14 June 2013

Aphaenogaster and Medicago

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Notes for week of June 10


One of the amazing aspects of google scholar citation alerts is that it pulls up patents in addition to scholarly articles. Transgenic Plants with Enhanced Agronomic Traits turned up this morning with this rather expansive description:

1. A recombinant DNA construct comprising a promoter that is functional in a plant cell and that is operably linked to a polynucleotide that, when expressed in a plant cell: (a) encodes a protein: i) having an amino acid sequence selected from the group consisting of SEQ ID NO: 45-68, and 70-88; ii) having an amino acid sequence having at least 90% identity over at least 90% of a reference sequence selected from the group consisting of 45-68, and 70-88 when said amino acid sequence is aligned to said reference sequence; or iii) that is a homolog of a protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 45-68, and 70-88; or (b) is transcribed into an RNA molecule that suppresses the level of an endogenous protein in said plant cell wherein said endogenous protein has an amino acid sequence of SEQ ID NO: 69 or is a homolog thereof; wherein said construct is stably integrated into plant chromosomal DNA. 

Without being an expert on patent law, looks like the are trying to patent a specific gene in group SEQ ID NO 45-68. Bradyrhizobium (my search term) comes up as a source of the potential promoter. So, should I (or UMN?) patent my Bradyrhizobium genomes when I publish them???

Wow, and this line

Yet another aspect of the invention provides anti-counterfeit milled seed having, as an indication of origin, plant cells of this invention.

makes it clear that they plan to track and prosecute the ‘patented’ genes.

Tool to draw custom Venn diagrams

Meeting with NG

  • discussed adaptive potential project
    • to avoid becoming overwhelmed, pilot study this year in MA
    • collect colonies at Harvard Forest, and nearby ‘warm’ site in Worchester
  • project version control
    • use github as planned
    • write up explanation using github user interface
    • include data in local directories, but hide in .gitignore
    • how to share data among collaborators? dropbox too small…server?
    • use amazon!!!



Updated Google Earth with sampling sites. Pursuing contacts in NY and VT for collecting at alternatives to state lands.

Working in github tutorial for version control of scripts.

P-value commentary

Went over responses with Cintia and Cristian. Tabulated ‘data’


Note - from discussion at Aphaenofest with AE and SD, should include sessionInfo() in every R script! Important for reproducibility 5+ years in future…


Update map script in climate-cascade project.

Tried to install rgdal library. First had to install gdal sudo apt-get install libgdal-dev and confirmed this worked by running gdal-config and seeing options. But when I tried to install rgdal, error message that “proj_api.h” not found in standard or given locations…

Success! First had to install libproj: sudo apt-get install libproj-dev suggested

To summarize, to install R package rgdal:

  1. install gdal using sudo apt-get install libgdal-dev in shell
  2. install proj using sudo apt-get install libproj-dev in shell
  3. install R library install.packages("rgdal")

Not clear how to plot MAT in ggplot so deferred for later…

P-value commentary


Aphaenogaster permits

Permission from Bard College Field Station (Hudsonia): Eric Kiviat (kiviat@bard.edu). Call in advance and check in at field station before sampling.

Left message at Cary Institute for Kelly ???

Green Mountain National Forest - 3 week permitting process. Called Killington and was told sampling would not be a problem! Score.

Contacted Ken Howard at Albany Sage College (recommendation from Amy Savage at Bard).

He has had collecting permits in past 2 years and gave new contact name. Also recommended some private sites:

  • Huyck Preserve, where Joan Herbers and Suzanne Foitzik have collected
  • Ann Lee Pond, next to Albany airport
  • Rattlesnake Mtn in Willsboro, NY as potential collecting site. Private land so not permit needed. http://www.lakechamplainregion.com/recreation/outdoors/hiking/rattlesnake-mountain-trail
  • field stations at Williams, Binghamton, Skidmore and Ithaca College


Add ImpactStory to publications page

Need to make columns for correct layout

Probably need to use bootstrap scaffolding


Barshis et al (2012) Genomic basis for coral resilience to climate change. PNAS

  • discussed relevance to Aphaenogaster transcriptome
  • we will have complete reaction norms for all genes, not simply two temperature points


Climate Cascade

Bingo - use Amazon S3 for data storage. Read files into R as described

P-val commentary



Installed kompozer for html using guide

Argh. Upgrade to R 3.0.1 to install devtools broke the rptR package. Had to install R 2.15.1 into /opt and run from there to repeat analyses. Emphasizes the need for sessionInfo() in R scripts!!

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