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Ivan Baxter - One of the best experts on this subject based on the ideXlab platform.

  • multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain Ionome
    Plant direct, 2019
    Co-Authors: Brian P Dilkes, Alexandra Asaro Fikas, Ivan Baxter
    Abstract:

    : The integrated responses of biological systems to genetic and environmental variation result in substantial covariance in multiple phenotypes. The resultant pleiotropy, environmental effects, and genotype-by-environmental interactions (GxE) are foundational to our understanding of biology and genetics. Yet, the treatment of correlated characters, and the identification of the genes encoding functions that generate this covariance, has lagged. As a test case for analyzing the genetic basis underlying multiple correlated traits, we analyzed maize kernel Ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads the Ionome, the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. We compared quantitative trait loci (QTL) determining single-element variation to QTL that predict variation in principal components (PCs) of multiple-element covariance. Single-element and multivariate approaches detected partially overlapping sets of loci. QTL influencing trait covariation were detected at loci that were not found by mapping single-element traits. Moreover, this approach permitted testing environmental components of trait covariance, and identified multi-element traits that were determined by both genetic and environmental factors as well as genotype-by-environment interactions. Growth environment had a profound effect on the elemental profiles and multi-element phenotypes were significantly correlated with specific environmental variables.

  • multivariate analysis reveals environmental and genetic determinants of element covariation in the maize grain Ionome
    bioRxiv, 2017
    Co-Authors: Alexandra Asaro, Brian P Dilkes, Ivan Baxter
    Abstract:

    Plants obtain elements from the soil through genetic and biochemical pathways responsive to physiological state and environment. Most perturbations affect multiple elements which leads the Ionome, the full complement of mineral nutrients in an organism, to vary as an integrated network rather than a set of distinct single elements. To examine the genetic basis of covariation in the accumulation of multiple elements, we analyzed maize kernel Ionomes from Intermated B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. We compared quantitative trait loci (QTL) determining single-element variation to QTL that predict variation in principal components (PCs) of multiple-element covariance. Single-element and multivariate approaches detected partially overlapping sets of loci. In addition to loci co-localizing with single-element QTL, multivariate traits within environments were controlled by loci with significant multi-element effects not detectable using single-element traits. Gene-by-environment interactions underlying multiple-element covariance were identified through QTL analyses of principal component models of Ionome variation. In addition to interactive effects, growth environment had a profound effect on the elemental profiles and multi-element phenotypes were significantly correlated with specific environmental variables.

  • should we treat the Ionome as a combination of individual elements or should we be deriving novel combined traits
    Journal of Experimental Botany, 2015
    Co-Authors: Ivan Baxter
    Abstract:

    It has been more than 10 years since the concept of the Ionome, all of the mineral nutrients in a cell tissue or organism, was introduced. In the intervening years, ionomics, high throughput elemental profiling, has been used to analyse over 400 000 samples from at least 10 different organisms. There are now multiple published examples where an ionomics approach has been used to find genes of novel function, find lines or environments that produce foods with altered nutritional profiles, or define gene by environmental effects on elemental accumulation. In almost all of these studies, the Ionome has been treated as a collection of independent elements, with the analysis repeated on each measured element. However, many elements share chemical properties, are known to interact with each other, or have been shown to have similar interactions with biological molecules. Accordingly, there is strong evidence from ionomic studies that the elements of the Ionome do not behave independently and that combinations of elements should be treated as the phenotypes of interest. In this review, I will consider the evidence that we have for the interdependence of the Ionome, some of its causes, methods for incorporating this interdependence into analyses and the benefits, drawbacks, and challenges of taking these approaches.

  • Single-kernel ionomic profiles are highly heritable indicators of genetic and environmental influences on elemental accumulation in maize grain (Zea mays).
    PLOS ONE, 2014
    Co-Authors: Ivan Baxter, Gregory Ziegler, Brett Lahner, Michael V. Mickelbart, Rachel Foley, John Danku, Paul R. Armstrong, David E. Salt, Owen A. Hoekenga
    Abstract:

    : The Ionome, or elemental profile, of a maize kernel can be viewed in at least two distinct ways. First, the collection of elements within the kernel are food and feed for people and animals. Second, the Ionome of the kernel represents a developmental end point that can summarize the life history of a plant, combining genetic programs and environmental interactions. We assert that single-kernel-based phenotyping of the Ionome is an effective method of analysis, as it represents a reasonable compromise between precision, efficiency, and power. Here, we evaluate potential pitfalls of this sampling strategy using several field-grown maize sample sets. We demonstrate that there is enough genetically determined diversity in accumulation of many of the elements assayed to overcome potential artifacts. Further, we demonstrate that environmental signals are detectable through their influence on the kernel Ionome. We conclude that using single kernels as the sampling unit is a valid approach for understanding genetic and environmental effects on the maize kernel Ionome.

  • Elemental concentrations in the seed of mutants and natural variants of Arabidopsis thaliana grown under varying soil conditions.
    PLOS ONE, 2013
    Co-Authors: Stephen C. Mcdowell, Ivan Baxter, David E. Salt, Garo Z. Akmakjian, Chris Sladek, David G. Mendoza-cózatl, Joe Morrissey, Nick Saini, Ron Mittler, John M. Ward
    Abstract:

    The concentrations of mineral nutrients in seeds are critical to both the life cycle of plants as well as human nutrition. These concentrations are strongly influenced by soil conditions, as shown here by quantifying the concentration of 14 elements in seeds from Arabidopsis thaliana plants grown under four different soil conditions: standard, or modified with NaCl, heavy metals, or alkali. Each of the modified soils resulted in a unique change to the seed Ionome (the mineral nutrient content of the seeds). To help identify the genetic networks regulating the seed Ionome, changes in elemental concentrations were evaluated using mutants corresponding to 760 genes as well as 10 naturally occurring accessions. The frequency of ionomic phenotypes supports an estimate that as much as 11% of the A. thaliana genome encodes proteins of functional relevance to ion homeostasis in seeds. A subset of mutants were analyzed with two independent alleles, providing five examples of genes important for regulation of the seed Ionome: SOS2, ABH1, CCC, At3g14280 and CNGC2. In a comparison of nine different accessions to a Col-0 reference, eight accessions were observed to have reproducible differences in elemental concentrations, seven of which were dependent on specific soil conditions. These results indicate that the A. thaliana seed Ionome is distinct from the vegetative Ionome, and that elemental analysis is a sensitive approach to identify genes controlling ion homeostasis, including those that regulate gene expression, phospho-regulation, and ion transport.

Hubert A. Gasteiger - One of the best experts on this subject based on the ideXlab platform.

  • proton conduction in pem fuel cell cathodes effects of electrode thickness and Ionomer equivalent weight
    Journal of The Electrochemical Society, 2010
    Co-Authors: Chunxin Ji, Daniel R Baker, Wenbin Gu, Jacob Jorne, Hubert A. Gasteiger
    Abstract:

    The dependence of electrode proton resistivity on electrode thickness, Pt loading, Ionomer loading, and Ionomer equivalent weight (EW) in proton exchange membrane (PEM) fuel cell cathodes was investigated using a Pt/Vulcan catalyst. For uniform electrodes, the electrode proton resistivity is independent of the electrode thickness and Pt loading but depends on the Ionomer loading and Ionomer EW. There is a strong dependence on the Ionomer EW when the Ionomer/carbon weight (I/C) ratio is lower than 0.8. The electrode proton resistivity strongly depends on relative humidity (RH) and the density of ―SO 3 H groups in the electrode. The electrode proton resistivity becomes nearly independent of Ionomer EW in electrodes when high I/C ratios are used. At low I/C ratios and low RH levels, electrodes with 850 EW Ionomer exhibit better performance than those with 1050 EW. On the contrary, 850 EW electrodes give lower performance under overhumidified conditions due to electrode flooding.

  • dependence of electrode proton resistivity on electrode thickness and Ionomer equivalent weight in cathode catalyst layer in pem fuel cell
    Meeting Abstracts, 2008
    Co-Authors: Chunxin Ji, Daniel R Baker, Wenbin Gu, Jacob Jorne, Hubert A. Gasteiger
    Abstract:

    developed to predict electrode performance can be used in a wide range of electrodes and electrode thicknesses. Since the equivalent weight (EW) of the Ionomer affects its proton conductivity, using Ionomers with different EW and measuring their corresponding electrode’s proton resistance can give us a better understanding of the impact of the Ionomer bulk proton resistivity on the electrode proton resistivity. While previous electrodes were made of 1050 EW Ionomer, the present work employed electrodes made of an Ionomer with lower EW. Lower electrode proton resistivities are expected for the electrodes made of low EW Ionomers. H cath R ,

Vadim N. Gladyshev - One of the best experts on this subject based on the ideXlab platform.

  • Systematic age‐, organ‐, and diet‐associated Ionome remodeling and the development of ionomic aging clocks
    Aging Cell, 2020
    Co-Authors: Bohan Zhang, Javier Seravalli, Dmitriy I Podolskiy, Marco Mariotti, Vadim N. Gladyshev
    Abstract:

    : Aging involves coordinated yet distinct changes in organs and systems throughout life, including changes in essential trace elements. However, how aging affects tissue element composition (Ionome) and how these changes lead to dysfunction and disease remain unclear. Here, we quantified changes in the Ionome across eight organs and 16 age groups of mice. This global profiling revealed novel interactions between elements at the level of tissue, age, and diet, and allowed us to achieve a broader, organismal view of the aging process. We found that while the entire Ionome steadily transitions along the young-to-old trajectory, individual organs are characterized by distinct element changes. The Ionome of mice on calorie restriction (CR) moved along a similar but shifted trajectory, pointing that at the organismal level this dietary regimen changes metabolism in order to slow down aging. However, in some tissues CR mimicked a younger state of control mice. Even though some elements changed with age differently in different tissues, in general aging was characterized by the reduced levels of elements as well as their increased variance. The dataset we prepared also allowed to develop organ-specific, Ionome-based markers of aging that could help monitor the rate of aging. In some tissues, these markers reported the lifespan-extending effect of CR. These aging biomarkers have the potential to become an accessible tool to test the age-modulating effects of interventions.

  • systematic age organ and diet associated Ionome remodeling and the development of ionomic aging clocks
    Aging Cell, 2020
    Co-Authors: Bohan Zhang, Javier Seravalli, Dmitriy I Podolskiy, Marco Mariotti, Vadim N. Gladyshev
    Abstract:

    Aging involves coordinated yet distinct changes in organs and systems throughout life, including changes in essential trace elements. However, how aging affects tissue element composition (Ionome) and how these changes lead to dysfunction and disease remain unclear. Here, we quantified changes in the Ionome across eight organs and 16 age groups of mice. This global profiling revealed novel interactions between elements at the level of tissue, age, and diet, and allowed us to achieve a broader, organismal view of the aging process. We found that while the entire Ionome steadily transitions along the young-to-old trajectory, individual organs are characterized by distinct element changes. The Ionome of mice on calorie restriction (CR) moved along a similar but shifted trajectory, pointing that at the organismal level this dietary regimen changes metabolism in order to slow down aging. However, in some tissues CR mimicked a younger state of control mice. Even though some elements changed with age differently in different tissues, in general aging was characterized by the reduced levels of elements as well as their increased variance. The dataset we prepared also allowed to develop organ-specific, Ionome-based markers of aging that could help monitor the rate of aging. In some tissues, these markers reported the lifespan-extending effect of CR. These aging biomarkers have the potential to become an accessible tool to test the age-modulating effects of interventions.

  • Genome-wide RNAi ionomics screen reveals new genes and regulation of human trace element metabolism
    Nature Communications, 2014
    Co-Authors: Mikalai Malinouski, Nesrin M. Hasan, Yan Zhang, Javier Seravalli, Andrei Avanesov, Svetlana Lutsenko, Vadim N. Gladyshev
    Abstract:

    The composition of trace elements in human cells (the Ionome) is an important component of metabolism. Here, the authors carry out a high-throughput, genome-wide analysis of the human Ionome and identify cellular regulators of important trace elements such as selenium, copper and iron.

Michael Eikerling - One of the best experts on this subject based on the ideXlab platform.

  • Microstructure of Catalyst Layers in PEM Fuel Cells Redefined: A Computational Approach
    Electrocatalysis, 2011
    Co-Authors: Kourosh Malek, Tetsuya Mashio, Michael Eikerling
    Abstract:

    This work comprises an extensive coarse-grained molecular dynamics study of self-organization processes that define the mesoscopic structure of catalyst layers used in polymer electrolyte fuel cells. The detailed structural analysis focuses on agglomeration of Pt-decorated primary particles of graphitized carbon black, formation of Ionomer domains, emergence of the porous network, and formation of interfaces between the distinct phases. Insights obtained enable us to decisively redraw the existing structural picture of the catalyst layer. As a key result, we found that Ionomer forms a thin adhesive film, which partially covers agglomerates of Pt/carbon. Densely arranged charged side chains of Ionomer form a highly ordered array on the Ionomer film surface. The preferential orientation of these charged side chains depends on the surface wetting properties of the agglomerates. As a major consequence, results on Ionomer structure and distribution, presented in this work, seem to invalidate the classical electrolyte-flooded agglomerate model that has been widely applied to catalyst layers in polymer electrolyte fuel cells. Instead, the structural analysis provided defines a need for novel models of proton transport, water distribution, and Pt effectiveness that account for the thin-film morphology of Ionomer and the specific arrangement of surface groups.

Chunxin Ji - One of the best experts on this subject based on the ideXlab platform.

  • proton conduction in pem fuel cell cathodes effects of electrode thickness and Ionomer equivalent weight
    Journal of The Electrochemical Society, 2010
    Co-Authors: Chunxin Ji, Daniel R Baker, Wenbin Gu, Jacob Jorne, Hubert A. Gasteiger
    Abstract:

    The dependence of electrode proton resistivity on electrode thickness, Pt loading, Ionomer loading, and Ionomer equivalent weight (EW) in proton exchange membrane (PEM) fuel cell cathodes was investigated using a Pt/Vulcan catalyst. For uniform electrodes, the electrode proton resistivity is independent of the electrode thickness and Pt loading but depends on the Ionomer loading and Ionomer EW. There is a strong dependence on the Ionomer EW when the Ionomer/carbon weight (I/C) ratio is lower than 0.8. The electrode proton resistivity strongly depends on relative humidity (RH) and the density of ―SO 3 H groups in the electrode. The electrode proton resistivity becomes nearly independent of Ionomer EW in electrodes when high I/C ratios are used. At low I/C ratios and low RH levels, electrodes with 850 EW Ionomer exhibit better performance than those with 1050 EW. On the contrary, 850 EW electrodes give lower performance under overhumidified conditions due to electrode flooding.

  • dependence of electrode proton resistivity on electrode thickness and Ionomer equivalent weight in cathode catalyst layer in pem fuel cell
    Meeting Abstracts, 2008
    Co-Authors: Chunxin Ji, Daniel R Baker, Wenbin Gu, Jacob Jorne, Hubert A. Gasteiger
    Abstract:

    developed to predict electrode performance can be used in a wide range of electrodes and electrode thicknesses. Since the equivalent weight (EW) of the Ionomer affects its proton conductivity, using Ionomers with different EW and measuring their corresponding electrode’s proton resistance can give us a better understanding of the impact of the Ionomer bulk proton resistivity on the electrode proton resistivity. While previous electrodes were made of 1050 EW Ionomer, the present work employed electrodes made of an Ionomer with lower EW. Lower electrode proton resistivities are expected for the electrodes made of low EW Ionomers. H cath R ,