# Matthew E. Jurek Week 6

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*Tony and I are interested in the third project. Using the equations derived in class today, we are going to look at two things in particular. The model of equations needs to include the influx of the chemostat. We will begin by incorporating this into the dni/dt equation by adding the influx to the tail end of the equation. Aside from that, it appears glutamate is coming from elsewhere as the graph of glutamate in the paper is of much larger scale. We feel there is a source of glutamate aside from the conversions discussed in class. As a result, we hope to incorporate this into the dx/dt equation after performing research on outside sources of glutamate within yeast. The described objectives are simply hypotheses at this point. It will be interesting to see how the models turn out. | *Tony and I are interested in the third project. Using the equations derived in class today, we are going to look at two things in particular. The model of equations needs to include the influx of the chemostat. We will begin by incorporating this into the dni/dt equation by adding the influx to the tail end of the equation. Aside from that, it appears glutamate is coming from elsewhere as the graph of glutamate in the paper is of much larger scale. We feel there is a source of glutamate aside from the conversions discussed in class. As a result, we hope to incorporate this into the dx/dt equation after performing research on outside sources of glutamate within yeast. The described objectives are simply hypotheses at this point. It will be interesting to see how the models turn out. | ||

*There is an amino acid permease gene family within yeast that includes [http://mcb.asm.org/content/19/8/5405.long| Ssy1]. This protein is able to sense extracellular amino acid concentrations. More importantly, this protein reacts within the yeast based on what it senses. Although the linked article goes into great detail regarding a number of scenarios that were tested regarding this protein, glutamate activity is what we're interested in. This article actually touches on changes in glutamate presence based on the various factors tested. The experiment is relevant as it may help us generate sources of glutamate outside of the reactions discussed in class. | *There is an amino acid permease gene family within yeast that includes [http://mcb.asm.org/content/19/8/5405.long| Ssy1]. This protein is able to sense extracellular amino acid concentrations. More importantly, this protein reacts within the yeast based on what it senses. Although the linked article goes into great detail regarding a number of scenarios that were tested regarding this protein, glutamate activity is what we're interested in. This article actually touches on changes in glutamate presence based on the various factors tested. The experiment is relevant as it may help us generate sources of glutamate outside of the reactions discussed in class. | ||

- | *As part of the project, we need to look at the influx of feed within the chemostat in order to complete the dni/dt equation. A previous [ | + | *As part of the project, we need to look at the influx of feed within the chemostat in order to complete the dni/dt equation. A previous [media:experiment.pdf| experiment] regarding yeast fed in a similar fashion was done. This paper describes how to calculate and model the flux within a chemostat, starting around page 65. There's several equations that could help us as we are also dealing with a chemostat. In addition to that, it explains a few theories regarding chemostats that may simplify our quest to find the feed flux. |

## Revision as of 00:27, 22 February 2013

Matthew E. Jurek BIOL398-03/S13

## Assignment Page

- BIOL398-03/S13:Week_2
- BIOL398-03/S13:Week 3
- BIOL398-03/S13:Week 4
- BIOL398-03/S13:Week_5
- BIOL398-03/S13:Week_6
- BIOL398-03/S13:Week_8
- BIOL398-03/S13:Week_9
- BIOL398-03/S13:Week_11
- BIOL398-03/S13:Week_12
- BIOL398-03/S13:Week_13
- BIOL398-03/S13:Week_14

## User Page

- Matthew E. Jurek Week 2
- Matthew E. Jurek Week 3
- Matthew E. Jurek Week 4
- Matthew E. Jurek Week 5
**Matthew E. Jurek Week 6**- Anthony J. Wavrin/Matthew E. Jurek Metabolic Pathways Project
- Matthew E. Jurek Week 8
- Matthew E. Jurek Week 9
- Matthew E. Jurek Week 11
- Matthew E. Jurek Week 12
- Matthew E. Jurek Week 13
- Matthew E. Jurek Week 14
- Final Presentation

## Project 1

- Tony and I are interested in the third project. Using the equations derived in class today, we are going to look at two things in particular. The model of equations needs to include the influx of the chemostat. We will begin by incorporating this into the dni/dt equation by adding the influx to the tail end of the equation. Aside from that, it appears glutamate is coming from elsewhere as the graph of glutamate in the paper is of much larger scale. We feel there is a source of glutamate aside from the conversions discussed in class. As a result, we hope to incorporate this into the dx/dt equation after performing research on outside sources of glutamate within yeast. The described objectives are simply hypotheses at this point. It will be interesting to see how the models turn out.
- There is an amino acid permease gene family within yeast that includes Ssy1. This protein is able to sense extracellular amino acid concentrations. More importantly, this protein reacts within the yeast based on what it senses. Although the linked article goes into great detail regarding a number of scenarios that were tested regarding this protein, glutamate activity is what we're interested in. This article actually touches on changes in glutamate presence based on the various factors tested. The experiment is relevant as it may help us generate sources of glutamate outside of the reactions discussed in class.
- As part of the project, we need to look at the influx of feed within the chemostat in order to complete the dni/dt equation. A previous [media:experiment.pdf| experiment] regarding yeast fed in a similar fashion was done. This paper describes how to calculate and model the flux within a chemostat, starting around page 65. There's several equations that could help us as we are also dealing with a chemostat. In addition to that, it explains a few theories regarding chemostats that may simplify our quest to find the feed flux.