FINALLY IN THE MOUNTAINS - Collections of mao li and zhui li (September 8, 2011)
After a 2 hour flight from Beijing to Xi'an, a three hour drive to Ankang, and then another 2 hour drive to Lan Gao, we were finally prepped to head into the mountains for some sample collections.
Our tour guide this time was Mr. Chen, whom you may remember from our trip to the same mountains on our last trip. We again went up to Nan Gong Mountain, and also ate lunch at the same location where we met the mayor last time.
We were able to collect all of our samples of Castanea seguinii (mao li) and C. henryi (zhui li) here, but had to wait until the next day to collect the C. mollissima (ban li) samples.
At this point, you may wonder about our sample collection methods. The idea for this trip is to collect different tissue material from all three species. For each of the three species, we want three fully healthy trees and three cankered trees (preferably ones with active cankers). This makes a total of 18 trees all together that we need to find.
When we find a tree, Andy uses a large cork borer, about 1/2" in diameter, to collect two cores of cambium tissue. He scrapes away much of the bark before coring into the tree. For the cankered trees, we also want material from both the healthy part of the tree as well as the active canker margin. By doing this, we can see if there is differential expression between the tissue around the blight and the other tissue in the tree. If done right, this can allow us to find activated areas of the genome that may be related to blight-resistance. For the healthy trees, we want to collect tissue from the trunk as well as leaf tissue. The leaf tissue will be used for genomic DNA extractions.
For the cores that are taken, two cores from each type of tissue, cankered and healthy, are taken. Each core is then cut into four wedges using a knife and the wedges are placed into a 50mL tube containing RNA later. Because we have no way to get ice, and keep it ice, while out in the mountains, the RNA later will act to keep the RNA and DNA from our samples from degrading until we can get them back to the lab in Beijing for extractions.
In addition to collecting the tissue samples, we also took several data points on each tree including 1) height; 2) dbh; 3) health (1-5, like last time); 4) form (1-5, like last time); and 5) GPS coordinates. Each tree was coded based on species and health, and we also took some general notes on the condition of the tree such as whether it was multi-stemmed, growing on the side of the road, or anything else of note.
Terrain in this part of China is very tough, which makes finding trees to sample somewhat more challenging. Because we wanted trees in very specific condition - large and healthy or large and with active cankers - Mr. Chen and I spent some time walking around and trying to find the most appropriate trees for sampling.
Some pictures are below. We'll be typing in the data when we get back to Beijing for the extractions. I'll be sure to update everyone on what all we sampled once we get that done.
A message from the hotel in Lan Gao where we stayed for one night. We used this as our base of operations between driving around the mountains of southern Shaanxi province.
How samples were taken in the field. Here we are in NanGongShan Park, just off the road at about 3500' in elevation. Andy is in the background taking stem sections from the tree with a large cork borer. Bill is sitting, labeling tubes filled with RNALater. Kathleen is on the left, dipping her knife into alcohol, sterilizing it so that she can use it to cut up the samples Andy takes from the tree (samples need to be small for the RNALater to work). On the right is Katy's hand w/ a lighter which she uses to flame the tools for sterilization. Amelia is not in the picture, but is helping to interpret our guide, Mr. Chen, as he finds new trees for sampling.
In this picture, we are all holding on for dear life on the slope. Here is a cankered C. henryi that Andy is getting ready for sample collection - as you can see he hangs on to the tree to stay steady. Kathleen had a hard time finding a flat spot for her cutting board where she would cut the stem disks into 4 pie segments. Bill is handing the labeled tube up to Kathleen so she can put the samples into it.
In the foreground, you can see the needles of a tree that is often found in these mountains, which we think is a species of Araucacia.
Here you can see the tally sheet along with what is left behind on the trees once a sample is taken. Both stems here are from a C. seguinii. The one on the left is quite cankered while the one on the right is healthy. Two tubes, then, were taken from this one tree and used for both DNA and RNA extraction.
Our group from the collections. Katie D'Amico, Bill Powell, Mr. Chen, (still getting name), Andy Newhouse, Ameila Zhang, Kathleen Baier, (still getting name).
Our tour guide this time was Mr. Chen, whom you may remember from our trip to the same mountains on our last trip. We again went up to Nan Gong Mountain, and also ate lunch at the same location where we met the mayor last time.
We were able to collect all of our samples of Castanea seguinii (mao li) and C. henryi (zhui li) here, but had to wait until the next day to collect the C. mollissima (ban li) samples.
At this point, you may wonder about our sample collection methods. The idea for this trip is to collect different tissue material from all three species. For each of the three species, we want three fully healthy trees and three cankered trees (preferably ones with active cankers). This makes a total of 18 trees all together that we need to find.
When we find a tree, Andy uses a large cork borer, about 1/2" in diameter, to collect two cores of cambium tissue. He scrapes away much of the bark before coring into the tree. For the cankered trees, we also want material from both the healthy part of the tree as well as the active canker margin. By doing this, we can see if there is differential expression between the tissue around the blight and the other tissue in the tree. If done right, this can allow us to find activated areas of the genome that may be related to blight-resistance. For the healthy trees, we want to collect tissue from the trunk as well as leaf tissue. The leaf tissue will be used for genomic DNA extractions.
For the cores that are taken, two cores from each type of tissue, cankered and healthy, are taken. Each core is then cut into four wedges using a knife and the wedges are placed into a 50mL tube containing RNA later. Because we have no way to get ice, and keep it ice, while out in the mountains, the RNA later will act to keep the RNA and DNA from our samples from degrading until we can get them back to the lab in Beijing for extractions.
In addition to collecting the tissue samples, we also took several data points on each tree including 1) height; 2) dbh; 3) health (1-5, like last time); 4) form (1-5, like last time); and 5) GPS coordinates. Each tree was coded based on species and health, and we also took some general notes on the condition of the tree such as whether it was multi-stemmed, growing on the side of the road, or anything else of note.
Terrain in this part of China is very tough, which makes finding trees to sample somewhat more challenging. Because we wanted trees in very specific condition - large and healthy or large and with active cankers - Mr. Chen and I spent some time walking around and trying to find the most appropriate trees for sampling.
Some pictures are below. We'll be typing in the data when we get back to Beijing for the extractions. I'll be sure to update everyone on what all we sampled once we get that done.
A message from the hotel in Lan Gao where we stayed for one night. We used this as our base of operations between driving around the mountains of southern Shaanxi province.
How samples were taken in the field. Here we are in NanGongShan Park, just off the road at about 3500' in elevation. Andy is in the background taking stem sections from the tree with a large cork borer. Bill is sitting, labeling tubes filled with RNALater. Kathleen is on the left, dipping her knife into alcohol, sterilizing it so that she can use it to cut up the samples Andy takes from the tree (samples need to be small for the RNALater to work). On the right is Katy's hand w/ a lighter which she uses to flame the tools for sterilization. Amelia is not in the picture, but is helping to interpret our guide, Mr. Chen, as he finds new trees for sampling.
In this picture, we are all holding on for dear life on the slope. Here is a cankered C. henryi that Andy is getting ready for sample collection - as you can see he hangs on to the tree to stay steady. Kathleen had a hard time finding a flat spot for her cutting board where she would cut the stem disks into 4 pie segments. Bill is handing the labeled tube up to Kathleen so she can put the samples into it.
In the foreground, you can see the needles of a tree that is often found in these mountains, which we think is a species of Araucacia.
Here you can see the tally sheet along with what is left behind on the trees once a sample is taken. Both stems here are from a C. seguinii. The one on the left is quite cankered while the one on the right is healthy. Two tubes, then, were taken from this one tree and used for both DNA and RNA extraction.
Our group from the collections. Katie D'Amico, Bill Powell, Mr. Chen, (still getting name), Andy Newhouse, Ameila Zhang, Kathleen Baier, (still getting name).
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