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| treat. All 12 days of hard work deserved a celebration and the students and mentors | | treat. All 12 days of hard work deserved a celebration and the students and mentors |
| bonded over frozen custard and ice cream.</p> | | bonded over frozen custard and ice cream.</p> |
| + | </div> |
| | | |
| + | <div class="text2"> |
| + | <h2>Week 4: June 19-23</h2> |
| + | <h3>Monday (06/19/17)</h3> |
| + | <p>After the weekend, the students met in the lab and initiated a second |
| + | digest. They were determined to get everything measured correctly and |
| + | leave minimal room for mistakes. This time around, the students were |
| + | much more knowledgeable about buffers and enzymes used and |
| + | proceeded carefully combining them with DNA. After the digest was complete, the |
| + | young scientists began prepping another gel for electrophoresis. Everything went |
| + | smoothly while the digest was completed and DNA was extracted and cut by the |
| + | enzymes. Next, the students prepped the DNA by adding a loading dye and then |
| + | proceeded to put it on the gel. After electrophoresis for 30 min, the gel was complete. |
| + | The LabPats were able to use this downtime for updating lab journals, creating new |
| + | and exciting logos, as well as continuing to work on the wiki. Next, another |
| + | experienced mentor helped with analyzing the gel and cutting out the DNA from the |
| + | gel. However, they were quite disappointed to learn that there were 3 bars, indicating |
| + | more base pairs than expected. The mentors ensured them that the gel still worked |
| + | and that they just needed to cut out the fluorescent band that was relevant. |
| + | Meticulous work was done to cut out the gel, and the labpats were finally able to let |
| + | out a sigh of relief once the gel was safely placed in the tube and put in the fridge to |
| + | be melted down tomorrow.</p> |
| | | |
| + | <h3>Tuesday (06/20/17)</h3> |
| + | <p>The students quickly resumed where they had left off to begin their gel |
| + | extraction. Two different protocols were used to see which one would |
| + | achieve a higher concentration. The teams were divided into Tina and Annie |
| + | working with Svetlana on (QIAEX II Agarose Gel Extraction) and Jason and Dallas (who |
| + | unfortunately was ill, so Annie and Tina tag teamed his sample) working with Mike on |
| + | QIAEX Gel Extraction Kit. The gel extractions were performed and the nano drop test |
| + | was performed. The only successful gel extractions were performed by the girls |
| + | (Svetlana’s protocol), so they took home the victory! The boys learned a lot from their |
| + | error and submitted defeat. The day was wrapped up by working hard designing the |
| + | wiki and learning how to code.</p> |
| + | |
| + | <h3>Wednesday (06/21/17)</h3> |
| + | <p>Today the students began their second Polymerase Chain Reaction (PCR). |
| + | Under the watchful eye of Dr. Harbaugh, the students independently finished |
| + | the PCR and loaded it into the thermocycler. Another small gel was prepared |
| + | and the PCR’s were taken out and loaded on the gel. The students meticulously loaded |
| + | the PCR’s onto the slits of the gel with incredible precision that truly showed their |
| + | growing expertise.</p> |
| + | <p>The students received the results they had been hoping for, which showed that the |
| + | Super folded GFP had been inserted into the bacteria. They then performed a PCR |
| + | Purification, which separated the massive amounts of DNA. The DNA was then |
| + | measured using the nano drop and these results were given:</p> |
| + | |
| + | <h3>Thursday (6/22/17)</h3> |
| + | <p>The day began with another PCR. Today, the students were ready to |
| + | completely do the PCR by themselves with little guidance from the mentors. |
| + | The standard protocol was followed and the PCR and ran another cycle in |
| + | the thermocycler. Meanwhile, another gel was prepared by the students. This time |
| + | around, the students were very efficient and the process went by very quickly. The gel |
| + | ended up giving too many bands, but the mentors conversed and decided to proceed |
| + | with the PCR purification anyways. After the lab work was done, the students decided |
| + | to meet with the other lab students to discuss current progress. The students created |
| + | discussion points and had a great discussion with the other lab.</p> |
| + | |
| + | <h3>Friday (6/23/17)</h3> |
| + | <p>The day began bright and early with two PCR digests. This time a PCR |
| + | Vector Digest was conducted on the same from yesterday and a PCR GFP |
| + | digest was done on the sample from Wednesday (6/21/17). After following |
| + | the protocol, the students were able to successfully perform the digests. After |
| + | a 2 hour wait (per the protocol), the young scientists performed a purification on the |
| + | GFP digest. The goal was to cut off end bits of the base pairs to allow the plasmid |
| + | connect again. During the students' lunch break, another meeting was held with teacher |
| + | leaders who wanted to know information about progress and future proceedings.</p> |
| </div> | | </div> |
| + | <div class="text"> |
| + | <h2>Week 5: June 26-30</h2> |
| + | <h3>Monday (6/26/17)</h3> |
| + | <p>The students began another week of hard work. They made a gel to run |
| + | their previous Plasmid Digest. Next, they looked at the gel under the blue |
| + | light and found the band they were looking for at 3.2k base pairs. Next they |
| + | scalpeled out the desired band and began a gel extraction using the QIAEX ll |
| + | Agarose Gel Extraction Protocol. After the gel extraction they tested their results on the |
| + | Spectrotropsesis. The first sample was lower than preferred and the next sample had a |
| + | very uneven graph, but with the desired numerals. Afterwards, the mentors discussed |
| + | and determined to still do a legation the next day and see the results.</p> |
| | | |
| + | <h3>Tuesday (6/27/17)</h3> |
| + | <p>Today was the student's first ligation. The goal was to put the sticky ends |
| + | back together to form a complete plasmid. A lot of math was done to |
| + | determine the exact ratios of sfGFP and PCR vector plasmid. Luckily, Dr. |
| + | Harbaugh was able to assist the students with newly introduced lab techniques. There |
| + | was another protocol and the students were able to follow it with no problem. They |
| + | then went to the conference room and had another meeting with the other labs and |
| + | teachers. This time, both labs gave extraordinary presentations about project progress |
| + | and end goal. The RH lab presented their abundance of lab work and myriad of |
| + | website/wiki work. The RX lab presented lab work and some technical website work. |
| + | Afterwards, the groups planned out agenda and discussed necessary steps to |
| + | complete the wiki page.</p> |
| + | |
| + | <h3>Wednesday (6/28/17)</h3> |
| + | <p>The students began the day with a new PCR. After examining the plates from |
| + | yesterday, it was determined that there indeed was green fluorescence on the |
| + | plates. However, a PCR was needed with a gel to determine whether or not it was |
| + | sfGFP or GFP. High in spirits, the students immediately went to work. First, they |
| + | created a Master Mix following the PCR Protocol for Phusion DNA Polymerase. They |
| + | did some tricky math and figured out exact proportions needed for nuclease-free water, |
| + | Phusion Buffer, DMSO, Kpn1(forward primer), BsrG1(reverse primer), as well as the |
| + | phusion DNA polymerase. They each used 6 colonies. Four students used green |
| + | colonies and then dipped it into the PCR and the LB Broth with chloramphenicol. This |
| + | method ensures that only the bacteria immune to chloramphenicol can survive. On the |
| + | gel, it should give a precise band of base pairs indicating sGFP or GFP. Another |
| + | student used 6 colonies without the green fluorescence. It acts as a control. When it is |
| + | run as a gel, there should be random bars that indicate there is no sGFP or GFP. Then |
| + | the samples were put into the thermocycler for 1.5 hours according to the protocol. |
| + | The students then had the endure a nerve raking wait as they wondered if the PCR had |
| + | gone successfully and whether the bacteria had sGFP or not. After preparing another |
| + | gel, the students meticulously put the samples on the 40 wells. After 30 minutes of |
| + | running the gel, the students came back to an ecstatic Dr. Goodson informing them |
| + | that the gel had turned out as planned and that they could proceed with the mini-prep |
| + | before sending in the DNA for sequencing. Everyone shared "elbow-fives" and were |
| + | relieved that all their hard work had not gone to waste!</p> |
| + | |
| + | <h3>Thursday (6/29/17)</h3> |
| + | <p>Today the students began to mini-prep the samples from the previous day. |
| + | Right from the start, the students noticed fluorescent green coming from |
| + | one of the tubes. This would foreshadow what they would see later in the |
| + | day. They began the mini-prep full of hope and concentrated on following the protocol |
| + | exactly to achieve the best possible results. They decided to first put the tubes over |
| + | the light and observed a lot of fluorescence (see picture). After about 2 hours, they |
| + | were finally done. They nano dropped the sample and observed an incredible amount |
| + | of DNA. Everyone cheered as they realized that the "response" component of the |
| + | project was successful.</p> |
| + | |
| + | <h3>Friday (6/30/17)</h3> |
| + | <p>Since all the lab work is currently done until the DNA sample is sent to Ohio State |
| + | University for DNA sequencing, the students had the whole day to make website |
| + | improvements and wiki renovations. New logos were also created as well as |
| + | graphics. The students will continue to add content to the wiki weekly.</p> |
| + | </div> |
| | | |
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