User:John M.L. Craven/Notebook/20.109 Mod 3, W/F Green Presentation: Difference between revisions

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{{Optimization of Extracellular Electron Transfer in Microbial Fuel Cells Using Geobacter sulfurreducens}} WORK IN PROGRESS
Optimization of Extracellular Electron Transfer in Microbial Fuel Cells Using ''Geobacter sulfurreducens''


==Background==
==Big Picture==


With increasing concerns in society about the depletion of fossil fuels and the harmful effects of carbon dioxide in the atmosphere, there is a great need for sources of energy from biological, renewable matter that will produce electricity and not be harmful to the environment. Microbial fuel cells, which use microorganisms to convert organic matter into fuel, may be a solution to this need if the process can be optimized for most applications of the technology. The objective of our project is to optimize the extracellular electron transfer capabilities of ''Geobacter sulfurreducens'' in microbial fuel cells. This will result in a more efficient process that can produce energy on a scale more competitive with current technologies. Specifically, we will create a genome scale metabolic network model of ''G. sulfurreducens'' in silico, study the intracellular dynamics of the species, determine the gene deletions that optimize extracellular electron transfer, measure the effects of these deletions on extracellular electron transfer, and examine genome wide effects of these deletions in vitro. We will do this using in silico metabolic flux analysis on a genome scale and with DNA microarray technology.


==Goals==
==Goals==
Line 11: Line 12:
#W --  
#W --  


However, we feel the original biological isolate is not necessarily where we should begin to understand how system-behavior is produced.  Specifically, in designing T7.2, the following five goals will drive our design; the first three goals revisit or extend goals motivating the design of [[T7.1]]. 
#Our design of T7.2 will enable the unique and selection-independent manipulation of each genetic element via restriction enzymes.
#We will specify a genome that does not include any functions that might be encoded via the physical coupling of multiple genetic elements.
#We will specify a genome that only includes elements that we believe contribute to phage gene expression.  Moving beyond our design of T7.1, we will actively erase or delete elements of unknown function.  In addition, efforts will be made to made to remove unknown genetic elements.
##reduced gene sets?
##codon shuffling?
#To attempt to make our modeling of gene expression easier, we will use standard synthetic elements in place of the natural elements that regulate transcription and translation. 
#We will make a genome that is more anemenable to measurements that are important to us, such as adding reporters of transcription and translation.
Taken together, our design of T7.2 should specify a genome that is simpler to model and manipulate, in which we have a putative function for each base pair of DNA involved in phage gene expression.  We hypothesize that as a result of the more parsimonious genome design, T7.2 will also encode a dynamic system that is easier to model and interact with, relative to the natural biological isolate.


==Meta Considerations==
==Meta Considerations==
===Standardization===  
===Standardization===  
We want to standardize certain functional genetic elements to make them easier to model.  For example, instead of further characterizing every different ribosome binding site and promoter, we can standardize on a set of that would take considerably less effort to characterize.
 
===Measurement===
===Measurement===
We want to increase the ability to measure different aspects of phage biology.  This may including mRNA and protein reporters, and/or optimizing DpnI restriction sites to ease entry assays. 
 
===Manipulability===
===Manipulability===
We need to increase our ability to make selection-independent changes to the genome easily.  We will take the some of the lessons we learned in T7.1 about the types and distribution of restriction sites needed.  
   
===Encoding===
===Encoding===
We want to reduce, to as large of an extent as possible, the number of genetic elements that are included in T7.2 that do not encode functions that we do not know about. 
 


==Designs==
==Designs==
See the [[T7.2/Design|Designs Page]] for further information.

Revision as of 18:48, 4 May 2009

Optimization of Extracellular Electron Transfer in Microbial Fuel Cells Using Geobacter sulfurreducens

Big Picture

With increasing concerns in society about the depletion of fossil fuels and the harmful effects of carbon dioxide in the atmosphere, there is a great need for sources of energy from biological, renewable matter that will produce electricity and not be harmful to the environment. Microbial fuel cells, which use microorganisms to convert organic matter into fuel, may be a solution to this need if the process can be optimized for most applications of the technology. The objective of our project is to optimize the extracellular electron transfer capabilities of Geobacter sulfurreducens in microbial fuel cells. This will result in a more efficient process that can produce energy on a scale more competitive with current technologies. Specifically, we will create a genome scale metabolic network model of G. sulfurreducens in silico, study the intracellular dynamics of the species, determine the gene deletions that optimize extracellular electron transfer, measure the effects of these deletions on extracellular electron transfer, and examine genome wide effects of these deletions in vitro. We will do this using in silico metabolic flux analysis on a genome scale and with DNA microarray technology.

Goals

which include:
  1. X--
  2. Y --
  3. Z --
  4. W --


Meta Considerations

Standardization

Measurement

Manipulability

Encoding

Designs

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