Talk:CH391L/S13/CleanGenomes

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**'''[[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?
the end result of this be better than starting with a non-minimized, ethanol resistant cell? And how long would each approach take?
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*'''[[User:Thomas Wall|Thomas Wall]] 19:00, 14 February 2013 (EST)''': I believe 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.
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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: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: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.

Revision as of 19:12, 14 February 2013

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.

  • 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?
    • 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?

  • 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.

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?

  • 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.

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.

Blattner Group

Neil R Gottel 17:25, 12 February 2013 (EST):I recommend that the work of the Blattner Lab on clean E. coli genomes should feature prominently in this article, since that's the state-of-the-art right now, and is a commercial product sold by Scarab Genomics. Is there a version of that sweet graphic that shows the deleted regions on the genome that we're allowed to use, because that'd be a great addition.

  • 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.

Readability

Neil R Gottel 17:25, 12 February 2013 (EST):At some points this article has turned into a wall of text, particularly for the section on estimating the number of essential genes. I think it'd be helpful if a few people took a subheading and cleaned it up (and documented what they did here). For my part, I rewrote the section on "Genome Synthesis".

  • Kevin Baldridge 14:00, 14 February 2013 (EST):I made a couple of minor edits in the transposable mutagenesis and mRNA disruption sections for readability and capitalization. Furthmore, I changed the last sentence in the comparative genomics section, to change it from underestimation to overestimation -- it seems that if you assume a gene is essential from conservation but it's not, that would be a false positive and thus overestimate the resulting number of essential genes
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