Computational characterization of differential kinase activity from phosphoproteomics datasets is critical for correctly inferring cellular circuitry and how signaling cascades are altered in drug ...treatment and/or disease. Kinase-Substrate Enrichment Analysis (KSEA) offers a powerful approach to estimating changes in a kinase's activity based on the collective phosphorylation changes of its identified substrates. However, KSEA has been limited to programmers who are able to implement the algorithms. Thus, to make it accessible to the larger scientific community, we present a web-based application of this method: the KSEA App. Overall, we expect that this tool will offer a quick and user-friendly way of generating kinase activity estimates from high-throughput phosphoproteomics datasets.
the KSEA App is a free online tool: casecpb.shinyapps.io/ksea/. The source code is on GitHub: github.com/casecpb/KSEA/. The application is also available as the R package "KSEAapp" on CRAN: CRAN.R-project.org/package=KSEAapp/.
mark.chance@case.edu.
Supplementary data are available at Bioinformatics online.
Protein footprinting mediated by mass spectrometry has evolved over the last 30 years from proof of concept to commonplace biophysics tool, with unique capabilities for assessing structure and ...dynamics of purified proteins in physiological states in solution. This review outlines the history and current capabilities of two major methods of protein footprinting: reversible hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (HRF), an irreversible covalent labeling approach. Technological advances in both approaches now permit high-resolution assessments of protein structure including secondary and tertiary structure stability mediated by backbone interactions (measured via HDX) and solvent accessibility of side chains (measured via HRF). Applications across many academic fields and in biotechnology drug development are illustrated including: detection of protein interfaces, identification of ligand/drug binding sites, and monitoring dynamics of protein conformational changes along with future prospects for advancement of protein footprinting in structural biology and biophysics research.
Atmospheric transport of trace elements and nutrients to the oceans Jickells, T. D.; Baker, A. R.; Chance, R.
Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences,
11/2016, Letnik:
374, Številka:
2081
Journal Article
Recenzirano
Odprti dostop
This paper reviews atmospheric inputs of trace elements and nutrients to the oceans in the context of the GEOTRACES programme and provides new data from two Atlantic GEOTRACES cruises. We consider ...the deposition of nitrogen to the oceans, which is now dominated by anthropogenic emissions, the deposition of mineral dust and related trace elements, and the deposition of other trace elements which have a mixture of anthropogenic and dust sources. We then consider the solubility (as a surrogate for bioavailability) of the various elements. We consider briefly the sources, atmospheric transport and transformations of these elements and how this results in strong spatial deposition gradients. Solubility of the trace elements also varies systematically between elements, reflecting their sources and cycling, and for some trace elements there are also systematic gradients in solubility related to dust loading. Together, these effects create strong spatial gradients in the inputs of bioavailable trace elements to the oceans, and we are only just beginning to understand how these affect ocean biogeochemistry.
This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’.
•The Challenge Hypothesis (CH) concerns the dynamics of male life-history strategies.•The CH predicts that testosterone (T) mediates shifts between mating and parenting.•In humans, pair-bonding and ...fatherhood generally correspond to lower T.•We meta-analyze 114 effects to quantify magnitudes of predicted CH effects in men.•We find both robust effects and evidence of selective reporting.
Males of many species must allocate limited energy budgets between mating and parenting effort. The Challenge Hypothesis provides a framework for understanding these life-history trade-offs via the disparate roles of testosterone (T) in aggression, sexual behavior, and parenting. It predicts that males pursuing mating opportunities have higher T than males pursuing paternal strategies, and in humans, many studies indeed report that men who are fathers and/or pair-bonded have lower T than childless and/or unpaired men. However, the magnitude of these effects, and the influence of methodological variation on effect sizes, have not been quantitatively assessed. We meta-analyzed 114 effects from 66 published and unpublished studies covering four predictions inspired by the Challenge Hypothesis. We confirm that pair-bonded men have lower T than single men, and fathers have lower T than childless men. Furthermore, men more oriented toward pair-bonding or offspring investment had lower T. We discuss the practical meaningfulness of the effect sizes we estimate in relation to known factors (e.g., aging, geographic population) that influence men’s T concentrations.
The framework hydrophobicity and flexibility of ZIF-8 are investigated by a detailed adsorption and diffusion study of a series of probe molecules including ethanol, 1-butanol, water, hexane isomers, ...xylene isomers, and 1,2,4-trimethylbenzene. The prospects for using ZIF-8 in biofuel recovery and hydrocarbon separations are discussed in terms of adsorption or kinetic selectivities. ZIF-8 shows extremely low water vapor uptakes and is especially suitable for vapor phase butanol-based biofuel recovery. The extraordinary framework flexibility of ZIF-8 is demonstrated by the adsorption of hydrocarbon molecules that are much larger than its nominal pore size, such as m-xylene, o-xylene and 1,2,4-trimethylbenzene. The calculation of corrected diffusion coefficients reveals an interesting spectrum of promising kinetic hydrocarbon separations by ZIF-8. These findings confirm that a molecular sieving effect tends to occur in the sorbate molecular size range of 4–6 Å rather than around the nominal ZIF-8 pore size of 3.4 Å, due to its surprising framework flexibility.
Alcohol (methanol, ethanol, 1-propanol, 2-propanol and 1-butanol) and water vapor adsorption in zeolitic imidazolate frameworks (ZIF-8, ZIF-71 and ZIF-90) with similar crystal sizes was ...systematically studied. The feasibility of applying these ZIF materials to the recovery of bio-alcohols is evaluated by estimating the vapor-phase alcohol-water sorption selectivity.
Nanoporous zeolitic imidazolate frameworks (ZIFs) form structural topologies equivalent to zeolites. ZIFs containing only one type of imidazole linker show separation capability for limited molecular ...pairs. We show that the effective pore size, hydrophilicity, and organophilicity of ZIFs can be continuously and drastically tuned using mixed-linker ZIFs containing two types of linkers, allowing their use as a more general molecular separation platform. We illustrate this remarkable behavior by adsorption and diffusion measurements of hydrocarbons, alcohols, and water in mixed-linker ZIF-8 x -90100–x materials with a large range of crystal sizes (338 nm to 120 μm), using volumetric, gravimetric, and PFG-NMR methods. NMR, powder FT-Raman, and micro-Raman spectroscopy unambiguously confirm the mixed-linker nature of individual ZIF crystals. Variation of the mixed-linker composition parameter (x) allows continuous control of n-butane, i-butane, butanol, and isobutanol diffusivities over 2–3 orders of magnitude and control of water and alcohol adsorption especially at low activities.
Emerging evidence indicates that gene products implicated in human cancers often cluster together in "hot spots" in protein-protein interaction (PPI) networks. Additionally, small sub-networks within ...PPI networks that demonstrate synergistic differential expression with respect to tumorigenic phenotypes were recently shown to be more accurate classifiers of disease progression when compared to single targets identified by traditional approaches. However, many of these studies rely exclusively on mRNA expression data, a useful but limited measure of cellular activity. Proteomic profiling experiments provide information at the post-translational level, yet they generally screen only a limited fraction of the proteome. Here, we demonstrate that integration of these complementary data sources with a "proteomics-first" approach can enhance the discovery of candidate sub-networks in cancer that are well-suited for mechanistic validation in disease. We propose that small changes in the mRNA expression of multiple genes in the neighborhood of a protein-hub can be synergistically associated with significant changes in the activity of that protein and its network neighbors. Further, we hypothesize that proteomic targets with significant fold change between phenotype and control may be used to "seed" a search for small PPI sub-networks that are functionally associated with these targets. To test this hypothesis, we select proteomic targets having significant expression changes in human colorectal cancer (CRC) from two independent 2-D gel-based screens. Then, we use random walk based models of network crosstalk and develop novel reference models to identify sub-networks that are statistically significant in terms of their functional association with these proteomic targets. Subsequently, using an information-theoretic measure, we evaluate synergistic changes in the activity of identified sub-networks based on genome-wide screens of mRNA expression in CRC. Cross-classification experiments to predict disease class show excellent performance using only a few sub-networks, underwriting the strength of the proposed approach in discovering relevant and reproducible sub-networks.
The proton gradient is a principal energy source for respiration-dependent active transport, but the structural mechanisms of proton-coupled transport processes are poorly understood. YiiP is a ...proton-coupled zinc transporter found in the cytoplasmic membrane of Escherichia coli. Its transport site receives protons from water molecules that gain access to its hydrophobic environment and transduces the energy of an inward proton gradient to drive Zn(II) efflux. This membrane protein is a well-characterized member of the family of cation diffusion facilitators that occurs at all phylogenetic levels. Here we show, using X-ray-mediated hydroxyl radical labelling of YiiP and mass spectrometry, that Zn(II) binding triggers a highly localized, all-or-nothing change of water accessibility to the transport site and an adjacent hydrophobic gate. Millisecond time-resolved dynamics reveal a concerted and reciprocal pattern of accessibility changes along a transmembrane helix, suggesting a rigid-body helical re-orientation linked to Zn(II) binding that triggers the closing of the hydrophobic gate. The gated water access to the transport site enables a stationary proton gradient to facilitate the conversion of zinc-binding energy to the kinetic power stroke of a vectorial zinc transport. The kinetic details provide energetic insights into a proton-coupled active-transport reaction.
PDF
