Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 · Mo17 (IBM) recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL) controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.The intake, transport, and storage of elements are key processes underlying plant growth and survival. A plant must balance mineral levels to prevent accumulation of toxic concentrations of elements, while taking up essential elements for growth. Food crops must strike similar balances to provide healthy nutrient contents of edible tissues. Adaptation to variation in soil, water, and temperature requires that plant genomes encode flexible regulation of mineral physiology to achieve homeostasis (McDowell et al. 2013). This regulation must be responsive to both the availability of each regulated element in the environment and the levels of these elements at the sites of use within the plant. Understanding how the genome encodes responses to element limitation or toxic excess in nutrient-poor or contaminated soils will help to achieve targeted crop improvements and sustain our rapidly growing human population (Cobb et al. 2013).The concentrations of elements in a plant sample provide a useful read-out for the environmental, genetic, and physiological processes important for plant adaptation. We and others developed highthroughput and inexpensive pipelines to detect and quantitate 20 different elemental concentrations by inductively coupled plasma mass spectrometry (ICP-MS). This process, termed ionomics, is the quantitative study of the complete set of mineral nutrients and trace elements in an organism (its ionome) (Lahner et al. 2003). In crop plants such as maize and soybean, seed element profiles mak...
Plants obtain soil-resident elements that support growth and metabolism from the water-flow facilitated by transpiration and active transport processes. The availability of elements in the environment interacts with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 × Mo17 (IBM) recombinant inbred population grown in 10 different environments, spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci (QTL) controlling seed elemental accumulation. While a set of these QTL was found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates, and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.
The cut-open oocyte Vaseline gap (COVG) voltage clamp technique allows for analysis of electrophysiological and kinetic properties of heterologous ion channels in oocytes. Recordings from the cut-open setup are particularly useful for resolving low magnitude gating currents, rapid ionic current activation, and deactivation. The main benefits over the two-electrode voltage clamp (TEVC) technique include increased clamp speed, improved signal-to-noise ratio, and the ability to modulate the intracellular and extracellular milieu. Here, we employ the human cardiac sodium channel (hNaV1.5), expressed in Xenopus oocytes, to demonstrate the cut-open setup and protocol as well as modifications that are required to add voltage clamp fluorometry capability. The properties of fast activating ion channels, such as hNaV1.5, cannot be fully resolved near room temperature using TEVC, in which the entirety of the oocyte membrane is clamped, making voltage control difficult. However, in the cut-open technique, isolation of only a small portion of the cell membrane allows for the rapid clamping required to accurately record fast kinetics while preventing channel run-down associated with patch clamp techniques. In conjunction with the COVG technique, ion channel kinetics and electrophysiological properties can be further assayed by using voltage clamp fluorometry, where protein motion is tracked via cysteine conjugation of extracellularly applied fluorophores, insertion of genetically encoded fluorescent proteins, or the incorporation of unnatural amino acids into the region of interest(1). This additional data yields kinetic information about voltage-dependent conformational rearrangements of the protein via changes in the microenvironment surrounding the fluorescent molecule.
1Plants obtain elements from the soil through genetic and biochemical pathways responsive 2 to physiological state and environment. Most perturbations affect multiple elements which leads 3 the ionome, the full complement of mineral nutrients in an organism, to vary as an integrated 4 network rather than a set of distinct single elements. To examine the genetic basis of covariation 5 in the accumulation of multiple elements, we analyzed maize kernel ionomes from Intermated 6 B73 x Mo17 (IBM) recombinant inbred populations grown in 10 environments. We compared 7 quantitative trait loci (QTL) determining single-element variation to QTL that predict variation 8 in principal components (PCs) of multiple-element covariance. Single-element and multivariate 9 approaches detected partially overlapping sets of loci. In addition to loci co-localizing with 10 single-element QTL, multivariate traits within environments were controlled by loci with 11 significant multi-element effects not detectable using single-element traits. Gene-by-environment 12 interactions underlying multiple-element covariance were identified through QTL analyses of 13 principal component models of ionome variation. In addition to interactive effects, growth 14 environment had a profound effect on the elemental profiles and multi-element phenotypes were 15 significantly correlated with specific environmental variables. 16 Author Summary 17A multivariate approach to the analysis of element accumulation in the maize kernel 18shows that elements are not regulated independently. By describing relationships between 19 element accumulation we identified new genetic loci invisible to single-element approaches. The 20 mathematical combinations of elements distinguish groups of plants based on environment, 21 demonstrating that observed variation derives from interactions between genetically controlled 22 factors and environmental variables. These results suggest that successful application of 23 available for use under a CC0 license.peer-reviewed) is the author/funder.
Cells are organized on length scales from Angstroms to microns. However, the mechanisms by which Angstrom-scale molecular properties are translated to micron-scale macroscopic properties are not well understood. We have shown that interactions between multivalent proteins and multivalent ligands can cause liquid-liquid demixing phase transitions, resulting in formation of micron-sized liquid droplets in aqueous solution and micron-sized puncta on membranes. These transitions appear to occur concomitantly with sol-gel transitions to form large, dynamic polymers within the droplets/puncta. I will discuss how such transitions may control the spatial organization and biochemical activity of actin regulatory signaling pathways, and contribute to formation of PML nuclear bodies in the mammalian nucleus. Our data suggest a general mechanism by which cells may achieve micron-scale organization based on interactions between multivalent macromolecules.
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