prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary.py, it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts.py, to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary.py but is also very fast in terms of CPU time and user friendly.
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
ABSTRACT A 16S rRNA gene database (http://greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
Indian Fig Cactus (Opuntia Ficus-Indica (L.) Miller) in the Americas: an Uncertain History
Abstract: 
 Opuntia ficus-indica (L.) Miller is a globally important cactus species with a long history of human use. In addition to the importance of O. ficus-indica as a food for humans and livestock, it also has long served a role in the production of cochineal, a once important textile dye. This cactus also is intimately interwoven into the story of Cactoblastis cactorum (Berg) (South American cactus moth), one of the best-known examples of biological weed control. In this regard, O. ficus-indica has been a target weed as well as an unintended host in C. cactorum invasion. Although the distribution and human-assisted movement of this cactus throughout much of the world is well documented, surprisingly little has been written about its history and movement within the Americas. Literature associated with Opuntia and their phytophagous pests in North and South America was examined in an attempt to determine the history of O. ficus-indica in the Americas. Available information suggests with some certainty that O. ficus-indica originated in present-day Mexico, but the timing of its introduction to South America is much less clear. Taxonomic difficulties associated with distinguishing among Opuntia species and the long pre-Columbian history of exchange between South American and Mesoamerican cultures are two primary complicating factors associated with dating the dispersal of this species to South America. Additionally, previous evidence in support of a pre-Columbian introduction to South America relied on questionable identification of insect-based textile dyes. These uncertainties are significant because clearer knowledge of the history of O. ficus-indica introduction to South America could provide a more complete biological and ecological context to efforts at managing this species in its native and introduced ranges, particularly with respect to the threat posed by C. cactorum in North American and Argentinean plantations.