14 June 2013
Aphaenogaster and MedicagoNext post Previous post
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
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.
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:
sudo apt-get install libgdal-devin shell
sudo apt-get install libproj-devin shell
Not clear how to plot MAT in ggplot so deferred for later…
Permission from Bard College Field Station (Hudsonia): Eric Kiviat (email@example.com). 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:
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
Bingo - use Amazon S3 for data storage. Read files into R as described
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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