Update

Blood: I performed the DNA extraction on all samples and will run horizontal agarose gel to see if there is a significant enough amount to warrant PCR amplification.

Algae: I helped Tony harvest his algal growth. Algal water was collected into falvon tubes and centrifuged. The supernatant was drained and the algal sediment was collected using a micrpippette and deposited into a metal pan. The pan was placed in an oven set at 70 degrees F for 45 minutes. Dried algae was scraped out of pan and collected in a beaker. The dried algal powder was ground using mortar and pestal (to make sure the cell walls were broken) and added to DIH2O a 30 cc syringe was used to remove water from beaker and inverted for 48 hours. The syringe shows 2 phases, a water phase and an oil phase. Oil extraction complete. The fish are still alive and happy and were added to the aquaponics fish family.

Protein: I began a new protein extraction and will run PAGE gels as soon as I read a couple more protocols. This week has been really busy with papers to write and exams in Calc and Chem.

Fish: The aquaponic fish are still quite happy with their salad bar root buffet and the addition of the algae fish. Half of the water was removed and replaced with DIH2O. I will check the pH when I return to lab next week. The fish have eaten almost all of the roots so I am going to grow more in the other tank.  I noticed that there were a couple of plants that had roots stuck in the holes. I thought I would be helpful and pull the roots through. I grabbed a container out of the tank and it slipped out of my hand. I spent the next 30 minutes cleaning it up. No plants were harmed in the making of this blog.

Update on blood, protein, algal infection, and fish

Blood: A protocol has been created and now I am waiting on primers. I collected blood, scalp hair, eyebrow hair, fingernail, and spit from myself, my daughter, and a friend that wishes to remain anonymous. we will call him Mr. XY. I will need to extract the DNA from these samples and then run a gel to see if DNA is present. Hopefully there will be a significant amount and I can proceed to PCR amplification.

Protein: I loaded a duplicate PAGE gel to the one that contains bands with 2 different biomarkers. Lane 8 contains 5uL Biorad Precision Plus Protein Dual Xtra Standards. This will measure proteins that range from 250kDa to 2 kDa.
Lane 1 contain 5uL of Fisher Bio Reagent. This measure proteins that range from 116 kDa to 14.4 kDa.
Running buffer was prepared with 100 mL 10x tris/glycerine/SDS buffer to 100 mL DIH2O. Gel ran at 140 volts for 1 hour and 30 minutes. 
Neither biomarker banded. I am not sure why but there could be many explanations. Possibilities include improper technique or equipment malfunction. I will research protocols and try again.

Algla infection: I was curious as to whether the bacteria that killed the algae is harmful to fish. If it is not, then it could possibly be used to eradicate unwanted algal growth from fish tanks. Two feeder fish were purchased from a local fish store and placed in a bowl containing 60 mL of contaminated algal water and 1 L of DIH2O. The bacteria are present. They are cocci, gram positive with a spikey appearance. As this bacteria matures the spikes grow into fimbrae that detach and float in the water. I took a 20 mL sample of water and introduced 2 antibiotic discs (penicillin and clindimycin) to see if the bacteria were affected. 48 hours later there were no bacteria present and the fish seem to be happy. Antibiotic discs were added to the infected water. After 6 days I came into the lab to see new algae growing in the once infected tank.

Fish: The plants have matured and the roots are growing through the holes in the bottom of the container and into the water. I placed the new plants into the tank and the fish immediately started nibbling. The pH is still steady at 8. Josh suggested removing half of the water and replacing it with DIH2O. I will do this next week. Two more fish were added to the tank in hopes that their excrement will lower pH.

Protein Extraction:
Through creative optimism and a little hard work, I received 2 biomarkers this week (Thank you Josh). One is from Fisher (measures protein MW of 116.0-14.4 kDa) and one from Biorad (measures protein MW of 250-2 kDa). My plan was to run these two biomarkers on a 4-20% Tris-HCL PAGE and then use it to measure the bands on the 4-20% Tris-HCL PAGE that I ran last week (2 identical gels). I loaded to 10 uL of Fisher into lane one and 10 uL of Biorad into lane 8. Running buffer was prepared using 100 mL 10x tris/glycerine/SDS buffer to 900 mL DI water. The gel ran at 100 volts for 2 hours. What resulted was each biomarker produced one band about 1/4 from the top of the gel. I am not sure why this happened. The electrophoresis tank did not make the usual high pitch noise that it does when it reaches maximum voltage but it stayed at a steady 100 volts and I could see continuous bubbles  so I didn't really worry about it. There are so many possibilities aas to why this run was not successful (equipment malfunction, defective product, and technique are at the top of my list so far). I will research this more and run a few more gels next week.

Blood: I am preparing to do a DNA extraction in order to visualize the double genome for blood type that I have been told that I have. I am meeting with Anil today to brainstorm some possible ideas.

Fish: The fish are still happy but the pH is still very stable at 8. They are also dependent on fish food and I would like them to eventually obtain optimal nutrition from the roots of the plants in the tank. Jeremy suggested that they do not like the plants that are growing and did a bit of research on fish palate. He discovered that fish enjoy bok choy, kale, arugula, and swiss chard. I used the extra tank to plant these. we will see if the fish enjoy their new salad bar.

Algal infection:
So after taking a water sample and staining it, I discovered that there is indeed bacteria present. They are cocci,Gram positive bacteria that look pretty scary under the microscope. I streaked a McKonkey plate to make sure that they are gram negative and I also streaked a MSA plate to see if they are halophiles given the salinity of the water, although this may have been a byproduct from the algal cell lysis.