iGEM 2019 — Team Baltimore_BioCrew

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# Team:Baltimore BioCrew/Notebook

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* team
  + [The Crew](https://2019.igem.org/Team%3ABaltimore_BioCrew/Team)
  + [Collaborations](https://2019.igem.org/Team%3ABaltimore_BioCrew/Collaborations)* Project
    + [Description](https://2019.igem.org/Team%3ABaltimore_BioCrew/Description)
    + [Design](https://2019.igem.org/Team%3ABaltimore_BioCrew/Design)
    + [Protocols](https://2019.igem.org/Team%3ABaltimore_BioCrew/Experiments)
    + [Notebook](https://2019.igem.org/Team%3ABaltimore_BioCrew/Notebook)
    + [Results](https://2019.igem.org/Team%3ABaltimore_BioCrew/Results)
    + [Improve](https://2019.igem.org/Team%3ABaltimore_BioCrew/Improve)
    + [Attributions](https://2019.igem.org/Team%3ABaltimore_BioCrew/Attributions)* parts
      + [Basic Parts](https://2019.igem.org/Team%3ABaltimore_BioCrew/Basic_Part)
      + [Composite parts](https://2019.igem.org/Team%3ABaltimore_BioCrew/Composite_Part)
      + [Parts Collection](https://2019.igem.org/Team%3ABaltimore_BioCrew/Part_Collection)* Human Practices
        + [Human Practices](https://2019.igem.org/Team%3ABaltimore_BioCrew/Human_Practices)
        + [Public Engagement](https://2019.igem.org/Team%3ABaltimore_BioCrew/Public_Engagement)* Awards
          + [Measurement](https://2019.igem.org/Team%3ABaltimore_BioCrew/Measurement)
          + [Model](https://2019.igem.org/Team%3ABaltimore_BioCrew/Model)* [Safety](https://2019.igem.org/Team%3ABaltimore_BioCrew/Safety)
          * [Judging Form](https://igem.org/2019_Judging_Form?id=3301)

- \*Wiki best viewed in Google Chrome

**Notebook**

* [Characterization](#section-1)

* [Creation](#section-2)

* [Improvement](#section-3)

* [Modeling](#section-4)

# Characterization

# Creation

# Improvement

# Modeling


[![](https://2019.igem.org/wiki/images/8/8b/HQ_page_logo.jpg)](https://2019.igem.org)

# Team:Baltimore BioCrew/Experiments

- [![navlogo](https://static.igem.org/mediawiki/2019/6/60/T--Baltimore_BioCrew--logottextsmaller.png)](https://2019.igem.org/Team%3ABaltimore_BioCrew)

* team
  + [The Crew](https://2019.igem.org/Team%3ABaltimore_BioCrew/Team)
  + [Collaborations](https://2019.igem.org/Team%3ABaltimore_BioCrew/Collaborations)* Project
    + [Description](https://2019.igem.org/Team%3ABaltimore_BioCrew/Description)
    + [Design](https://2019.igem.org/Team%3ABaltimore_BioCrew/Design)
    + [Protocols](https://2019.igem.org/Team%3ABaltimore_BioCrew/Experiments)
    + [Notebook](https://2019.igem.org/Team%3ABaltimore_BioCrew/Notebook)
    + [Results](https://2019.igem.org/Team%3ABaltimore_BioCrew/Results)
    + [Improve](https://2019.igem.org/Team%3ABaltimore_BioCrew/Improve)
    + [Attributions](https://2019.igem.org/Team%3ABaltimore_BioCrew/Attributions)* parts
      + [Basic Parts](https://2019.igem.org/Team%3ABaltimore_BioCrew/Basic_Part)
      + [Composite parts](https://2019.igem.org/Team%3ABaltimore_BioCrew/Composite_Part)
      + [Parts Collection](https://2019.igem.org/Team%3ABaltimore_BioCrew/Part_Collection)* Human Practices
        + [Human Practices](https://2019.igem.org/Team%3ABaltimore_BioCrew/Human_Practices)
        + [Public Engagement](https://2019.igem.org/Team%3ABaltimore_BioCrew/Public_Engagement)* Awards
          + [Measurement](https://2019.igem.org/Team%3ABaltimore_BioCrew/Measurement)
          + [Model](https://2019.igem.org/Team%3ABaltimore_BioCrew/Model)* [Safety](https://2019.igem.org/Team%3ABaltimore_BioCrew/Safety)
          * [Judging Form](https://igem.org/2019_Judging_Form?id=3301)

- \*Wiki best viewed in Google Chrome

**PROTOCOLS**

* [Anderson Promoters](#section-1)

* [MAFF](#section-2)

* [Killswitch](#section-3)

* [General Protocols](#section-4)

* [General Recipes](#section-5)

# Anderson Promoters Protocols

## Experimentation Overview

After we had selected different Anderson Promoters of varying strength, we began our work. Our first step was a simple resuspension of the 5 promoters out of the distribution plate. After the DNA was suspended, we proceeded to ligate and insert into competent cells. After we had established colonies,

## Protocols

# MAFF Protocols

## Experimentation Overview

Our two MAFF genes, BT2268 and BT2269, were synthesized and ordered with 6x his tags for purification. We proceeded to run a gel electropheresis in order to confirm our genes were the proper length, which ended up being successful. After the genes had been inserted into *E. Coli*, we ran an SDS-Page in order to check for protein expression.

## Protocols

# Killswitch Protocols

## Experimentation Overview

In addition to the basic SynBio protocols (resuspension, ligation, transformation, gel electropheresis, etc.), we also planned to run experiments to determine the efficacy of both the original and the redesigned killswitches. While we were able to test the original killswitch multiple times, we were unable to test the redesigned version before wiki freeze due to synthesis errors.

## Protocols

## Media Recipes

# General Protocols

### Gel Electropheresis

#### Pouring the Gel

1. Slowly measure out agarose on scale (for a standard 1% gel, use 1 g of agarose. For other concentrations, calculate accordingly). Stay within ~.05 g of 1 g.
2. Mix agarose powder with 100 mL 1xTAE in a microwavable flask.
3. Microwave for 1-3 min until the agarose is completely dissolved, stopping every 30 seconds to swirl the flask. Keep an eye on it to make sure it does not overboil. Wear oven mitts when handling the flask.
4. Place agarose solution on counter until the flask can be comfortably held
5. Set up the gel tray with the well comb in place, as one person slowly pours the agarose solution into the well. Avoid bubbles.
6. Let gel sit for 20-30 minutes until completely solidified (the gel will be milky white and opaque).

#### Loading Samples

1. Add equal amount of loading buffer to each of your samples.
2. Place the agarose gel into the electrophoresis unit.
3. Fill gel box with 1xTAE until the gel is covered and container is filled.
4. Carefully load a molecular weight ladder into the first lane of the gel. Place your elbow on the counter to prop yourself up so you can look at the gel from an angle to see the wells. Place the tip of the pipette tip just above the well and slowly push so the sample fills the entire well.
5. Load the rest of the samples in this manner.
6. Run the gel at 80-150 V until the dye line is approximately 75-80% of the way down the gel for about 1 hour. NOTE: Black is negative, red is positive. Always Run to Red.
7. Turn OFF power, disconnect the electrodes from the power source, and then carefully remove the gel from the gel box.
8. Visualize your DNA fragments under UV light.

### Plasmid Purification

 [Plasmids were purified via the QIAprep Spin Mini Prep Kit Protocol](https://www.qiagen.com/us/resources/download.aspx?id=22df6325-9579-4aa0-819c-788f73d81a09&lang=en)

### Restriction Digest

Master mix:

1. 76 uL H2O
2. 20 uL 10x NEB2
3. 1 uL EcoR1
4. 1 uL Pst1
5. 1 uL Dpn1
6. 1 uL BSA

Mix together:

1. 10 uL Sample DNA
2. 10 uL Master Mix

### Ligation

Mix together:

1. 2 uL plasmid
2. 3.5 uL insert
3. 1 uL T4 Ligase buffer
4. 0.5 uL T4 Ligase
5. 4.5 uL H2O

### Transformation

[We used the iGEM Parts Registry Transformation Protocol](https://static.igem.org/mediawiki/parts/6/67/IGEM_Registry_-_Transformation_Protocol.pdf)

### Colony PCR

Master Mix:

1. 316.8ul dIH20
2. 44ul Taq Buffer
3. 22ul foreward primer
4. 22ul reverse primer
5. 33ul dNTPs
6. 2.2ul Taq

Add 1ul DNA to 19ul Master Mix
Settings:
1 Cycle

1. 95°C - 1min

30 Cycles

1. 95°C - 30s
2. 55°C - 45s
3. 72°C - 45s

1 Cycle

1. 72°C - 2min

Hold at 4°C

### Protein Resuspension and Protein Gel Electropheresis

1. Resuspend protein sample in a 1:1 ratio of sample to cracking buffer
2. Place resuspended sample in boiling water for 5 minutes
3. Load samples into protein gel
4. Run at 100v
5. Run until the gel is about 75-80% of the way down the gel
6. Remove gel from electrodes and plastic casing
7. Wash gel with purified water about 3 times, agitating the vessel the gel and water are in slightly to wash thoroughly, while not tearing the gel
8. Stain the gel with Simplyblue dye

### Spin Column Purification of 6xHis-tagged proteins

1. Resuspend a pellet derived from 5ml cell culture volume in 630 ul Lysis buffer (NPl-10). Add 70ul Lysozyme Stock Solution (10mg/ml) and add 3 units/ml culture volume Benzonase Nuclease
2. Incubate for 15-30min
3. Centrifuge lysate at 12000 x g for 15-30 min at 4 degrees C. Collect the supernatant.
4. Save 20 ul of the lysate for SDS-PAGE analysis
5. Equilibrate the Ni-NTA spin column with 600 ul buffer NPl-10. Centrifuge for 2 minutes at 2900 rpm. Spin without lid to ensure it is done in two minutes
6. Load up to 600 ul of the cleared lysate containing the His-Tagged protein onto the (pre-equilibrated) Ni-NTA spin columns. Spin for 5 minutes at about 1600 rpm, and collect the flow-through. To ensure efficient binding, don’t go higher than 1600 rpm, though do it with an open lid
7. Wash the column twice with 600 ul Buffer NPl-20. Centrifuge for 2 min. at about 2900 rpm. Save the flow-through for analysis by SDS-PAGE
8. Elute the protein twice with 300ul Buffer NPl-500. Centrifuge for 2 minutes at about 2900, and collect the eluate. Most of the protein will be in the first eluate. The rest will be in the second. 300ul each time

# General Recipes

[![](https://2019.igem.org/wiki/images/8/8b/HQ_page_logo.jpg)](https://2019.igem.org)

# Team:Baltimore BioCrew/Results

- [![navlogo](https://static.igem.org/mediawiki/2019/6/60/T--Baltimore_BioCrew--logottextsmaller.png)](https://2019.igem.org/Team%3ABaltimore_BioCrew)

* team
  + [The Crew](https://2019.igem.org/Team%3ABaltimore_BioCrew/Team)
  + [Collaborations](https://2019.igem.org/Team%3ABaltimore_BioCrew/Collaborations)* Project
    + [Description](https://2019.igem.org/Team%3ABaltimore_BioCrew/Description)
    + [Design](https://2019.igem.org/Team%3ABaltimore_BioCrew/Design)
    + [Protocols](https://2019.igem.org/Team%3ABaltimore_BioCrew/Experiments)
    + [Notebook](https://2019.igem.org/Team%3ABaltimore_BioCrew/Notebook)
    + [Results](https://2019.igem.org/Team%3ABaltimore_BioCrew/Results)
    + [Improve](https://2019.igem.org/Team%3ABaltimore_BioCrew/Improve)
    + [Attributions](https://2019.igem.org/Team%3ABaltimore_BioCrew/Attributions)* parts
      + [Basic Parts](https://2019.igem.org/Team%3ABaltimore_BioCrew/Basic_Part)
      + [Composite parts](https://2019.igem.org/Team%3ABaltimore_BioCrew/Composite_Part)
      + [Parts Collection](https://2019.igem.org/Team%3ABaltimore_BioCrew/Part_Collection)* Human Practices
        + [Human Practices](https://2019.igem.org/Team%3ABaltimore_BioCrew/Human_Practices)
        + [Public Engagement](https://2019.igem.org/Team%3ABaltimore_BioCrew/Public_Engagement)* Awards
          + [Measurement](https://2019.igem.org/Team%3ABaltimore_BioCrew/Measurement)
          + [Model](https://2019.igem.org/Team%3ABaltimore_BioCrew/Model)* [Safety](https://2019.igem.org/Team%3ABaltimore_BioCrew/Safety)
          * [Judging Form](https://igem.org/2019_Judging_Form?id=3301)

- \*Wiki best viewed in Google Chrome

**Results**

* [Summary of Results](#section-1)

* [Future Work](#section-2)

# Summary of Results

### *B. Theta* Genes

Our goal was to help repopulate the gut microbiome after antibiotics. During our research, we discovered Mucous Associated Functional Factors (MAFF) proteins, proteins synthesized by *B. theta*, that support the symbiosis of many bacterial species within the gut and maintain the health of the epithelial cell lining. As *B. theta* is anaerobic, difficult to grow in a lab, and is extremely sensitive (thus often wiped out of the gut after antibiotics), we decided that a MAFF supplement would be the best solution to the problem. Thus, we aimed to synthesize the MAFF proteins in *E. coli* by creating two plasmids (K3301012 and K3301013) each capable of expressing one of two MAFF proteins. The two genes for the proteins are BT2268 and BT2269, which we used to develop the basic parts BBa\_K3301001 and BBa\_K3301002.

During our work, we found it difficult to synthesize the plasmid containing BT2268. Due to its length, we ordered the gene in two parts that would be later linked by a BamHI restriction site. However, the star activity and lack of inactivation temperature for this enzyme made the gene impossible to ligate reliably into one piece, and thus all transformation efforts failed. As a result, we focused our energy on BT2269.

Here are our results:
After digestion, ligation, and transformation, positive BT2269 colonies grew. After extracting and digesting plasmids from the colonies with EcoRI and PstI, a gel was run. On it, we saw a band of about 2kbp, the size we expected, thus indicating that a successful uptake of the BT2269 gene and mechanisms to produce it into Ecoli.

![](https://static.igem.org/mediawiki/2019/thumb/6/6a/T--Baltimore_BioCrew--gelwetlab2.jpeg/800px-T--Baltimore_BioCrew--gelwetlab2.jpeg)

Plasmids were digested with EcoRI and PstI and run on a gel. A band of about 2kbp was displayed, signaling a correct transformation.

### Killswitch

After disappointing results while testing the original killswitch, we focused our attention to the redesigned version. After some trouble with synthesis due to the complexity of the construct, we eventually got our DNA shipped after we changed out the terminator for something less complex. A positive gel electropheresis told us that our DNA was as long as it should be. After colonies were grown successfully, we proceeded to run a new experiment.

![](https://static.igem.org/mediawiki/2019/thumb/4/4d/T--Baltimore_BioCrew--kscolony.jpeg/450px-T--Baltimore_BioCrew--kscolony.jpeg)

![](https://static.igem.org/mediawiki/2019/1/1b/T--Baltimore_BioCrew--finaldata.png)

![](https://static.igem.org/mediawiki/2019/thumb/5/5a/T--Baltimore_BioCrew--kspics.jpeg/800px-T--Baltimore_BioCrew--kspics.jpeg)

This data clearly follows a visible trend. There is an immediate jump in the OD of each sample, save one, as the xylose concentration goes above 0%, as now the bacteria is expressing the antitoxin. After that initial jump, the reading start to even out, with some OD readings growing. This tells us that the initial jump is around the xylose concentration needed to maintain a colony.

# Future Work

We aim to continue to expand upon this project by

-Purifying the MAFF protein from the positive colonies

-Ensuring the reproducibility of our data

-Finding a new method of ligating BTT268 so we can synthesize it