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	Team HTHS_Trussville_AL

Official Team Profile

The Hewitt-Trussville High School team consists of seven students in the Biomedical Sciences Academy. Trussville, Alabama is rural community of approximately 20,000 people found eighteen miles northwest of Birmingham in Jefferson County, and Hewitt-Trussville High School has approximately 1300 students. Over the last four years, we have navigated our way through the Project Lead The Way biomedical sciences curriculum and worked together in labs. The seven members of our team are all 2014 seniors including Jessica Bacon, Darcy Echols, Nicole Hardesty, Nikki Newman, Sikandar Raza, Connor Staggs, and Chloe Wilks. We also have an amazing mentor from the Hudson-Alpha Institute of Biotechnology, Dr. Bob Zahorchak. But, most importantly, we want to save the endangered snail populations in the Cahaba River by developing a cheap and efficent phosphate detection plasmid for the Alabama Department of Environmental Managaement to use.

Due to rising use of chemical based fertilizers, the runoff of harmful chemicals such as phosphate (PO43-) and nitrate (NO3-) into public water sources has increased. This accumulation of chemicals in streams and lakes is harmful to the environment. PO43- runoff in rivers is detrimental to aquatic life forms such as the Leptoxis compacta, a gastropod that was believed to have been extinct in 2000; however, in May of 2011 the Leptoxis compacta was rediscovered in the Cahaba River. PO43- is a food source for algae and as the levels of PO43- increase, the number of algae blooms increase and cover the surface of the water. This blocks sunlight so the energy cannot get to the bottom of the river. Currently tests are chemical in nature and specific to only certain forms of PO43- (testing only organic phosphate or orthophosphate). This research revolves around the creation of a biological plasmid to test for all forms of PO43- in a sample of water. Using a shuttle vector, the plasmid is first grown in E. coli, and then transferred into a specific type of yeast called S. cerevaise, which contains an outer sensor for PO43- .The sensor tests for the presence of PO43- because it is a food source for the yeast. If PO43- is present, then the yeast uses it for energy development; however, if no phosphate is present in the environment, then the sensor sends a cascading signal to a protein called Pho4, which binds to a gene called Pho5 to initiate the phosphate starvation cycle. This mechanism allows the yeast to produce its own phosphate.

The plasmid that is inserted into S. cerevaise contains the genetic sequence for the Pho5 promoter that when activated will turn on a Red Florescent Protein (RFP). The Pho5 promoter will be removed from one plasmid using the restriction enzymes EcoRI and BamHI. An adaptor will then be used to convert the sticky end produced by BamHI into a second compatible EcoRI sticky end. After performing Polymerase Chain Reaction, this fragment of DNA will then be inserted into a new plasmid using 3A assembly. The new plasmid will already posses the RFP gene and antibiotic resistance which will be used to make competent cells. The recombinant plasmid will then be grown in E. coli before being shuttled into the yeast cells. The Pho5 promoter in the new plasmid will then be able to receive the Pho4 protein if it is initiated when PO43- is not present. When the Pho4 is bound to the Pho5 on the plasmid, the RFP gene will be activated. The RFP will cause the yeast to turn bright red, signaling that there is no PO43- present; if the yeast does not turn bright red, then PO43- is present in the environment. Therefore the plasmid serves as a qualitative and quantitative method to test for the presence of PO43- in a water sample, which in turn creates a biological mechanism that is not hazardous to monitor levels of PO43- .

Notebook

2013

August 26, 2013:

1. Determine if the Pho Sensor is the one the group wants to use

2. Find the yeast plasmid vector to put the sequence into

3. Determine the restriction enzyme needed to cut the plasmid (and put the sequence in)

4. Get RFP (Red Fluorescent Protein) DNA sequence

5. Find and determine if the inverter DNA sequence will work

6. Gibson Assembly

7. Put plasmid through PCR

8. Test with electrophoresis

9. Cut sequences out of gels if working

10. Inject plasmid into yeast

11. Grow Yeast

12. Test Yeast

13. Develop standardization test for red color

14. Water quality test

September 17, 2013

To Do’s:

                   1. Download new software (Tinkercell and GENtle)

                   2. Redo Gantt Chart

                   3. Redraw plasmid

                   4. Start list of potential questions and problems

                   5. Finish scholarly article reviews

                   6. Put DNA sequences into software

                               Find Pho5 sequence and promoter

                               Find RFP sequence

                              Find Plasmid

                              Verify origin of replication

                              Verify antibiotic resistance 
                              
                              antibiotic vs. antifungal 
   
                 7. Discuss restriction enzymes

September 23, 2013:

-First skype meeting with Dr. Zahorchak

-Remove inverter from the plasmid

October 2, 2013:

To Do’s Before Visit to Hudson Alpha:

               1. Fix the Gantt Chart

               2. Make a flow chart of the process

               3. Need software for tomorrow so we can   look at it for plasmid creation.

               4. Need to be able to discuss the following topics on complex levels:
                              Restriction Enzymes
                              Plasmids
                              PCR
                             Competent Cells
                             What to use in place of antibiotics?
                             What is a promoter and ribosome binding site?

              5. Look through the following on parts registry 
                             Plasmids
                             Yeast Parts

October 3, 2013:

Questions:

1) Is phosphate consistent throughout a river or are there different concentrations at certain spots?

2) Orthophosphate vs. Polyphosphate

3) Pho 89, Pho84”p”, and Pho87/Pho90

4) Are there more sensors than just those?

5) Target the transmitters so there could be a more colored result for the phosphate levels.

6) Will the stored phosphate in the vacuoles affect our plasmid?

7) Pho84 and excess amounts of phosphate

8) Could we turn off/bypass Pho4

9) Increase CDK?

10) How does the algae know that phosphate is in the water? Possible back up?

Answers Dr. Zahorchak:

Ortho PO4-2 vs. Poly PO4-2 OH | Ortho: 2PO4-2 attached to each other

(bases sugar)--OH--P=O

| OH

Why trying to engineer these systems? ⇇

Detect PO4-2 (if it is present)

fertilizer has a lot of PO4-2

Check latest ADEM reports for water quality

How to detect levels?

Determine sensitivity (down the road)

What level will it switch on/off

Qualitative data first

Stored PO4-2 in a cell vacuole? Does that affect the test?

Yes

Think of a way to grow the yeast so that the cell can’t store subsistence in the vacuole (not a major priority right now)

Make both programs compatible to use

Pick One

    GENtle

Wait to measure different levels of color

Increase CDK?

       Do not want to mess with this
       Learn more about

Yeast Transformation Lab?

        Either make your own kit or buy competent cells (pros/cons)
        Competent Cells
                 Using antifungal to kill yeast that do not accept the plasmid

Check biobricks for the yeast and vector

Check for yeast iGEM projects from before/previous years

iGEM material=free

Make a list of what we need

Include sequences

What is this?

       Restriction Enzymes

Notes from Dr. Zahorchak:

Pho5 regulates phosphotase

What enzyme(s) are included in the pathway?

What if one of the sites you need is internal to Pho5?

Find Pho5 promoter (BLast)

Might need to find the exon.

Need the entire Pho5 promoter

Figure out if everything is on the RFP after Pho5 gene is fused

Answers from Dr. Zahorchak (continued):

Chemical test

     Converts PO4 to ortho

Would our test look for orthophosphate or all forms?

Test strips ($6) only test for ortho Chemical test ($45) converts all forms of phosphate into orthophosphate then tests

Goals Before Christmas:

1)Finish Research

2)plug everything into GENtle and run simulations

3)materials

4)methods (plasmid methods)

5)Begin Plasmid construction

October 9, 2013:

Meeting and Discussion with Dr. Zahorchak:

-Plasmid→ Antifungal DNA, Pho5, RFP DNA, Terminator Sequence

-Restriction Enzyme Site

-Gentle→ Plasmid, Pho5, Antifungal, RFP, entire plasmid

-Why would we add RFP before Pho5?

-Antifungal Agents

    -Amphotericin B
    -Aculeacin
    -Mulundocondin
    -Tunicamycin
    -Fluconazole
    -Itraconazole
    -Ketoconazole
    -Miconazole
    -Flucytosine
    -Terbinafine
    -Amcrofine

2014

January 15th 2014
January 16th 2014
January 21st 2014
January 27th 2014
February 3rd 2014
February 6th 2014
February 10th 2014
February 17th 2014
February 18th 2014
February 19th 2014
February 20th 2014
April 16th 2014
May 9th 2014
May 12th 2014
May 21st 2014

Results/Conclusions

What did you achieve over the course of your semester?

Safety

What safety precautions did your team take? Did you take a safety training course? Were you supervised at all times in the lab?

Attributions

Who worked on what?

Human Practices

What impact does/will your project have on the public?

Fun!

What was your favorite team snack?? Have a picture of your team mascot?

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Team:HTHS Trussville AL