Team:BYU Provo/Results/Modeling

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__NOTOC__==Basic Design==
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__NOTOC__==Bacteriophage Plaques==
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===Basic Design===
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[[File:BYUModelingDesign.JPG|360px|right|link=https://static.igem.org/mediawiki/2013/c/c9/BYUModelingDesign.JPG]]
Experiments with bacteriophage growth is often performed either in liquid broth or in solid agar medium. In contrast to the relative uniform distribution of phages in liquid broth, phages form individual clearings in bacterial lawn within solid agar medium. These clearings are termed plaques. They are the product of bacterial cell lysis as phage replicate and spread outward.  
Experiments with bacteriophage growth is often performed either in liquid broth or in solid agar medium. In contrast to the relative uniform distribution of phages in liquid broth, phages form individual clearings in bacterial lawn within solid agar medium. These clearings are termed plaques. They are the product of bacterial cell lysis as phage replicate and spread outward.  
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For our modeling experiments, we hypothesized that multiple experimental factors may influence the size of plaque formation in solid agar medium (Fig. 1). We decided to start with identifying the relationships between plaque sizes and each of these factors. With these data, we can generate a mathematical model that take into account all experimental variability. Such model can be used by researcher to design the optimal experimental conditions that will produce plaques of the ideal size for their experiments.
For our modeling experiments, we hypothesized that multiple experimental factors may influence the size of plaque formation in solid agar medium (Fig. 1). We decided to start with identifying the relationships between plaque sizes and each of these factors. With these data, we can generate a mathematical model that take into account all experimental variability. Such model can be used by researcher to design the optimal experimental conditions that will produce plaques of the ideal size for their experiments.
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===Experimental Results===
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Many experimental
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[[File:BYUModelingPlatePics.JPG|380px|right|link=https://static.igem.org/mediawiki/2013/2/22/BYUModelingPlatePics.JPG]]
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A viral plaque is a visible structure formed within a cell culture, such as bacterial cultures within some nutrient medium (e.g. agar). The bacteriophage viruses replicate and spread, thus generating regions of cell destructions known as plaques.
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We decided to start with determining the relationship between phage plaque size and phage particle size. Specifically, 0.5 mL of E coli B liquid culture (OD 600 = 0.5) was transfected with 20uL of the respective phage (T1, T3, T4, and T7) at approximately the same concentration for 10 minutes. After this, the bacteria/phage mixture was plated on standard LB plates using x1 top agar. Plates were allowed to solidify at room temperature for 30 minutes, before they were placed in an incubator at 37 Celsius for 24 hours. Following incubation, pictures of plates were taken with Alphaimager and plaque sizes were measured using [http://rsbweb.nih.gov/ij/ ImageJ].
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A plaque is developed as a part of infection of one cell by a single virus particle that is followed by the replication of that virus, and finally, the death of the cell. The newly replicated virus particles will later infect and then kill surrounding cells.
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===Data Analysis===
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Data analysis gives the following results:
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[[File:BYUModelingTable.JPG|750px|left|link=https://static.igem.org/mediawiki/2013/6/67/BYUModelingTable.JPG]]
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Fig. 3 verifies our hypothesis that there is an inverse relationship between plaque sizes and phage particle size. This further confirms our method of selection (using different concentrations of agar) in our creation of mutant T4 and T7 phage library.
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==Cholera Team==
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===Next Step===
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To further model phage plaque sizes we will
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* test whether or not our mutant phage confirm to the same plaque size - phage particle size relationship.
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* start modeling experiments in which one of the other experimental factors (temperature, bacterial concentration, agar concentration, incubation time) act as the independent variable.
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Latest revision as of 23:06, 27 September 2013


Modeling Results


Results Overview
Judging Criteria
* Bronze
* Silver
* Gold
Experimental Results
Modeling Results
Parts Submitted

Bacteriophage Plaques

Basic Design

BYUModelingDesign.JPG

Experiments with bacteriophage growth is often performed either in liquid broth or in solid agar medium. In contrast to the relative uniform distribution of phages in liquid broth, phages form individual clearings in bacterial lawn within solid agar medium. These clearings are termed plaques. They are the product of bacterial cell lysis as phage replicate and spread outward.

For our modeling experiments, we hypothesized that multiple experimental factors may influence the size of plaque formation in solid agar medium (Fig. 1). We decided to start with identifying the relationships between plaque sizes and each of these factors. With these data, we can generate a mathematical model that take into account all experimental variability. Such model can be used by researcher to design the optimal experimental conditions that will produce plaques of the ideal size for their experiments.


Experimental Results

BYUModelingPlatePics.JPG

We decided to start with determining the relationship between phage plaque size and phage particle size. Specifically, 0.5 mL of E coli B liquid culture (OD 600 = 0.5) was transfected with 20uL of the respective phage (T1, T3, T4, and T7) at approximately the same concentration for 10 minutes. After this, the bacteria/phage mixture was plated on standard LB plates using x1 top agar. Plates were allowed to solidify at room temperature for 30 minutes, before they were placed in an incubator at 37 Celsius for 24 hours. Following incubation, pictures of plates were taken with Alphaimager and plaque sizes were measured using [http://rsbweb.nih.gov/ij/ ImageJ].



Data Analysis

Data analysis gives the following results:

BYUModelingTable.JPG

Fig. 3 verifies our hypothesis that there is an inverse relationship between plaque sizes and phage particle size. This further confirms our method of selection (using different concentrations of agar) in our creation of mutant T4 and T7 phage library.


Next Step

To further model phage plaque sizes we will

  • test whether or not our mutant phage confirm to the same plaque size - phage particle size relationship.
  • start modeling experiments in which one of the other experimental factors (temperature, bacterial concentration, agar concentration, incubation time) act as the independent variable.




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