DNA might not be as big of a problem.
		+	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 11:10, 17 February 2013 (EST)''':I agree that it's much harder to build something than to selectively lose parts to get adaptation. Should we be thinking about building a '''maximal genome'''? As long as it survived with a ton of new genes, then it would be far more likely to have the potential to evolve useful functions.
		+
		+	==Environmental Dependence ==
		+
	'''[[User:Max E. Rubinson\|Max E. Rubinson]] 10:34, 14 February 2013 (EST)''': Shouldn't a "clean" or "minimal" genome refer to the minimum set of genes that an organism needs to survive and reproduce ''in a defined environment''?		'''[[User:Max E. Rubinson\|Max E. Rubinson]] 10:34, 14 February 2013 (EST)''': Shouldn't a "clean" or "minimal" genome refer to the minimum set of genes that an organism needs to survive and reproduce ''in a defined environment''?
	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I'm sorry that I didn't fix this sooner. I've been Internet deprived for the last 1.5 days and I'm just reading everyone's comments. I'm typing this through an iPAD, since the place I'm staying at doesn't have Internet access, so if I make any mistakes let me know. Thanks for bringing this up, totally forgot about it.		*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I'm sorry that I didn't fix this sooner. I've been Internet deprived for the last 1.5 days and I'm just reading everyone's comments. I'm typing this through an iPAD, since the place I'm staying at doesn't have Internet access, so if I make any mistakes let me know. Thanks for bringing this up, totally forgot about it.