Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

<p>Abstract</p> <p>Background</p> <p>For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly.</p> <p>Results</p> <p>We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform.</p> <p>Conclusions</p> <p>By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.</p

Phytoplankton blooms weakly influence the cloud forming ability of sea spray aerosol

After many field studies, the establishment of connections between marine microbiological processes, sea spray aerosol (SSA) composition, and cloud condensation nuclei (CCN) has remained an elusive challenge. In this study, we induced algae blooms to probe how complex changes in seawater composition impact the ability of nascent SSA to act as CCN, quantified by using the apparent hygroscopicity parameter (κapp). Throughout all blooms, κapp ranged between 0.7 and 1.4 (average 0.95 ± 0.15), consistent with laboratory investigations using algae‐produced organic matter, but differing from climate model parameterizations and in situ SSA generation studies. The size distribution of nascent SSA dictates that changes in κapp associated with biological processing induce less than 3% change in expected CCN concentrations for typical marine cloud supersaturations. The insignificant effect of hygroscopicity on CCN concentrations suggests that the SSA production flux and/or secondary aerosol chemistry may be more important factors linking ocean biogeochemistry and marine clouds.Key PointsChanges in seawater and sea spray composition did not strongly affect expected CCN concentrationsBlooms may impact clouds more strongly through changes in aerosol flux or secondary chemistryModel parameterizations likely overestimate changes in cloud nuclei due to primary marine organicsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134444/1/grl54978_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134444/2/grl54978-sup-0001-supinfo.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134444/3/grl54978.pd

Oceanic emissions of dimethyl sulfide and methanethiol and their contribution to sulfur dioxide production in the marine atmosphere

Oceanic emissions of dimethyl sulfide (CH3SCH3, DMS) have long been recognized to impact aerosol particle composition and size, the concentration of cloud condensation nuclei (CCN), and Earth's radiation balance. The impact of oceanic emissions of methanethiol (CH3SH, MeSH), which is produced by the same oceanic precursor as DMS, on the volatile sulfur budget of the marine atmosphere is largely unconstrained. Here we present direct flux measurements of MeSH oceanic emissions using the eddy covariance (EC) method with a high-resolution proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToFMS) detector and compare them to simultaneous flux measurements of DMS emissions from a coastal ocean site. Campaign mean mixing ratios of DMS and MeSH were 72&thinsp;ppt (28&ndash;90&thinsp;ppt interquartile range) and 19.1&thinsp;ppt (7.6&ndash;24.5&thinsp;ppt interquartile range), respectively. Campaign mean emission fluxes of DMS (FDMS) and MeSH (FMeSH) were 1.13&thinsp;ppt&thinsp;m&thinsp;s&minus;1 (0.53&ndash;1.61&thinsp;ppt&thinsp;m&thinsp;s&minus;1 interquartile range) and 0.21&thinsp;ppt&thinsp;m&thinsp;s&minus;1 (0.10&ndash;0.31&thinsp;ppt&thinsp;m&thinsp;s&minus;1 interquartile range), respectively. Linear least squares regression of observed MeSH and DMS flux indicates the emissions are highly correlated with each other (R2=0.65) over the course of the campaign, consistent with a shared oceanic source. The campaign mean DMS to MeSH flux ratio (FDMS:FMeSH) was 5.5&thinsp;&plusmn;&thinsp;3.0, calculated from the ratio of&nbsp;304 individual coincident measurements of FDMS and FMeSH. Measured FDMS:FMeSH was weakly correlated (R2=0.15) with ocean chlorophyll concentrations, with FDMS:FMeSH reaching a maximum of 10.8&thinsp;&plusmn;&thinsp;4.4 during a phytoplankton bloom period. No other volatile sulfur compounds were observed by PTR-ToFMS to have a resolvable emission flux above their flux limit of detection or to have a gas-phase mixing ratio consistently above their limit of detection during the study period, suggesting DMS and MeSH are the dominant volatile organic sulfur compounds emitted from the ocean at this site. The impact of this MeSH emission source on atmospheric budgets of sulfur dioxide (SO2) was evaluated by implementing observed emissions in a coupled ocean&ndash;atmosphere chemical box model using a newly compiled MeSH oxidation mechanism. Model results suggest that MeSH emissions lead to afternoon instantaneous SO2 production of 2.5&thinsp;ppt&thinsp;h&minus;1, which results in a 43&thinsp;% increase in total SO2 production compared to a case where only DMS emissions are considered and accounts for 30% of the instantaneous SO2 production in the marine boundary layer at the mean measured FDMS and FMeSH. This contribution of MeSH to SO2 production is driven by a higher effective yield of SO2 from MeSH oxidation and the shorter oxidation lifetime of MeSH compared to DMS. This large additional source of marine SO2 has not been previously considered in global models of marine sulfur cycling. The field measurements and modeling results presented here demonstrate that MeSH is an important contributor to volatile sulfur budgets in the marine atmosphere and must be measured along with DMS in order to constrain marine sulfur budgets. This large additional source of marine&ndash;reduced sulfur from MeSH will contribute to particle formation and growth and CCN abundance in the marine atmosphere, with subsequent impacts on climate. &nbsp;</p

Identification of platform-independent gene expression markers of cisplatin nephrotoxicity.

Within the International Life Sciences Institute Committee on Genomics, a working group was formed to focus on the application of microarray technology to preclinical assessments of drug-induced nephrotoxicity. As part of this effort, Sprague-Dawley rats were treated with the nephrotoxicant cisplatin at doses of 0.3-5 mg/kg over a 4- to 144-hr time course. RNA prepared from these animals was run on a variety of microarray formats at multiple sites. A set of 93 differentially expressed genes associated with cisplatin-induced renal injury was identified on the National Institute of Environmental Health Sciences (NIEHS) custom cDNA microarray platform using quadruplicate measurements of pooled animal RNA. The reproducibility of this profile of statistically significant gene changes on other platforms, in pooled and individual animal replicate samples, and in an independent study was investigated. A good correlation in response between platforms was found among the 48 genes in the NIEHS data set that could be matched to probes on the Affymetrix RGU34A array by UniGene identifier or sequence alignment. Similar results were obtained with genes that could be linked between the NIEHS and Incyte or PHASE-1 arrays. The degree of renal damage induced by cisplatin in individual animals was commensurate with the number of differentially expressed genes in this data set. These results suggest that gene profiles linked to specific types of tissue injury or mechanisms of toxicity and identified in well-performed replicated microarray experiments may be extrapolatable across platform technologies, laboratories, and in-life studies

Terahertz field control of in-plane orbital order in La0.5Sr1.5MnO4

In-plane anisotropic ground states are ubiquitous in correlated solids such as pnictides, cuprates and manganites. They can arise from doping Mott insulators and compete with phases such as superconductivity; however, their origins are debated. Strong coupling between lattice, charge, orbital and spin degrees of freedom results in simultaneous ordering of multiple parameters, masking the mechanism that drives the transition. Here we demonstrate that the orbital domains in a manganite can be oriented by the polarization of a pulsed THz light field. Through the application of a Hubbard model, we show that domain control can be achieved by enhancing the local Coulomb interactions, which drive domain reorientation. Our results highlight the key role played by the Coulomb interaction in the control and manipulation of orbital order in the manganites and demonstrate a new way to use THz to understand and manipulate anisotropic phases in a potentially broad range of correlated materials.Peer ReviewedPostprint (published version

Genome-Wide ENU Mutagenesis in Combination with High Density SNP Analysis and Exome Sequencing Provides Rapid Identification of Novel Mouse Models of Developmental Disease

BACKGROUND Mice harbouring gene mutations that cause phenotypic abnormalities during organogenesis are invaluable tools for linking gene function to normal development and human disorders. To generate mouse models harbouring novel alleles that are involved in organogenesis we conducted a phenotype-driven, genome-wide mutagenesis screen in mice using the mutagen N-ethyl-N-nitrosourea (ENU). METHODOLOGY/PRINCIPAL FINDINGS ENU was injected into male C57BL/6 mice and the mutations transmitted through the germ-line. ENU-induced mutations were bred to homozygosity and G3 embryos screened at embryonic day (E) 13.5 and E18.5 for abnormalities in limb and craniofacial structures, skin, blood, vasculature, lungs, gut, kidneys, ureters and gonads. From 52 pedigrees screened 15 were detected with anomalies in one or more of the structures/organs screened. Using single nucleotide polymorphism (SNP)-based linkage analysis in conjunction with candidate gene or next-generation sequencing (NGS) we identified novel recessive alleles for Fras1, Ift140 and Lig1. CONCLUSIONS/SIGNIFICANCE In this study we have generated mouse models in which the anomalies closely mimic those seen in human disorders. The association between novel mutant alleles and phenotypes will lead to a better understanding of gene function in normal development and establish how their dysfunction causes human anomalies and disease.This work was enabled by the Australian Phenomics Network and partly supported by funding from the Australian Government’s National Collaborative Research Infrastructure Strategy, a Strategic Grant from the Faculty of Medicine, Nursing and Health Sciences at Monash University, and the Victorian Government’s Operational Infrastructure Support Program. IS acknowledges support through the NH&MRC R. Douglas Wright and ARC Future Fellowship schemes. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Regional Similarities and NOx‐Related Increases in Biogenic Secondary Organic Aerosol in Summertime Southeastern United States

During the 2013 Southern Oxidant and Aerosol Study, Fourier transform infrared spectroscopy (FTIR) and aerosol mass spectrometer (AMS) measurements of submicron mass were collected at Look Rock (LRK), Tennessee, and Centreville (CTR), Alabama. Carbon monoxide and submicron sulfate and organic mass concentrations were 15–60% higher at CTR than at LRK, but their time series had moderate correlations (r ~ 0.5). However, NOx had no correlation (r = 0.08) between the two sites with nighttime‐to‐early‐morning peaks 3–10 times higher at CTR than at LRK. Organic mass (OM) sources identified by FTIR Positive Matrix Factorization (PMF) had three very similar factors at both sites: fossil fuel combustion‐related organic aerosols, mixed organic aerosols, and biogenic organic aerosols (BOA). The BOA spectrum from FTIR is similar (cosine similarity > 0.6) to that of lab‐generated particle mass from the photochemical oxidation of both isoprene and monoterpenes under high NOx conditions from chamber experiments. The BOA mass fraction was highest during the night at CTR but in the afternoon at LRK. AMS PMF resulted in two similar pairs of factors at both sites and a third nighttime NOx‐related factor (33% of OM) at CTR but a daytime nitrate‐related factor (28% of OM) at LRK. NOx was correlated with BOA and LO‐OOA for NOx concentrations higher than 1 ppb at both sites, producing 0.5 ± 0.1 μg/m3 for CTR‐LO‐OOA and 1.0 ± 0.3 μg/m3 for CTR‐BOA additional biogenic OM for each 1 ppb increase of NOx.Key PointsAerosol concentration and composition are largely similar at two different forested sites during summertime in the southeastern United StatesFTIR of ambient biogenic SOA factors are similar to isoprene and monoterpene chamber experiment, supporting NOx‐related oxidation pathwaysNOx increases biogenic SOA by 0.5 ± 0.1 μg/m3 for CTR‐LO‐OOA and 1.0 ± 0.3 μg/m3 for CTR‐BOA for each ppb NOx above 1 ppb at Centreville but not at Look Rock (where NOx was usually below 1 ppb)Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146465/1/jgrd54860-sup-0001-SI.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146465/2/jgrd54860.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146465/3/jgrd54860_am.pd

The First Provenance Challenge

The first Provenance Challenge was set up in order to provide a forum for the community to help understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions