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AgBase

    [AgBase](https://agbase.arizona.edu/index.html) Version 2.0 is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products including gene ontology annotations. Its long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase uses controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species.

    Data from: Ploidy determination of buffel grass accessions in the USDA National Plant Germplasm System collection by flow cytometry

      The DNA content of 568 accessions of buffel grass in the USDA National Plant Germplasm System was determined through flow cytometry to predict their ploidy levels. Based on DNA content, 308 accessions were determined as tetraploids with 36 chromosomes, 139 as pentaploids with 45 chromosomes, 20 as hexaploids with 54 chromosomes, two as septaploids with 63 chromosomes, and 99 as aneuploids. Chromosome counts of selected plants confirmed ploidy levels from DNA findings. Chromosome number of euploid plants could be predicted from the DNA data.

      2DLEAF

        A 2D mechanistic model of CO2 and water vapor movement in a leaf and photosynthesis.

        UPIC

          Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers.

          IncA-C Alignment

            IncA/C plasmids are a class of plasmids from Enterobacteraciae that are relatively large (49 to >180 kbp), are readily transferred by conjugation, and carry multiple antimicrobial resistance genes. Reconstruction of the phylogeny of these plasmids has been difficult because of the high rate of remodeling by recombination-mediated horizontal gene transfer (HGT). We hypothesized that evaluation of nucleotide polymorphisms relative to the rate of HGT would help to develop a clock to show if anthropic practices have had significant influences on the lineages of the plasmid. A system was developed to rapidly sequence up to 191 known open27 reading-frames from each of 39 recently isolated IncA/C plasmids from a diverse panel of Salmonella enterica and Escherichia coli. With these data plus sequences from Genbank we were able to distinguish six distinct lineages that had extremely low numbers of polymorphisms within each lineage, especially among the largest group designated as Lineage 1. Two regions, each about half the plasmid in size, could be distinguished with a separate lineal pattern. The distribution of Lineage 1 showed that it has migrated extremely rapidly with fewer polymorphisms than can be expected in two-thousand years. Remodeling by frequent HGT was evident with a pattern that appeared to have the highest rate just upstream of the putative conjugation origin of transfer (ori-T). It seems likely that when an IncA/C plasmid is transferred also adjacent to a multiple antimicrobial resistance gene cassette.