Modeling the Glutamate Metabolic Pathway in

Modeling the Glutamate Metabolic Pathway in Modeling the Glutamate Metabolic Pathway in - Start

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Modeling the Glutamate Metabolic Pathway in - Description

Saccharomyces. . cerevisiae. . to Resemble Experimental Data. Anthony . Wavrin. & Matthew . Jurek. Department of Biology. Loyola Marymount University. February 28. th. , 2013. Outline. The addition of other factors to create a more accurate nitrogen metabolism model. ID: 713808 Download Presentation

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Modeling the Glutamate Metabolic Pathway in




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Presentations text content in Modeling the Glutamate Metabolic Pathway in

Slide1

Modeling the Glutamate Metabolic Pathway in Saccharomyces cerevisiae to Resemble Experimental Data

Anthony

Wavrin

& Matthew

Jurek

Department of Biology

Loyola Marymount University

February 28

th

, 2013

Slide2

OutlineThe addition of other factors to create a more accurate nitrogen metabolism modelGlutamine,

-

ketoglutarate

, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from ter Schure et al. (1995)Adding more variables to minimize deviation from experimental data

 

Slide3

OutlineThe addition of other factors to create a more accurate nitrogen metabolism model

Glutamine,

-

ketoglutarate, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from

ter

Schure et al. (1995)Adding more variables to minimize deviation from experimental data

 

Slide4

The Role of Aspartate Within the Model

The

unproportional

increase in glutamate, with respect to -ketoglutarate and glutamine, indicates another possible source of glutamate.  

ter

Schure

et al.

(1995)

J.

Bacteriol

.

177(22):6672

Slide5

OutlineThe addition of other factors to create a more accurate nitrogen metabolism model

Glutamine,

-

ketoglutarate, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from ter

Schure

et al. (1995)Adding more variables to minimize deviation from experimental data

 

Slide6

Glutamine, -Ketoglutarate

,

Glutamate

, Aspartate, and Internal Nitrogen 

Glutamine (z),

-

ketoglutarate () , and glutamate (m) are the three parameters that are modeled to fit experimental data.

Aspartate (asp) is modeled as an additional source of glutamate.

Internal nitrogen (

n

i

)

is factored in to increase relationships between

g

lutamine,

-

ketoglutarate

, and

glutamate.

 

Slide7

OutlineThe addition of other factors to create a more accurate nitrogen metabolism model

Glutamine,

-

ketoglutarate, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from

ter

Schure et al. (1995)Adding more variables to minimize deviation from experimental data

 

Slide8

Differential Equations Defining the Model

 

Slide9

OutlineThe addition of other factors to create a more accurate nitrogen metabolism model

Glutamine,

-

ketoglutarate, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from

ter

Schure et al. (1995)Adding more variables to minimize deviation from experimental data

 

Slide10

Constants Utilized Within the Model Constants

Role

k

xMain determinant of maximum rate of reactionKxThe concentration at which k1/2 occursnextConcentration of nitrogen in feed

Slide11

Constants in Equations at Steady StateInitial Concentrations: a, z, m,

= 5 and

n

i = 20

 

 

 

 

 

Slide12

OutlineThe addition of other factors to create a more accurate nitrogen metabolism model

Glutamine,

-

ketoglutarate, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from

ter

Schure et al. (1995)Adding more variables to minimize deviation from experimental data

 

Slide13

Model Reaching Steady State

Time

Time

TimeTime

Time

Concentration

Concentration

Concentration

Concentration

Concentration

Slide14

OutlineThe addition of other factors to create a more accurate nitrogen metabolism model

Glutamine,

-

ketoglutarate, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from ter

Schure

et al. (1995)Adding more variables to minimize deviation from experimental data 

Slide15

Time

Time

Time

Concentration

Concentration

Concentration

ter

Schure

et al.

(1995)

J.

Bacteriol

.

177(22):6672

Model vs.

ter

Schure

et al.

Slide16

OutlineThe addition of other factors to create a more accurate nitrogen metabolism model

Glutamine,

-

ketoglutarate, glutamate, aspartate, and internal nitrogen as state variablesDifferential equations that model the dynamicsImportance of constants in regulating steady statesGraphic representation of reaching and maintaining steady statesResults more accurately depict data from

ter

Schure et al. (1995)Adding more variables to minimize deviation from experimental data

 

Slide17

Further ExperimentationIncorporating glutamine and glutamate as nitrogen transporters and translation of proteins.

Modeling

-

ketoglutarate into the Citric Acid Cycle.Examine and incorporate the expression rates of GDH1, GDH2, GDH3, GLN1, and GLT1.

 

Slide18

AcknowledgementsA special thanks to Dr. Dahlquist for the biological background necessary to model this system and Dr. Fitzpatrick for his assistance in the logistics of modeling.

Slide19

References John, E. H. and Flynn, K. J. (2000) Modelling phosphate transport and assimilation in microalgae; how much complexity is warranted?. Ecol. Modelling, 125, 145–157.

Schilling, C. H., Schuster, S.,

Palsson

, B. O. & Heinrich, R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, 296–303 (199).ter Schure, E.G., Sillje, H.H.W., Verkleij, A.J., Boonstra, J., and Verrips, C.T. (1995) Journal of Bacteriology 177: 6672-6675.


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