# BME494s2013 Project Team1

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We used a microscopy imaging technique to determine the production rate of GFP yeast.  Based on our collected data we were able to determine a "real" value for the maximum GFP production rate for the given conditions. We used a microscopy imaging technique to determine the production rate of GFP yeast.  Based on our collected data we were able to determine a "real" value for the maximum GFP production rate for the given conditions. - +
+ [[Image:DJMyeast010.jpg|300px|Raw Data of Yeast at 10 hours]] + [[Image:DJMyeast016.jpg|300px|Raw Data of Yeast at 16 hours]] + [[Image:DJMyeast022.jpg|300px|Raw Data of Yeast at 22 hours]] Line 449: Line 452: [[Image:Data_with_4th_degree_poly_fit.png|400px|Data with 4th Degree Polynomial "Best Fit"]] [[Image:Data_with_4th_degree_poly_fit.png|400px|Data with 4th Degree Polynomial "Best Fit"]]

- + DJMyeast010.jpg [[Image:Best_Fit_Derivative_Plot.png|400px|Plot of the Derivative of the "Best Fit" Polynomial]] [[Image:Best_Fit_Derivative_Plot.png|400px|Plot of the Derivative of the "Best Fit" Polynomial]] Ideally, the GFP production rate measured by this method could be entered as a value for [which parameter] in the Ceroni et al. model. Ideally, the GFP production rate measured by this method could be entered as a value for [which parameter] in the Ceroni et al. model.

## Overview & Purpose

Escherichia coli, commonly referred to as E. coli, has many different strains. The most commonly known serotypes of these bacteria can cause serious food poisoning or even fatality in humans. However, most strains are completely harmless. These strains are usually found in the gut of the host and help by producing K2 and helping with digestion. The presence of these bacteria is very beneficial for it helps to prevent pathogenic bacteria from being present in the intestine.[1]

The Lac switch that we have created in the genetic coding of E. coli bacteria produces a glowing blue color that initially runs off of glucose and eventually runs off of lactose. With this technology, we can create a glow stick that can be used in emergency kits that will provide light in dire situations. By using a non-harmful strain of E. coli, we can create an environmental conscious and biodegradable glow stick that will not cause harm to the surroundings.

This technology will prove to be very helpful for hunters or those who are outdoors for they will not have to worry about disposing of their light source. Used like a regular glow stick, the different components of the device will remain separated and will be mixed together to produce light once a certain amount of force is applied.

## Background

Natural Lac Operon with Various Parts [2]

The lac operon itself is a set of genes found in certain bacterias' DNA that is required for the transport and metabolism of lactose. Most commonly found in Escherichia coli, the operon was the first example of a group of genes under the control of an operator region to which a lactose repressor (LacI) binds.

The Lac operon functions as a single transcription unit and in its basic form comprises of an operator, a promoter, and one or more structural genes such as a regulator or terminator that are transcribed into one polycistronic mRNA. Typically, the structural genes include LacZ, LacY, and LacA.

• LacZ encodes β-galactosidase, an intracellular enzyme that cleaves the disaccharide lactose into glucose and galactose.
• LacY encodes β-galactoside permease, a membrane-bound transport protein that pumps lactose into the cell.
• LacA encodes β-galactoside transacetylase, an enzyme that transfers an acetyl group from acetyl-CoA to β-galactosides.

"Only LacZ and LacY appear to be necessary for lactose catabolism" [3].

When the bacteria are transferred to lactose-containing medium, allolactose (which forms when lactose is present in the cell) binds to the LacI repressor, inhibits the binding of the repressor to the operator, and allows transcription of mRNA for enzymes involved in lactose metabolism and transport across the membrane as seen in the image.

The main idea is that E. coli (the most common medium when investigating the Lac operon) conserves its resources by not making many Lac proteins when other more easily-accepted sugars, such as glucose, are available [4]. This was tested by Jacques Monod during World War II. He tested the combinations of different sugars for E. coli and discovered that when the bacteria are grown with glucose and lactose, glucose would get metabolized first during the bacteria's growth phase I and then lactose during growth phase II.

This means that if glucose and lactose are available for the cell, transcription will occur but at a slow rate. Obviously, if there is no lactose at all, transcription will be repressed. As long as lactose is available, transcription will happen as the LacI repressor is never binded to the operator. Thus, when these Lac proteins are made with the presence of lactose and the corresponding genes act as a switch, this mechanism can be seen as an engineering application, and in this case, used to trigger a color change within the cell. As in the case for our group, the lac operon device contained the necessary promoters, ribosome-binding sites, terminators, a LacI repressor, a cyan fluorescent protein, and a vector backbone based on the Type IIS assebmly strategy and would turn a bright cyan color when exposed to lactose. This "switch" function can have a multitude of possibilities, and one of these uses is focused on in the page.

Basic Components of a Lac Operon [1]

## Design: Our genetic circuit

### Our gene switch

To create our gene switch, we chose to replace β-galactosidase with a gene coding for a variant of GFP (green fluorescent protein). The switch is active or “on” in the presence of IPTG (Isopropylthiogalactoside) and causes the production of a cyan fluorescent color. Additionally, we did not want our switch to be influenced by the presence of glucose so we chose a promoter that is not sensitive to the CAP-cAMP complex and as a result IPTG is the sole input that causes an effect to the switch.

#### Device Structure and Parts

The BioBricks for our design came from the Registry of Standard Biological Parts. Our system utilized two main BioBricks along with an appropriate vector backbone (see figure below).

IPTG-Inducible Lac Promoter
Part BBa_K418003
This BioBrick contains the genetic coding region for the LacI repressor protein along with a promoter adapted from the natural Lac Operon. When LacI binds to the pLac regulator and PLlac01 hybrid regulator, it inhibits transcription. When IPTG binds to LacI, it inhibits the LacI operation and therefore promotes transcription.
The components of this BioBrick are:

• A constitutive promoter: causes transcription
• A ribosome binding site: place for ribosomes to attach during transcription.
• Gene coding for LacI repressor protein: gene that is transcribed to create the LacI repressor.
• Terminators: end the transcription process.
• LacI regulated promoter: initiates the next part of the transcription process. Note: This promoter is negatively regulated by the LacI protein and therefore, transcription will only take place when the LacI protein is NOT present.

Cyan Fluorescent Protein
Part BBa_K411225
This BioBrick contains the genes for the expression of the enhanced cyan fluorescent protein (derived from A. victoria GFP) and is regulated by the IPTG-Inducible Lac Promoter (BBa_K418003).
The components of the BioBrick are:

• A ribosome binding site: place for ribosomes to attach during gene transcription.
• Gene coding for Cyan Fluorescent Protein: gene that is transcribed to create cyan fluorescent protein.
• Terminators: end the transcription process.

Vector Backbone
Part pSB1A3-1
This part was chosen as the vector backbone of our device. pSB1A3-1 is a high copy number plasmid. The replication origin is a pUC19-derived pMB1 (copy number of 100-300 per cell). The terminators bracketing pSB1A3 MCS are designed to prevent transcription from inside the MCS from reading out into the vector.

Circuit_Diagram_of_Sweet_Cyan_Switch.PNG

## Building: Assembly scheme

Mutagenesis process[5]

The assembly strategy employed in the design of this device is a Type IIS assembly strategy. The steps and procedures involved in this single-pot assembly are described below.

### Mutagenesis

One of the parts chosen by our group contains a BsmBI cut site, which would disrupt the digestion and ligation process further along the assembly strategy. In order to counteract this, the part is subjected to mutagenesis to alter a selected base pair within the DNA to eliminate the BsmBI cut site while keeping the integrity of the coding sequence intact.

This site-directed base substitution is performed using two primers with centrally located substitution sites to alter the selected base pair on a methylated plasmid.

After the part has completed the mutagenesis, the DNA sequence (which is linear at this point in time) undergoes in vitro recombination reaction. The host cell then "circularizes" the mutated part DNA and digests the original methylated plasmid. If the methylation of the original plasmid is skipped, an additional purification step would be necessary to extract the mutated plasmid.[5]

PCR Reaction Table
Reagent [Brick 1] [Brick 2] [Vector]
Template DNA 0.2 μL 0.2 μL 0.2 μL
10 μM Forward Primer 1.0 μL 1.0 μL 1.0 μL
10 μM Reverse Primer 1.0 μL 1.0 μL 1.0 μL
2x GoTaq Green Mix 25 μL 25 μL 25 μL
H2O 22.8 μL 22.8 μL 22.8 μL
Total Volume 50 μL 50 μL 50 μL

### PCR

PCR, or polymerase chain reaction, is then used to amplify the DNA sequences and create modular fragments for ease of assembly.

A DNA fragment is combined with its forward and reverse primers, nucleotides, and DNA polymerase. This mixture is then inserted into a thermal cycler, which cycles the internal temperature with predetermined values. These changes in temperature cause the DNA to separate, the primers to pair with their respective DNA strands, the DNA polymerase to activate, and a new DNA strand to be formed.

The thermal cycling procedure, listed below, is continued until the specified fragment is amplified sufficiently for use.

Thermal Cycling

• 90°C, 3 minutes
• [95°C, 15 seconds; 55°C, 15 seconds; 72°C, 30 seconds] × 30
• 72°C, 3 minutes
• 4°C, ∞

Digestion/Ligation Reaction Table
Reagent Assembly Negative Control
PCR fragment 1 (vector) 1.0 μL 1.0 μL
PCR fragment 2 1.0 μL --
PCR fragment 3 1.0 μL --
10x T4 ligase buffer 1.0 μL 1.0 μL
10x T4 ligase 0.25 μL 0.25 μL
BsmBI 0.5 μL 0.5 μL
H2O 5.25 μL 7.25 μL
Total Volume 10 μL 10 μL

### Digestion and ligation reaction

The Type IIS assembly strategy employs a single-pot assembly, wherein digestion and ligation occur in tandem. To prevent the futile digestion/ligation loop that could result from this assembly strategy, the BsmBI restriction enzyme is used. BsmBI is useful in this scenario because its binding site is remote from its cutting site.

In the digestion and ligation reaction, BsmBI binds to its binding site, CGTCTC, and cuts at a location further along the DNA strand. This creates a 4 base pair "sticky overhang." Complementary "sticky overhangs" then pair up and are connected by the ligase.

The thermal cycling procedure used in the digestion and ligation reaction is shown below.

Thermal Cycling

• [45°C, 2 minutes; 16°C, 5 minutes] × 25
• 60°C, 10 minutes
• 80°C, 20 minutes
• 4°C, ∞

### Parts and primers

The following table lists the BioBricks used in the construction of the Sweet Cyan device. The individual parts can be found with a simple search of the part IDs at the Parts Registry.

BioBrick parts used in the device assembly
Name ID Size
IPTG inducible lac promoter cassette [Brick 1] BBa_K418003 1416 bp
RBS + CFPlva + term. X2 [Brick 2] BBa_K411225 917 bp
BioBrick plasmid backbone [Vector] pSB1A3 2155 bp

The following table lists the primers used in the mutagenesis and PCR procedures of device assembly.

Primers used in the device assembly
Part/Purpose Forward (5' to 3') Reverse (5' to 3')
[Brick 1] CACACCACGTCTCATAGATTGACAGCTAGCTCA CACACCACGTCTCATGTGCTCAGTATCTT
[Brick 2] CACACCACGTCTCAAAAGAGGAGAAATAC CACACCACGTCTCATAGTTATAAACGCAGAAAG
[Vector] CACACCACGTCTCAACTAGTAGCGGCCGC CACACCACGTCTCATCTAGATGCGGCCGC
[Brick 1] Mutagenesis ATCAGCTGTTGCCCGCCTCACTGGTGAAAAG TCTTTTCACCAGTGAGGCGGGCAACAGCTGA

## Testing: Modeling and GFP imaging

Network diagram illustration of the lac model (Julia)

### A lac switch model

We used a previously published synthetic switch, developed by Ceroni et al.[6], to understand how our system could potentially be modeled and simulated. The graphic to the left depicts the relationships between the parameters of the lac operon switch described by Ceroni using a network diagram illustration. The parameters shown in the illustration relate to cell processes and could be used in forming a cohesive mathematical model of the cell's operation.

In order to approximate the behavior of this set-up, a mathematical model can be developed based upon the relationships between the processes found in the cell. These relationships can be expressed in mathematical terms using numbers that relate to the system, including creation or decay rates, concentrations, or various constants. The actual values for these parameters can be sourced from experimentation, literature, or a predefined steady-state.

If a model is well-defined and the necessary parameters known, a person may use the model to ascertain the state of a cell at a given point in time. For example, if an experimenter wanted to know the decay of the GFP protein molecules at a given point in time in a single cell, the following equation could be written using the notation found in the table below.

Decay = G × λG/L

The formula takes the concentration of the GFP protein in molecules per cell ("G") and multiplies it by the protein degradation rate in minutes-1 (G/L"). This results in a decay value for GPF in molecules per minute per cell.

The Ceroni et al. model and the network diagram illustration use the table of variables and parameters seen below in their representation of the lac switch. The variables related to a particular cell process are located near to that process in the network diagram illustration.

Lac switch model: Important variables and parameters[6]
Variable Description Units
I IPTG concentration mM
G GFP protein concentration molecules/cell
LF free LacI molecules molecules/cell
LI LacI molecules bound to IPTG molecules/cell
MG mRNA molecules of GFP molecules/cell
ML mRNA molecules of LacI molecules/cell
DFG/L free Repressor/Reporter plasmids plasmids/cell
DLG/L Repressor/Reporter plasmids bound to LacI molecules plasmids/cell
DIG/L Repressor/Reporter plasmids bound to induced LacI molecules plasmids/cell
D0G number of Reporter plasmids per cell plasmids/cell
D0L number of Repressor plasmids per cell plasmids/cell
αG GFP rate of synthesis minutes-1
AL LacI rate of synthesis minutes-1
αMG GFP transcription rate minutes-1
αML LacI transcription rate minutes-1
KLx equilibrium binding constant of the LacI-Ox complex molecules/cell
KIx equilibrium binding constant for the binding of induced LacI molecule to the Ox operator sequence molecules/cell
KLI equilibrium binding constant for binding IPTG-LacI mM
τLI time constant of LacI binding to operator sequences minutes
τDI time constant of induced-LacI binding to operator sequences minutes
τDL time constant of LacI-IPTG binding minutes

Figure 1: Original Bgal Concentration vs. Time with I = 0.32
Figure 2: Bgal Concentration vs. Time with I = 0.045
Figure 3: Bgal Concentration vs. Time with I = 0.064

### An interactive model

We used a model of the natural Lac operon to understand how changing the parameter values changes the behavior of the system. By changing the initial concentration of input (IPTG in this case), we were able to estimate the threshold that produces an "on" state in the system.

Initially, the code had the concentration at 0.32 which is seen in the β-galactoside (Bgal concentration) vs. time plot (Figure 1). This value was changed again to 0.045 in determining the threshold that produces this "on" state (Figure 2). After proceeding to go up and down with these a values, a threshold was indeed found where the output concentration of IPTG was sustained and is about 0.064 (Figure 3).

Because the rate at which β-galactosidase is being produced must interact with the degradation rate of β-galactosidase, the production starts to cap off at around time = 100 with an approaching βgal concentration of about 4.52 x 10-4 as seen in the original model. As the initial concentration of IPTG goes down (say 0.045), this time goes down to less than 10 with the output decreasing after a peak of concentration (2.298 x 10-5) as the input decreases. Even at this point however, the output of IPTG is still not quite sustained although a pattern is evident. As soon as the concentration gets to around 0.064, visible equilibrium is seen between production and degradation at a time of around 10 and a concentration of about 2.56 x 10-5 and thus a threshold is found.

This model assumes that IPTG stays constant over time although realistically IPTG would of course fluctuate or run out as time would go on. Some more terms/variables are taken into account as well:

Terms of Interest with Matlab Model
Variable Description
μ Dilution of input IPTG or [IPTG]/cell volume, with IPTG diffusion
γβ Degradation of βgal protein (the β-galactosidase) concentration that is being produced
αM Production rate that M (the mRNA) is being transcribed
αβ Production rate that βgal (the β-galactosidase) is being translated
cell (= 1) Bacterial cell volume of 1

### Collecting imperical values to improve the model

Sarah
We used a microscopy imaging technique to determine the production rate of GFP yeast. Based on our collected data we were able to determine a "real" value for the maximum GFP production rate for the given conditions.

- show plot of data and discuss outcome. - include some of the pictures of the raw data - wrap up section to explain how the curves could be improved

DJMyeast010.jpg Ideally, the GFP production rate measured by this method could be entered as a value for [which parameter] in the Ceroni et al. model.

## Stakeholder Assessment

Stakeholder Matrix

SUPPORTS & UNDERSTANDS
text

DOES NOT SUPPORT & UNDERSTANDS
A group that understands the technology behind the device but would not support its construction and use could be competition, stakeholders in current technology that meet the customer needs that this new device would try and cater to. Also, scientists, engineers, and healthcare personnel who know the implications of using E. coli in a biodegradable device may oppose its commercialization, as mistakes made in production or consumer handling of the product could prove harmful to human and environmental health.

Public and laymen knowledge of E. coli may consist of only what they hear in the news, which often relates to food contamination scares; for this reason, stakeholders of the device itself may not support its production if they believe that widespread stigma may prevent successful marketing and sales campaigns.

SUPPORTS & DOES NOT UNDERSTAND
text

DOES NOT SUPPORT & DOES NOT UNDERSTAND
In general, when the common person hears about E. coli, they assume that it is the strain that causes great harm to the human species. Because of this, those who do not fully understand that many strains of E. coli that are harmless to humans exist. By using a biodegradable device that is powered with E. coli, it runs a risk that the average consumer would shy away from this type of light source because of the generalized fear of the bacteria. Therefore, those who do not fully understand that there are completely harmless types of E. coli and that they can be quite useful in our everyday life would not support such a product. This product would lack their support simply because of lack of knowledge and a general public opinion towards E. coli.

## Our Team

Emily Byrne
• My name is Emily Byrne, and I am a student majoring in biomedical engineering. I am taking BME 494 because I am interested in genetic engineering, synthetic biology, and their potential to impact the clinical setting. An interesting fact about me is that I enjoy painting and woodworking.

Sarah K. Halls

• My name is Sarah K. Halls, and I am a student majoring in Biomedical Engineering. I am taking BME 494 because I enjoy cell and tissue Engineering work and hope to start my career in this field of study. An interesting fact about me is that I did an internship at Harvard University working on cell patterning.

Sean Hector

• My name is Edgil Hector (Sean), and I am a student majoring in biomedical engineering. I am taking BME 494 because the subject is relevant to my interests, and the class counts as a required technical elective. An interesting fact about me is that I am the most indecisive human being on the planet.

Julia Smith

• My name is Julia Smith, and I am a senior majoring in Biomedical Engineering. I am taking BME 494 because I am extremely interested in synthetic biology. An interesting fact about me is that in addition to my nerdy side and love of academic learning, I train reining horses.

## Works Cited

1. http://en.wikipedia.org/wiki/Escherichia_coli [e-coli-wiki]
2. http://www.studyblue.com/notes/note/n/microbiology-exam-2/deck/2183983 [microbio-exam]
3. http://en.wikipedia.org/wiki/Lac_operon [lac-op-wiki]
4. Benno Muller-Hill. The Lac Operon. Walter de Gruyter. isbn:3110148307. [Muller-Hill-1996]
5. http://tools.invitrogen.com/content/sfs/manuals/geneart_site_directed_mutagenesis_man.pdf [invitrogen]
6. Ceroni F, Furini S, Giordano E, and Cavalcanti S. . pmid:21070658. [Ceroni-2010]