Week 12, Semester 2

This week is focused on expanding my extraction protocols to include additional bacterial species. To date, E. coli has been the sole species utilized for all extractions and polymerase chain reactions(PCRs). The additional species that have been included are : Pseudomonas aeruginosa, Proteus vulgaris, and Staphylococcus aureus. The two former were chosen due both to availability and their status as gram-negative bacteria; the protocol I am using for extractions was specifically developed for application against gram-negative species, due to the structural differences that exist between gram-negative and gram-positive species. S. aureus, though gram-positive, was selected both to test to efficacy of the gram-negative protocol against a positive species and to be used as the base species for design of a gram-positive specific protocol. It is expected that my current protocol will be ineffective at producing DNA from a gram-positive organism due to the gram-negative specificity of the cell lysing agents used in the developed protocol, thus a separate protocol will have to be designed.

Until the next blog, please enjoy the following links.

Everything you always wanted to know about unlocking and sequencing the human genome can be found at this fascinating Smithsonian website:
http://www.genome.gov/smithsonian/

Gain access to my personal favorite scientific study, the Gombe Research Project, which Dr. Jane Goodall has been conducting for more than 50 years; use Google Earth to enjoy the panoramic views of chimpanzee individuals, their family groups, and the Tanzanian park within which they reside.
http://www.google.com/maps/about/behind-the-scenes/streetview/treks/gombe-tanzania/

Photo credit: Fanni, photographed by Anup Shah for National Geographic Magazine.
Access additional photos and background information at:
http://ngm.nationalgeographic.com/ngm/0304/feature4/zoom4.html

Week 11, Semester 2-A Much-Needed Break

Hello! Last week, I was able to join our fellow scholars and faculty advisors for a welcome bit of rest and relaxation on our first field trip of the semester. We piled into the van and headed for Dreamy Draw Park and Recreation Area to hunt for an (alleged) alien crash site, do a little hiking and geo-caching, and eat lunch courtesy of Phoenix College. Who knew exercise and getting a sunburn could be so fun?

Even though the nearest Starbucks drive-through was miles away, somehow we managed to have a great time, use GPS, and learn about ephemeral desert washes before the day was over. No alien life forms were spotted, but somehow it didn't matter when I looked around at the smiling faces of this semester's team of scholars and faculty and realized once again how lucky I am to be part of this crew. It saddens me to think that another semester has almost come and gone, and before long this program, for me, will have concluded.

Next week I will pick up my research again, and begin drafting this semester's research paper. Until then, please enjoy these candid pics from our outing.

Week 10, Semester 2

Hello! And welcome back to this blog.

This week has been focused on reviewing the data collected thus far and determining the next steps of my research project. I have decided to analyze genomic sequences of the various bacteria named in my abstract for sequence correlations; this will allow me to predict a primer design that will result in DNA amplification during the polymerase-chain reaction (PCR) process. This design prediction is in line with my original project hypothesis, which is that there are universal primers for PCR usage which will successfully amplify DNA from seven common bacterial species (all species are named in my abstract; see blog Week 6, Semester 1 for details.)

After primer design is complete, the next phase of this project is to repeat the procedures used to conduct extractions on E. coli. The entire protocol testing process will not be repeated; only the protocol and precipitate solutions found to be successful at extracting E. coli will be used on the six remaining species. Then, bacterial samples from all seven species will be submitted for PCR amplification using the specific primers that were designed.

This next phase begins in earnest in Week 11. For my remaining lab time this week, I will be joining the Biology staff and other S-STEM scholars on a much-needed off-site field trip to the Dreamy Draw Park & Recreation Area. For those of you who are unable to attend, please enjoy this shot of our beautiful desert, taken from within the park.

Week 9, Semester 2.

Colorized low-temperature electron micrograph, E. coli. https://www.flickr.com/photos/microbeworld/5981923914/

Welcome back to this blog!

This week's focus consists of running a polymerase-chain reaction (PCR) on the DNA samples previously discussed in the Week 5, Semester 2 edition of this blog. It remains to be seen if the primers utilized were successful at the DNA amplification process, for as of publication time the PCR was still in progress; thus the results had not been analyzed.

The next phase of this project will proceed beginning next week with the extension of the extraction protocol to other bacterial species endemic to this lab. The methodology utilized for E. coli extractions and testing will be repeated with each additional species; every phase of the project from extraction, to electrophoresis gel, to spectrometer reading, to finally PCR will be repeated with each additional species to identify any correlations or errors in the methodology used and results obtained. 

After the multi-species extractions have been finished, the project will conclude for the semester with an analysis of the genomic sequences specific to each bacterial species. The primers selected for the initial E. coli PCR's were referenced as being universal in the work Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes (Frank, et. al, 2008) and were therefore selected for further testing. However, it is hypothesized that further examination of the individual genomes is warranted to determine if a new primer design is needed for application to species other than E. coli.

Further details to follow on the next blog issue.

Week 8, Semester 2. Success!

Hello! And welcome back to my blog.

This week, I resumed testing of samples previously extracted from E. coli bacterium. Both protocols submitted for analysis utilized a 0.3 ml TBS and 10 µl SDS solution to lyse the cells, a 55°C heating and ice cooling method combined with a protein precipitation solution to reduce protein contamination and an isopropanol/ethanol wash to precipitate chromosomal DNA and clean the DNA pellet.The protocols differed in the substances used for protein precipitation; protocol one (P1) utilized proteinase K, and protocol two (P2) utilized a guanadine hydrochloride/sodium acetate solution. They also differed in length of precipitation in isopropanol; P1 was in solution for five minutes while P2 remained in solution @ -20°C for five days.

The samples were placed in an electrophoresis gel for analysis. The gels were created @ a ratio of 20 g agarose/100 ml 1 X TAE buffer ratio, with 4 µl of 10,000x concentration SYBY green DNA stain added to solution post-heating.

The spectrometer was also used to measure ultraviolet absorbance ratios of the four samples. Samples were subjected to 260 nm, 280 nm, and 320 nm consecutively.

Results:

DNA!

All four samples showed banding in the gel; P1 sample two contained the most clearly visible banding. The photo that follows is of the samples. The clarity is a bit off due to the age of the camera used to capture the image.

Calculations from the spectrometer readings to follow on my next blog. Happy learning!

Week 7-Semester 2.Mathopolis

Hello! Lab work is progressing, albeit at a slower pace than I would prefer. However, previous efforts to accelerate the pace of my project have shown that a consistent, repeated, and measured approach is most conducive to accurate results. Whether double- and triple-checking all calculations before beginning a protocol, or repeatedly verifying the settings on a pipette as I work, I have found that adhering to an established technique is the key to both finding and repeating accurate results.

Luckily for me, I have been inundated by the structured world of math this semester. I am taking Chemistry, Physics, and Trigonometry concurrently, so I spend quite a bit of time weekly honing my mathematical skills. This focus has transferred over to my research here in the lab and increased my proficiency at performing the calculations needed to move forward with my project.

This week has been heavily focused on gaining and retaining math skills, but I did focus on extractions as well. I was also able to finally utilize the recipe for the protein precipitation solution provided by Cori Leonetti, our in-house microbiologist. Unfortunately, due to a scheduling conflict with some classes, I was unable to access all the equipment needed to complete my protocols until late in the week. Therefore, the results of this week's work remain to be seen; until the process has been completed, here is the solution I am using to precipitate proteins from my DNA samples.

4.2 M Guanidinium Hydrochloride
0.9 M Sodium Acetate
4.8 pH target
De-ionized water to reach total volume of 50 mL

I calculated the molarity of the solution targeting a final volume of 50 mL. The GuHCl was in an 8.0 M solution; the sodium acetate was in solid form, so I used a mole-mass conversion to calculate the amount needed. I then mixed, observed for solubility, and added de-ionized water until nearly at final volume. I then measured the pH. The result was approximately 6.3, so I added HCL by dropper until the pH was reduced until it reached the desired result. I then added the remaining de-ionized water to achieve full volume and re-measured the pH for a final result.

More on the usage of this solution and further extractions to follow. Until then, please enjoy the following:

Week 6-Semester 2. Reference Guide #1

Hello! This week again finds that my DNA extractions and subsequent absorbance readings conducted using the spectrophotometer will fall on Friday, the day after this blog is due. As a result, any data collection and methodology conducted this week will appear in a later blog post.

Part of my research project this semester is to become personally proficient in the use of all lab equipment and also guide any students that follow in the operation of the previously mentioned (on this blog) “lost” spectrophotometer by compiling detailed instructions for usage. Therefore, this week’s post will be a brief process analysis about using the Helios spectrophotometer to take live UV absorbance ratio readings.

The reader should be cautioned that there are additional methods for taking readings, such as programming and saving fixed methods, and other nuances within the settings menu that may affect sequence progression of individual wells and absorbance ratio levels. This additional information will be included in future blog posts. In the interim, I have pre-set and saved the settings needed to conduct the following protocol. If implemented as described, without any changes to the settings menu, the user can quickly and easily take accurate live absorbance readings.

Quick guide to live reads:

Notes/overview:

·         The Helios needs 10-15 minutes to warm up before being used.

·         The user should not leave the lid open or peer into the bay for an extended length of time; safety goggles with UV protection are recommended.

·         Bacterial DNA solutions should be at a 1µl DNA/99µl diluting liquid ratio (total volume 100µl). Molecular biology-grade water works best due to its purity.

·         The control sample should be 100 µl of the same liquid used to dilute the DNA sample.

·         Due to an inherent flaw in the design of the Helios, both control and DNA samples may need to be increased to 200µl total volume each to improve data collection.

·         One reading will be taken of the control sample @ 260 nm to set a baseline.

·         Each DNA sample will be subjected to three nm readings in the following order: 260 (to measure DNA presence), 280 (to measure protein contamination), and 320 (to measure turbidity, i.e. additional contaminants). It is important to begin with the 260 nm setting, as any DNA will be degraded by the higher wavelengths, and accurate measurements will be negatively affected by using a different progression sequence.

·         The user should record absorbance ratios given by each nm level in order to later calculate DNA purity and concentration.

Begin:

1)      Insert control cuvette into well #1. Place cuvettes containing DNA samples in wells 2-7 as needed.

2)      Make sure well #1 is aligned in anterior position (between UV bulbs).

3)      Program control sample:

a)      Set UV nm @ 260 nm for zero-base reading by pressing “nm” on LED display.

b)      Type desired nm wavelength (260) in display. Hit enter.

c)      Press zero-base key to set read at zero.

d)     LED display should read 0.000 A 260 nm. Record data by writing it down (or print by pressing print key on LED display.)

4)      Program DNA samples:

a)      Use right arrow key to advance to desired well.

b)      Set initial read @ 260 nm as outlined in step 3.

c)      Display will show absorbance reading @ 260 nm. Record data.

d)     Re-set nm @ 280 nm. Record data.

e)      Re-set nm @ 320. Record data.

f)       Repeat steps 4a-e for additional wells.

The procedure is as simple as that! Good luck with your samples!

Please enjoy this excellent website from the Smithsonian about DNA. Website is also photo credit:

 http://www.genome.gov/smithsonian/