The weather has been relatively pleasant for October. Tuesday morning there was frost on the Crescent harbor dock , but none on the island.
Tuesday mornings commute birds included one forked tail petrel, a few mew gulls and a kittiwake . The goldeneyes were near the Galankin dock.
Wednesday morning saw 2 Harlequins and a few mew gulls. There was one kingfisher, one glaucous winged gull on a piling, and goldeneyes next to the island dock.
Thursday morning was a little quiet for birds, just the goldeneyes by the dock and gulls that were too far away to identify.
I should have tended to my spore cultures on Sunday or used antibiotics in the media as the bacteria have the run of the Amanita cultures. I still have one Amanita in the refrigerator, so I should be able to try again. I looked in the park on Tuesday for a last specimen or two, but no luck. The winter chanterelles, Lactarius deliciosus and the Tricholoma were still fruiting. Also saw several golden-crowned kinglets and a small flock of black turnstones.
We ran the second step of the nested PCR with a lower annealing temperature (51 C instead of 57C)) and 35cycles instead of 30 in an attempt to get an amplification product that is definately a AM fungus. Apparently, the lower the temperatures, the more strigent the binding conditions, so the binding of primer to DNA template is more specific. We ran the gels of the PCR products on Wednesday. Chris and Lacy's products have some interesting bands, especially from Trichophorum, Josh and Caleb's came up with nothing. Only one of their postive controls had a band and it was a different size than that of the other group with the same primers. Not good. I may have to watch them even more carefully. They were having a ridiculously difficult time labeling their tubes that day, the muddle must have continued through the mixing process. Fortunately everyone's negative controls were clean. Even if we struggle to get the PCR process to work for us, we can at least see the fungi in the cleared and stained roots. The photograph is of a cleared and stained root from Trichophorum caespitosum. The most abundant fungi are in the dark septate group which we don't have specific primers for at this point. I've been corresponding with someone in Kansas who works with this group and he hasn't been successful in his attempts to develop specific group wide primers. The dark septate endophytes fungi are in the Ascomycetes, but are in different orders, genera and species, so it isn't a surprise that there aren't any specific primers. It would have been nice to be surprised.
Thursday I learned how to purify the extracted DNA with a sepharose column. Sepharose is a beaded form of agarose to which the impurities in the sample bind. The column needs to be conditioned (seems like getting the moisture level correct) by adding sterile distilled water and centrifuging and discarding the water three times. The zebra column is a small tube about an 1.5 inch tall with a beak-like (think moss beak) at the bottom that sits in a collection tube. Lastly the DNA is added to the column, centrifuged and collected in a clean collection tube. We purified Carex livida and Cornus suecica in hopes of getting good amplification. We are also going to try some different primers tomorrow.
Also on Thursday started the DNA extraction process from the yellow Amanita muscaria and Craterellus tubaeformis. We are hoping that one of these fungi has a laccase gene (lignin degraders) and can be used as a good positive control in the search for laccase genes in the DNA isolated from the muskeg and forest soils.
Did a little wandering around searching for birds on Tuesday and Thursday. Both days I stopped at swan lake. Didn't manage to find the reported grebe. My eyes just don't have the right search image yet. Will try again tomorrow. Did see the 2 coots, a shoveler (Tuesday), many scaups, and the cackling goose that has decided to hang out with the larger hybrid ducks. I shouldn't neglect the mallards, who faithfully greet my every arrival. At Wednesday night ballet, Joe told me about seeing swans fly overhead (how fitting, too bad I didn't have a white tutu). Drove out to Starrigavan Thursday afternoon in hopes that they were there...always a dreamer. Did see 2 horned grebes, one hooded merganser, several buffleheads, lots of mallards,4 song sparrows, a winter wren, and ample glaucous winged and thayers' gulls. My one bird observation besides the commute on Wednesday was 2 northern flickers flying over HPR when I was driving to Cheryls to solve my costume emergency.
Checked the channel Thursday afternoon on my way in to UAS. The gull population was very thinned out by the ramp. There were 14 longtails, a goldeneye and 2 pelagic cormorants in the count zone.
Tuesday I went to the Forest Service to return Mary's flora and look at Brad's collection of odd weeds and composites he collected from Kosciusko island. I'm still thinking about the plant that looked alot like a multi-headed Aparigidium (now Microseris). It fits Microseris except for the multiple flower heads. I had to look at the characteristics for Taraxacum to make sure we weren't ignoring that possibility. The fruits didn't look quite right. It took me awhile to persuade Brad to keep a small part of the collection here, so that we could look at it more closely (the bulk of it goes to UAF). Unfortunately, I ran out of time and energy to look at it that day and haven't gone back yet.
I did decide that I needed to construct my own key to the composites that occur in southeast, since the genera have changed so considerably.
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