Intro to Using Galaxy for Bioinformatics

Talk given at IU Galaxy for Bioinformatics Workshop 09/17/13This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432, Craig Stewart, PI. William Barnett, Matthew Hahn, and Michael Lynch, co-PIs. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute. Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencie

RNA-Seq Demo on Galaxy

Talk given at the IU Bioinformatics Clinic, July 2014.This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432, Craig Stewart, PI. William Barnett, Matthew Hahn, and Michael Lynch, co-PIs. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute. Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencie

RNA-Seq Demo on Galaxy

Workshop given during the 2015 Bioinformatics Clinic at Indiana University, August 2015This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432, Craig Stewart, PI. William Barnett, Matthew Hahn, and Michael Lynch, co-PIs. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute. Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencies

Moving Large Data to Galaxy

Talk given at the IU Bioinformatics Clinic July 2014This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432, Craig Stewart, PI. William Barnett, Matthew Hahn, and Michael Lynch, co-PIs. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute. Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencie

Galaxy for Data Provenance

Talk given at the IU Bioinformatics Clinic, July 2014This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432, Craig Stewart, PI. William Barnett, Matthew Hahn, and Michael Lynch, co-PIs. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute. Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencie

Automating work in Galaxy

Workshop given during the 2015 Bioinformatics Clinic at Indiana University, August 2015This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432, Craig Stewart, PI. William Barnett, Matthew Hahn, and Michael Lynch, co-PIs. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute. Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencies

The gain and loss of chromosomal integron systems in the Treponema species

BACKGROUND: Integron systems are now recognized as important agents of bacterial evolution and are prevalent in most environments. One of the human pathogens known to harbor chromosomal integrons, the Treponema spirochetes are the only clade among spirochete species found to carry integrons. With the recent release of many new Treponema genomes, we were able to study the distribution of chromosomal integrons in this genus. RESULTS: We find that the Treponema spirochetes implicated in human periodontal diseases and those isolated from cow and swine intestines contain chromosomal integrons, but not the Treponema species isolated from termite guts. By examining the species tree of selected spirochetes (based on 31 phylogenetic marker genes) and the phylogenetic tree of predicted integron integrases, and assisted by our analysis of predicted integron recombination sites, we found that all integron systems identified in Treponema spirochetes are likely to have evolved from a common ancestor—a horizontal gain into the clade. Subsequent to this event, the integron system was lost in the branch leading to the speciation of T. pallidum and T. phagedenis (the Treponema sps. implicated in sexually transmitted diseases). We also find that the lengths of the integron attC sites shortened through Treponema speciation, and that the integron gene cassettes of T. denticola are highly strain specific. CONCLUSIONS: This is the first comprehensive study to characterize the chromosomal integron systems in Treponema species. By characterizing integron distribution and cassette contents in the Treponema sps., we link the integrons to the speciation of the various species, especially to the pathogens T. pallidum and T. phagedenis

A comparative analysis of pulp-derived nanocelluloses for 3D bioprinting facial cartilages

Nanocelluloses have attracted significant interest in the field of bioprinting, with previous research outlining the value of nanocellulose fibrils and bacterial nanocelluloses for 3D bioprinting tissues such as cartilage. We have recently characterised three distinct structural formulations of pulp-derived nanocelluloses: fibrillar (NFC), crystalline (NCC) and blend (NCB), exhibiting variation in pore geometry and mechanical properties. In light of the characterisation of these three distinct entities, this study investigated whether these structural differences translated to differences in printability, chondrogenicity or biocompatibility for 3D bioprinting anatomical structures with human nasoseptal chondrocytes. Composite nanocellulose-alginate bioinks (75:25 v/v) of NFC, NCC and NCB were produced and tested for print resolution and fidelity. NFC offered superior print resolution whereas NCB demonstrated the best post-printing shape fidelity. Biologically, chondrogenicity was assessed using real time quantitative PCR, dimethylmethylene blue assays and histology. All biomaterials showed an increase in chondrogenic gene expression and extracellular matrix production over 21 days, but this was superior in the NCC bioink. Biocompatibility assessments revealed an increase in cell number and metabolism over 21 days in the NCC and NCB formulations. Nanocellulose augments printability and chondrogenicity of bioinks, of which the NCC and NCB formulations offer the best biological promise for bioprinting cartilage

Telomere formation on macronuclear chromosomes of Oxytricha trifallax and O. fallax: alternatively processed regions have multiple telomere addition sites

BACKGROUND: Ciliates employ massive chromatid breakage and de novo telomere formation during generation of the somatic macronucleus. Positions flanking the 81-MAC locus are reproducibly cut. But those flanking the Common Region are proposed to often escape cutting, generating three nested macronuclear chromosomes, two retaining "arms" still appended to the Common Region. Arm-distal positions must differ (in cis) from the Common Region flanks. RESULTS: The Common-Region-flanking positions also differ from the arm-distal positions in that they are "multi-TAS" regions: anchored PCR shows heterogeneous patterns of telomere addition sites, but arm-distal sites do not. The multi-TAS patterns are reproducible, but are sensitive to the sequence of the allele being processed. Thus, random degradation following chromatid cutting does not create this heterogeneity; these telomere addition sites also must be dictated by cis-acting sequences. CONCLUSIONS: Most ciliates show such micro-heterogeneity in the precise positions of telomere addition sites. Telomerase is believed to be tightly associated with, and act in concert with, the chromatid-cutting nuclease: heterogeneity must be the result of intervening erosion activity. Our "weak-sites" hypothesis explains the correlation between alternative chromatid cutting at the Common Region boundaries and their multi-TAS character: when the chromatid-breakage machine encounters either a weak binding site or a weak cut site at these regions, then telomerase dissociates prematurely, leaving the new end subject to erosion by an exonuclease, which pauses at cis-acting sequences; telomerase eventually heals these resected termini. Finally, we observe TAS positioning influenced by trans-allelic interactions, reminiscent of transvection