Olympic B3 Science Summer Camp 2015
Biotechnology, Biodiversity and Bioinformatics
June 12th - June 26th
Pictures of Individuals and Class Activities are posted frequently -- Also a Blog by Gypsy Ruano
Our Facebook page has even more pictures but fewer captions and can be found at this link Requires Login
First Blog Entry (camera was not charged so pictures are missing).
Wednesday, June 11 th, 2014. The B3 Summer Science Camp Blog
First day of the B3 program was today and we learned a lot about the American Chestnut Tree. This magnificent tree used to be very abundant in the early 1800s 1900s
from Maine to some parts of Florida. But unfortunately due to a fungus (blight) brought to the U.S. from China , this species of tree was brought to near extinction. Luckily there are still a few trees in Crowders
Mountain that are still authentic American Chestnuts. We will be going there next class to extract samples from these saplings. Hopefully the samples we take help us get one step closer to finding a way to get rid of this fungal blight. The American Chestnut Foundation has already started cross breeding many American Chestnuts with Chinese Chestnuts since they are the
most immune to the blight while still being an American Chestnut. Hearing many of the people speak today about this issue makes all of us willing to help and make a difference in restoring the American Chestnut Tree. ----- Gypsy Ruano
June 15 th
Field Trip to Crowder's Mountain State Park to collect samples for analysis
The goal of this field trip was to see the native habitat of a few remaining wild American Chestnuts and to collect some of their leaves.
All have been affected by the blight, so we also hoped to collect some of the fungus, looking for bark rubbings and soil samples.
Ranger Kelly Cook was our guide for this trip, which started at the Linwood parking lot and took us to the peak of Crowder's Mountain.
The temperature was predicted to reach ~100, so we looked for trees lower on the trail than in previous years - there were some that had been marked by Mr Steve Barilovits.
Terry Rabinowitz and Jon Shea of UNC Charlotte accompanied us.
A group picture starts us out, the first at the Linwood parking lot.
We were accompanied by 2 UNC Charlotte scientists, Jon Shea, and Terry Rabinowitz (shown in the second row, 3,4) TACF official Steve Barilovits (5, back row), and Ranger Kelly Cook (below).
Ranger Cook
Our first tree was on the Tower Trail, about 1.0 mile up. Luckily we had GPS coordinates to find it.
Collecting samples involves bagging leaves, scraping the bark gently to collect material in small tubes and collecting soil. Everything is stored on dry ice until we take it back to the lab for processing.
Monday, June 15 th, 2015. The B3 Summer Science Camp Blog
Today we go to Crowder's mountain and at first I thought that everyone was going to come in shorts ... Then I saw everyone in pants and thought to myself "good job B3".
At 8:00 am sharp we departed the school and the journey to see the American Chestnut in person was becoming a reality. We quickly got to crowders mountain and the scenery was beautiful , the bugs thought
we were beautiful too since they were all on us in the matter of seconds. As soon as we sat down , we sprayed ourselves down with bug spray and sunscreen. We Took a picture of course,
because who doesn't love pictures? Shortly after we began our journey, We first zeroed in the GPS coordinates and began looking for the first of the saplings. The first one was a bit difficult
to find, but eventually we found them and successfully retrieved our data. The second one was right nearby while the third sapling was a mile ahead and down a steep hill. On our way to the
third sprout you could see trail fit perfectly with the trees, we also saw a part of the actual Crowder's Mountain; that was pretty neat. When we got to where the third sapling was we
noticed it was taller than the others. After that we proceeded to appreciate nature and walk down the hill to the bus. This was a great experience for everyone including myself and I'd say
Crowder's Mountain was an absolute success.
----- Gypsy Ruano
June 16 th
Lab day - practicing basic skills for molecular biology methods.
The goal of todays lab is to learn how to read lab directions (protocols), follow them properly, and get used to the tools that are used.
Precision and accuracy are essential, and there are a lot of finicky details when you are first using the tools.
Checking each other and then checking our readings using statistical tests are two ways to make sure we are doing it right.
Brett weighing a small volume from a micropipettor on a microbalance, while Gypsy mixes a solution.
Ethan preparing the Parafilm for the weighing step, while Hannah and Iain share notebook and measuring duties.
Kajal and Raechel collaborating; Nicole and Sanjana making sure the solution does not spill (and Ethan and Maegan in the background)
Kim and Caleb temporarily distracted by the photographer; Kaeli and Lucinda concentrating.
Excellent at concentration: Meagan wuth her notebook, and Tripp labelling tubes (one of the two TAs, Maria was being the phtographer today)
Tuesday, June 16 th, 2015. The B3 Summer Science Camp Blog
This was our first day of pipetting here at B-3 , some of us had experience and some did not. This is was the time where we sharpen our skills or started learning the art of pipetting.
There are three types of Pipettes that range from 0-10 , 10-100 and 1000 , using these pipettes we measured water and glycerol to get a feel of what is it to use them.
After successfully mastering the pipettes we moved into using the serological pipettes which Ethan really sucked at but other than that all serological pipettes have different
volumes going from 2mL , 5mL and 10mL we then used these pipettes to again extract water and glycerol for practice. After a second success we started mixing different solutions
which you need to make *complicated enzyme reactions*.
----- Gypsy Ruano
June 17 th
Lab day - starting to prepare DNA from Chestnut leaves
Nucleic acids (DNA and RNA) have to be purified away from all of the starches, proteins and small molecules of the cells.
Some of the small molecules would damage the DNA, so we add a lot of chemicals to inhibit those reactions.
Breaking open the cells releases enzymes that can damage the DNA, so we keep everything cold, using dry ice.
Brett, and Kim and Caleb grinding plant tissue and dry ice in a mortar; the prefect plant paste.
Adding chemicals as you go (Meagan and Ethan) and more dry ice (Maria, in a cloud and without glasses -tsk tsk),
Scraping down the pestle (Lucinda and Kaeli) and inspecting progress (Kajal and Raechel)
Chloroform is added in the hood, with safety gear (Lucinda) and then the solution is vortexed (Kim)
You should get a nice green solution (Raechel) and then you centrifuge the solution, when you take it out the tube has layers (Maegan and Ethan demonstrate)
While waiting for the centrifuge, notebooks were updated and calculations carried out (Maria and Nadia, Nicole and Sanjana).
Wednesday, June 17 th, 2015. The B3 Summer Science Camp Blog
Today in B-3 we quickly got to work and started extracting the DNA from our leaves. We first crushed our leafs with dry ice
into a powder form, next while we were mixing it we put in PVP & Sorbitol. After than we put .50 of BME and .50 of Tween. Next we put
in 2.5 ml of GB , using all of these chemicals we started to break down the leaf even more. After the leaf was extracted we proceeded
to put in double the amount of CTAB after that we put in in the water bath. After we all removed our samples from the water bath, it
was time to put the chloroform in our samples. The amount of chloroform we put in was based on the amount of leaf extract we already
had, for example if someone had 4 mL of their leaf extract then they would put in 4 pipettes full of chloroform. After the chloroform
it was time to spin! Spin the mixture that is, we either shaked the tube for 10 minutes which took work or put the tube on our vortex
machine for ten minutes.
----- Gypsy Ruano
June 18 th
Lab day - continuing to process DNA from Chestnut leaves
Today we remove proteins that like to stick to DNA, using an enzyme and high salt, and we remove the RNA using an enzyme RNAase.
After rmoving the fragments of protein and RNA left by the enzymes we concentrate the DNA with isopropanol.
DNA is soluble in water but not in 40% isopropanol, so by adding it we can precipitate the DNA, collect it and resuspend it in clean buffer.
We also prepared agarose gels, which let us see how long our DNA fragments are, to use on Monday.
Many hands help make our solutions (aliquots are made for each team).
Sample prep begins by adding the enzymes and heating the tubes (Lucinda, Kaeli and Maegan, and Nicole and Sanjana)
We modified our vortexers to hold many small microfuge tubes at the same time, (modification, then in action)
After centrifuging the DNA we get a pellet, it has to be resuspended in buffer (Maegan demonstrates)
Resuspended Samples are inspected (Kim and Caleb, Raechel and Kajal) and spun down if necessary
We poured the agarose gels at the end of the day (gel casting, Nicole and Sanjana demonstrate), and stored them in a refrigerator over the weekend.
Thursday, June 18 th, 2015. The B3 Summer Science Camp Blog
Holding place for Blog entry.
----- Gypsy Ruano
June 19 th
Field Trip to the Pryor Farm near Edneyville
Today we travel to an experimental orchard near Asheville, to participate in some field science.
Our main goal is to do some infections of young trees in a cross with the fungal pathogen.
We will return in September to see how resistant the young trees seem to be.
Group at the start (Raechel hidden); the hosting scientist is Dr. Paul Sisco, formerly a professor at NCSU and a volunteer scientist with the American Chestnut Foundation.
The Pryor Farm is on a ridge, the views were great.
Dr. Sisco showed us the reproductive parts of the chestnuts, the male catkins (left) and female flowers (right, near his fingers)
Tom Saielli, a staff scientist was bagging the flowers to make a controlled cross with a Chinquapin pollin.
The first and second-year plantings are close together because many trees don't survive.
Trees challenged with fungus develop trunk lesions if resistance is low, (good resistance on right).
Our main task is to carry out the fungal inoculation of 26 young trees. First the trunk is surface sterilized and so is a spatula.
Next a plug is taken from a plate of fungus and applied to the place where the bark was taken from the trunk.
The final step is to tape over the infection site. The group heads off to get started.
Friday, June 19 th, 2015. The B3 Summer Science Camp Blog
