No abstract

Photosynthetic characteristics of three species of Sphagnum common in the foothills of the Brooks Range on the North Slope of Alaska were investigated. Generally, light-saturated rates of net photosynthesis decreased in the order S. squarrosum, S. angustifolium, and S. warnstorfii when plants were grown under common growth chamber conditions. For field-grown S. angustifolium, average light compensation point at 10°C was 37 μmol ms photosynthetic photon flux density (PPFD), and light saturation occurred between 250 and 500 μmol m s. At 20°C, compensation point increased to 127 μmol ms and the PPFD required for light saturation increased to approximately 500 μmol ms, while maximum rates of CO uptake increased only slightly. Light response curves of chamber-grown plants exhibited substantially lower compensation points and higher light-saturated rates of CO assimilation than field-grown material, due perhaps to a higher percentage of green, photosynthetically competent tissue. All three species exhibited broad responses to temperature, with optima near 20°C, and maintained at least 75% of maximum assimilation between approx. 13° and 30°C. Rates at 5°C were approx. 50% of maximum. Studies of the microclimate of Sphagnum at the field research site suggest that CO uptake should occur at near light-saturated rates during the day in open tussock tundra but that PPFD may often be limiting under Salix and Betula canopies in a water track drainage. Simulations using a simple model provided a seasonal estimate of 0.78 g dry weight (DW) of S. angustifolium produced from each initial g of photosynthetic tissue under willow canopies, assuming no water limitations. Although the simulation model suggests that production would be 66% higher in open tussock tundra, S. angustifolium is rarely found in this potentially more stressful habitat. To explain the relative abundance of Sphagnum in shaded water track areas as compared to open tussock tundra, we postulate that the vascular plant canopies provide protection from adverse effects of high temperatures, excess irradiance and reduced water availability. Under conditions of normal water availability, removal of the vascular plant cover did not affect the tissue water content of S. squarrosum, but resulted in a strong decrease in photosynthetic capacity, accompanied by chlorophyll bleaching. These results suggest that photoinhibition may limit production under certain conditions.

Proteogenomics combines large-scale genomic and transcriptomic data with mass-spectrometry-based proteomic data to discover novel protein sequence variants and improve genome annotation. In contrast with conventional proteomic applications, proteogenomic analysis requires a number of additional data processing steps. Ideally, these required steps would be integrated and automated via a single software platform offering accessibility for wet-bench researchers as well as flexibility for user-specific customization and integration of new software tools as they emerge. Toward this end, we have extended the Galaxy bioinformatics framework to facilitate proteogenomic analysis. Using analysis of whole human saliva as an example, we demonstrate Galaxy’s flexibility through the creation of a modular workflow incorporating both established and customized software tools that improve depth and quality of proteogenomic results. Our customized Galaxy-based software includes automated, batch-mode BLASTP searching and a Peptide Sequence Match Evaluator tool, both useful for evaluating the veracity of putative novel peptide identifications. Our complex workflow (approximately 140 steps) can be easily shared using built-in Galaxy functions, enabling their use and customization by others. Our results provide a blueprint for the establishment of the Galaxy framework as an ideal solution for the emerging field of proteogenomics.

Background and aims Plant litter chemistry is a key driver of decomposition in peatlands. This study explored the relative contributions of phylogeny and environment to litter chemistry of peat mosses (Sphagnum), the key peat-forming plants on earth. Methods Fifteen Sphagnum species, representing three taxonomic sections ACUTIFOLIA, CUSPIDATA and SPHAGNUM, were sampled across a wide range of hydro-geochemical conditions. For all species we characterised chemical composition within (i) inorganic elements, (ii) carbohydrate polymers (iii) non-carbohydrates. Results The variation in carbohydrates was mostly explained by taxonomic section, suggesting phylogenetic conservation of carbohydrate composition. ACUTIFOLIA species invested relatively more in pectins, whereas CUSPIDATA and SPHAGNUM species invested more in hemicellulose. The composition of non-carbohydrates was mainly influenced by environment , except for some constituents for which the variation was more correlated to phylogeny. Finally, the variation in inorganic element concentrations mostly reflected hydro-geochemical conditions within and between peatlands. Conclusions The separation into an environmentally independent, phylogenetically conserved group of compounds (structural carbohydrates) and an environmentally dependent, variable group of compounds (inorganic elements, non-carbohydrates) has important implications both for understanding patterns in and for upscaling of spatially variable ecosystem processes associated with peat decomposition such as carbon se-questration, nutrient cycling and greenhouse gas emissions.

Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism (e.g. human), revealing insights into the molecular functions conferred by these communities. Compared to conventional proteomics, metaproteomics presents unique data analysis challenges, including the use of large protein databases derived from hundreds or thousands of organisms, as well as numerous processing steps to ensure high data quality. These challenges limit the use of metaproteomics for many researchers. In response, we have developed an accessible and flexible metaproteomics workflow within the Galaxy bioinformatics framework. Via analysis of human oral tissue exudate samples, we have established a modular Galaxy-based workflow that automates a reduction method for searching large sequence databases, enabling comprehensive identification of host proteins (human) as well as "meta-proteins" from the nonhost organisms. Downstream, automated processing steps enable basic local alignment search tool analysis and evaluation/visualization of peptide sequence match quality, maximizing confidence in results. Outputted results are compatible with tools for taxonomic and functional characterization (e.g. Unipept, MEGAN5). Galaxy also allows for the sharing of complete workflows with others, promoting reproducibility and also providing a template for further modification and enhancement. Our results provide a blueprint for establishing Galaxy as a solution for metaproteomic data analysis. All MS data have been deposited in the ProteomeXchange with identifier PXD001655 (http://proteomecentral.proteomexchange.org/dataset/PXD001655).