01 November 2013

genome and DNA

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Week's notes


Correcting proofs for MEE paper

Lab meeting - comments on NSF GRF proposals

Biology Seminar - Mike Willig UConn


Lawrence et al. (2012) Species interactions alter evolutionary responses to a novel environment. PLoS Biology 10:e1001330.

  • nice experimental study of species interactions influencing evolution
  • microbes always mainted large (10^6) population sizes. relevance to fragmented populations in natural settings?

Colautti, R.I. & Barrett, S.C.H. (2013). Rapid Adaptation to Climate Facilitates Range Expansion of an Invasive Plant. Science, 342, 364–366.

  • nice study. good to see that things I do can be published in Science! they do use aster models, but buried in the supplemental methods


Sent off proofs to MEE

Job applications

Annual report for climate-cascade grant

To characterize the thermal transcriptome of the Aphaenogaster picea-rudis complex, RNA was extracted from ants of two colonies, with 12 samples subjected to temperatures from 0 to 38 Celsius. We have completed a preliminary assembly of the transcriptome, resulting in 126,172 transcripts which were reduced to eliminate redundancy to 73,943 transcripts with a mean length of 821 and a total length of 60,773,272 bp. Allowing for partial assembly of genes and multiple isoforms, this is on the order of transcripts we would expect. We mapped reads from each of the twelve temperatures to this transcriptome, and identified transcripts showing differential expression (Figure 1). We are in process of completing this analysis and writing the manuscript.

To evaluate local adaptation across the range of the A. picea-rudis complex, field crews from three institutions (University of Tennessee: Lacy Chick; North Carolina State University: Lauren Nichols, Clint Penick; University of Vermont: Andrew Nguyen, Mike Herrmann, Federico Lopez, John Stanton-Geddes) collected 3 to 12 colonies at 29 sites from Georgia to Maine, spanning a range of 12 degrees latitude and 12 degrees Celsius (Figure 2). These colonies were shipped to North Carolina State University and reared for 8 weeks in two climate-controlled chambers, 20 and 26 Celsius. At this point, 16 individual workers were removed from each colonies and one set was heat-shocked at 37 C for one hour. All samples were flash frozen in liquid nitrogen and shipped to UVM for RNA extraction and sequencing, which is in progress. In addition, samples were collected for protein stability assays and cuticular hydrocarbons.

In addition, to explore the genetic variation for heat tolerance within a northern Aphaenogaster population, I collected larvae from 50 ant colonies at Harvard Forest and transferred them into 10 host colonies in the lab. After the larvae were reared and developed into workers, I tested their CTmax. An undergraduate (Nicole Redmond) is currently extracting DNA from all these ants which will we use to identify siblings. With the genetic relatedness matrix created from the sequence data, we will partition phenotype variance for heat tolerance into genetic and environmental components, and use this information to infer the potential for this population to adapt to future climate change.

A second undergraduate (Riley Harding) is working on an independent project examining the effects of heat stress on foraging behavior.

Finally, we started work to sequence a genome for Aphaenogaster.


Amazon academic grants for RStudio server at UVM?

Plant-Insect-Interactions Groups

Discussed Lawrence et al (2013) paper

  • cool system and nice results, especially the idiosyncratic responses among species
  • relevance of microbial communities that were severly-bottlenecked to adaptation in natural systems?
  • assumes all evolutionary change is due to mutation


Started extraction with modified protocol from Qiagen Genomic-tip kit



Marked ants with Riley.


First round of Genomic-tip extraction using 10 Aphaenogaster.

Modified protocol the “Tissue prep” for Genomic-tip extraction and used the G2 buffer for homogenization. Eluted in 100ul H20


Submitted UVM job application

Taught HIV case to Human Genetics class.



Heat-shocked the ‘green’ ants at 42C for one hour.


Second attempt at Genomic-tip extraction. To save valuable Aphaenogaster, used 10 Pogo. Eluted in 100ul H20.

Nanodrop results

Sample Concentration (ng/ul) 260/280
MB2 6.1 1.34
Pogo 22.3 0.56

Neither sample has adequate quality based on 260/280 (pure DNA 1.7 - 1.9) though the MB2 sample isn’t terribly far…

Total mass DNA for 100ul MB2 = 600 ng. If I need 10ug for PacBio, at this level of extraction would need 17 times this sample, which would be 170 ants. Don’t have this many ants in the colony…


Climate-cascade meeting

Read Jeremy’s Genetics manuscript


Alison Brody


things to do…


covered Sara’s class while she was at EcoGenomics conference

Ecolunch - Alison Brody

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