Influence fields: a quantitative framework for representation and analysis of active dendrites

Rathour RK, Narayanan R. Influence fields: a quantitative framework for representation and analysis of active dendrites. J Neurophysiol 107: 2313-2334, 2012. First published January 18, 2012; doi:10.1152/jn.00846.2011.-Neuronal dendrites express numerous voltage-gated ion channels (VGICs), typically with spatial gradients in their densities and properties. Dendritic VGICs, their gradients, and their plasticity endow neurons with information processing capabilities that are higher than those of neurons with passive dendrites. Despite this, frameworks that incorporate dendritic VGICs and their plasticity into neurophysiological and learning theory models have been far and few. Here, we develop a generalized quantitative framework to analyze the extent of influence of a spatially localized VGIC conductance on different physiological properties along the entire stretch of a neuron. Employing this framework, we show that the extent of influence of a VGIC conductance is largely independent of the conductance magnitude but is heavily dependent on the specific physiological property and background conductances. Morphologically, our analyses demonstrate that the influences of different VGIC conductances located on an oblique dendrite are confined within that oblique dendrite, thus providing further credence to the postulate that dendritic branches act as independent computational units. Furthermore, distinguishing between active and passive propagation of signals within a neuron, we demonstrate that the influence of a VGIC conductance is spatially confined only when propagation is active. Finally, we reconstruct functional gradients from VGIC conductance gradients using influence fields and demonstrate that the cumulative contribution of VGIC conductances in adjacent compartments plays a critical role in determining physiological properties at a given location. We suggest that our framework provides a quantitative basis for unraveling the roles of dendritic VGICs and their plasticity in neural coding, learning, and homeostasis.

Cell Surface Assembly of HIV gp41 Six-Helix Bundles for Facile, Quantitative Measurements of Hetero-oligomeric Interactions

Helix helix interactions are fundamental to many biological signals and systems and are found in homo- or heteromultimerization of signaling molecules as well as in the process of virus entry into the host. In HIV, virus-host membrane fusion during infection is mediated by the formation of six-helix bundles (6HBs) from homotrimers of gp41, from which a number of synthetic peptides have been derived as antagonists of virus entry. Using a yeast surface two-hybrid (YS2H) system, a platform designed to detect protein-protein interactions occurring through a secretory pathway, we reconstituted 6HB complexes on the yeast surface, quantitatively measured the equilibrium and kinetic constants of soluble 6HB, and delineated the residues influencing homo-oligomeric and hetero-oligomeric coiled-coil interactions. Hence, we present YS2H as a platform for the facile characterization and design of antagonistic peptides for inhibition of HIV and many other enveloped viruses relying on membrane fusion for infection, as well as cellular signaling events triggered by hetero-oligomeric coiled coils.

Quantitative estimation of mechanical and optical properties from ultrasound assisted optical tomography data

We demonstrate quantitative optical property and elastic property imaging from ultrasound assisted optical tomography data. The measurements, which are modulation depth M and phase phi of the speckle pattern, are shown to be sensitively dependent on these properties of the object in the insonified focal region of the ultrasound (US) transducer. We demonstrate that Young's modulus (E) can be recovered from the resonance observed in M versus omega (the US frequency) plots and optical absorption (mu(a)) and scattering (mu(s)) coefficients from the measured differential phase changes. All experimental observations are verified also using Monte Carlo simulations. (c) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). DOI: 10.1117/1.JBO.17.10.101507]

Quantitative interactions between the A-type K+ current and inositol trisphosphate receptors regulate intraneuronal Ca2+ waves and synaptic plasticity

Key points center dot Active calcium signal propagation occurs when an initial calcium trigger elicits calcium release through endoplasmic reticulum (ER) receptors. A high concentration of the calcium trigger in thin-calibre dendrites would suppress release of calcium through hippocampal inositol trisphosphate receptors (InsP3Rs). center dot Could the high-density expression of A-type K+ channels in thin-calibre dendrites be a mechanism for inhibiting this suppression, thereby restoring the utility of the ER as a substrate for active calcium propagation? center dot Quantitative analyses involving experimentally constrained models reveal a bell-shaped dependence of calcium released through InsP3Rs on the A-type K+ channel density, during the propagation of a calcium wave. center dot A-type K+ channels regulated the relative contribution of ER calcium to the induction of synaptic plasticity in the presence of model metabotropic glutamate receptors. center dot These results identify a novel form of interaction between active dendrites and the ER membrane and suggest that A-type K+ channels are ideally placed for inhibiting the suppression of InsP3Rs in thin-calibre dendrites. Abstract The A-type potassium current has been implicated in the regulation of several physiological processes. Here, we explore a role for the A-type potassium current in regulating the release of calcium through inositol trisphosphate receptors (InsP3R) that reside on the endoplasmic reticulum (ER) of hippocampal pyramidal neurons. To do this, we constructed morphologically realistic, conductance-based models equipped with kinetic schemes that govern several calcium signalling modules and pathways, and constrained the distributions and properties of constitutive components by experimental measurements from these neurons. Employing these models, we establish a bell-shaped dependence of calcium release through InsP3Rs on the density ofA-type potassium channels, during the propagation of an intraneuronal calcium wave initiated through established protocols. Exploring the sensitivities of calcium wave initiation and propagation to several underlying parameters, we found that ER calcium release critically depends on dendritic diameter and that wave initiation occurred at branch points as a consequence of a high surface area to volume ratio of oblique dendrites. Furthermore, analogous to the role ofA-type potassium channels in regulating spike latency, we found that an increase in the density ofA-type potassium channels led to increases in the latency and the temporal spread of a propagating calcium wave. Next, we incorporated kinetic models for the metabotropic glutamate receptor (mGluR) signalling components and a calcium-controlled plasticity rule into our model and demonstrate thatthe presence of mGluRs induced a leftward shift in a BienenstockCooperMunro-like synaptic plasticity profile. Finally, we show that the A-type potassium current could regulate the relative contribution of ER calcium to synaptic plasticity induced either through 900 pulses of various stimulus frequencies or through theta burst stimulation. Our results establish a novel form of interaction between active dendrites and the ER membrane, uncovering a powerful mechanism that could regulate biophysical/biochemical signal integration and steer the spatiotemporal spread of signalling microdomains through changes in dendritic excitability.

Stretching single polymer chains of donor-acceptor foldamers: toward the quantitative study on the extent of folding

Single-molecule force spectroscopy has proven to be an efficient tool for the quantitative characterization of flexible foldamers on the single-molecule level in this study. The extent of folding has been estimated quantitatively for the first time to the best of our knowledge, which is crucial for a better understanding of the ``folding-process'' on single-molecule level. Therefore, this study may provide a guidance to regulate folding for realizing rational control over the functions of bulk materials.

Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice

Rice landraces are lineages developed by farmers through artificial selection during the long-term domestication process. Despite huge potential for crop improvement, they are largely understudied in India. Here, we analyse a suite of phenotypic characters from large numbers of Indian landraces comprised of both aromatic and non-aromatic varieties. Our primary aim was to investigate the major determinants of diversity, the strength of segregation among aromatic and non-aromatic landraces as well as that within aromatic landraces. Using principal component analysis, we found that grain length, width and weight, panicle weight and leaf length have the most substantial contribution. Discriminant analysis can effectively distinguish the majority of aromatic from non-aromatic landraces. More interestingly, within aromatic landraces long-grain traditional Basmati and short-grain non-Basmati aromatics remain morphologically well differentiated. The present research emphasizes the general patterns of phenotypic diversity and finds out the most important characters. It also confirms the existence of very unique short-grain aromatic landraces, perhaps carrying signatures of independent origin of an additional aroma quantitative trait locus in the indica group, unlike introgression of specific alleles of the BADH2 gene from the japonica group as in Basmati. We presume that this parallel origin and evolution of aroma in short-grain indica landraces are linked to the long history of rice domestication that involved inheritance of several traits from Oryza nivara, in addition to O. rufipogon. We conclude with a note that the insights from the phenotypic analysis essentially comprise the first part, which will likely be validated with subsequent molecular analysis.

Quantitative Strain and Compositional Studies of InxGa1-xAs Epilayer in a GaAs-based pHEMT Device Structure by TEM Techniques

In GaAs-based pseudomorphic high-electron mobility transistor device structures, strain and composition of the InxGa1 (-) As-x channel layer are very important as they influence the electronic properties of these devices. In this context, transmission electron microscopy techniques such as (002) dark-field imaging, high-resolution transmission electron microscopy (HRTEM) imaging, scanning transmission electron microscopy-high angle annular dark field (STEM-HAADF) imaging and selected area diffraction, are useful. A quantitative comparative study using these techniques is relevant for assessing the merits and limitations of the respective techniques. In this article, we have investigated strain and composition of the InxGa1 (-) As-x layer with the mentioned techniques and compared the results. The HRTEM images were investigated with strain state analysis. The indium content in this layer was quantified by HAADF imaging and correlated with STEM simulations. The studies showed that the InxGa1 (-) As-x channel layer was pseudomorphically grown leading to tetragonal strain along the 001] growth direction and that the average indium content (x) in the epilayer is similar to 0.12. We found consistency in the results obtained using various methods of analysis.

Quantitative estimation of density variation in high-speed flows through inversion of the measured wavefront distortion

A simple method employing an optical probe is presented to measure density variations in a hypersonic flow obstructed by a test model in a typical shock tunnel. The probe has a plane light wave trans-illuminating the flow and casting a shadow of a random dot pattern. Local slopes of the distorted wavefront are obtained from shifts of the dots in the pattern. Local shifts in the dots are accurately measured by cross-correlating local shifted shadows with the corresponding unshifted originals. The measured slopes are suitably unwrapped by using a discrete cosine transform based phase unwrapping procedure and also through iterative procedures. The unwrapped phase information is used in an iterative scheme for a full quantitative recovery of density distribution in the shock around the model through refraction tomographic inversion. Hypersonic flow field parameters around a missile shaped body at a free-stream Mach number of 5.8 measured using this technique are compared with the numerically estimated values. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)

Interplay of male traits, male mating strategies and female mate choice in the Asian elephant, Elephas maximus

Elaborate male traits with no apparent adaptive value may have evolved through female mate discrimination. Tusks are an elaborate male-only trait in the Asian elephant that could potentially influence female mate choice. We examined the effect of male body size, tusk possession and musth status on female mate choice in an Asian elephant population. Large/musth males received positive responses from oestrous females towards courtship significantly more often than did small/non-musth males. Young, tusked non-musth males attempted courtship significantly more often than their tuskless peers, and received more positive responses (though statistically insignificant) than did tuskless males. A positive response did not necessarily translate into mating because of mate-guarding by a dominant male. Female elephants appear to choose mates based primarily on traits such as musth that signal direct fertility benefits through increased sperm received than for traits such as tusks that may signal only indirect fitness benefits.

A quantitative imaging-based screen reveals the exocyst as a network hub connecting endocytosis and exocytosis

The coupling of endocytosis and exocytosis underlies fundamental biological processes ranging from fertilization to neuronal activity and cellular polarity. However, the mechanisms governing the spatial organization of endocytosis and exocytosis require clarification. Using a quantitative imaging-based screen in budding yeast, we identified 89 mutants displaying defects in the localization of either one or both pathways. High-resolution single-vesicle tracking revealed that the endocytic and exocytic mutants she4 Delta and bud6 Delta alter post-Golgi vesicle dynamics in opposite ways. The endocytic and exocytic pathways display strong interdependence during polarity establishment while being more independent during polarity maintenance. Systems analysis identified the exocyst complex as a key network hub, rich in genetic interactions with endocytic and exocytic components. Exocyst mutants displayed altered endocytic and post-Golgi vesicle dynamics and interspersed endocytic and exocytic domains compared with control cells. These data are consistent with an important role for the exocyst in coordinating endocytosis and exocytosis.

QUANTITATIVE OH PLANAR LASER INDUCED FLUORESCENCE DIAGNOSTICS OF SYNGAS AND METHANE COMBUSTION IN A CAVITY COMBUSTOR

The current work reports quantitative OH species concentration in the cavity of a trapped vortex combustor (TVC) in the context of mixing and flame stabilization studies using both syngas and methane fuels. Planar laser induced fluorescence (PLIF) measurements of OH radical obtained using a Nd: YAG pumped dye laser are quantified using a flat flame McKenna burner. The momentum flux ratio (MFR), defined as the ratio of the cavity fuel jet momentum to that of the guide vane air stream, is observed to be a key governing parameter. At high MFRs similar to 4.5, the flame front is observed to form at the interface of the fuel jet and the air jet stream. This is substantiated by velocity vector field measurements. For syngas, as the MFR is lowered to similar to 0.3, the fuel-air mixing increases and a flame front is formed at the bottom and downstream edge of the cavity where a stratified charge is present. This trend is observed for different velocities at similar equivalence ratios. In case of methane combustion in the cavity, where the MFRs employed are extremely low at similar to 0.01, a different mechanism is observed. A fuel-rich mixture is now observed at the center of the cavity and this mixture undergoes combustion. On further increase of the cavity equivalence ratio, the rich mixture exceeds the flammability limit and forms a thin reaction zone at the interface with air stream. As a consequence, a shear layer flame at the top of the cavity interface with the mainstream is also observed. The equivalence ratio in the cavity also determines the combustion characteristics in the case of fuel-air mixtures that are formed as a result of the mixing. Overall, flame stabilization mechanisms have been proposed, which account for the wide range of MFRs and premixing in the mainstream as well.

Quantitative metabolic profiling of NMR spectral signatures of branched chain amino acids in blood serum

Branched Chain Amino Acids (BCAAs) are related to different aspects of diseases like pathogenesis, diagnosis and even prognosis. While in some diseases, levels of all the BCAAs are perturbed; in some cases, perturbation occurs in one or two while the rest remain unaltered. In case of ischemic heart disease, there is an enhanced level of plasma leucine and isoleucine but valine level remains unaltered. In `Hypervalinemia', valine is elevated in serum and urine, but not leucine and isoleucine. Therefore, identification of these metabolites and profiling of individual BCAA in a quantitative manner in body-fluid like blood plasma/serum have long been in demand. H-1 NMR resonances of the BCAAs overlap with each other which complicates quantification of individual BCAAs. Further, the situation is limited by the overlap of broad resonances of lipoprotein with the resonances of BCAAs. The widely used commercially available kits cannot differentially estimate the BCAAs. Here, we have achieved proper identification and characterization of these BCAAs in serum in a quantitative manner employing a Nuclear Magnetic Resonance-based technique namely T-2-edited Correlation Spectroscopy (COSY). This approach can easily be extended to other body fluids like bile, follicular fluids, saliva, etc.

Plant reproductive traits mediate tritrophic feedback effects within an obligate brood-site pollination mutualism

Plants, herbivores and parasitoids affect each other directly and indirectly; however, feedback effects mediated by host plant traits have rarely been demonstrated in these tritrophic interactions. Brood-site pollination mutualisms (e.g. those involving figs and fig wasps) represent specialised tritrophic communities where the progeny of mutualistic pollinators and of non-mutualistic gallers (both herbivores) together with that of their parasitoids develop within enclosed inflorescences called syconia (hence termed brood-sites or microcosms). Plant reproductive phenology (which affects temporal brood-site availability) and inflorescence size (representing brood-site size) are plant traits that could affect reproductive resources, and hence relationships between trees, pollinators and non-pollinating wasps. Analysing wasp and seed contents of syconia, we examined direct, indirect, trophic and non-trophic relationships within the interaction web of the fig-fig wasp community of Ficus racemosa in the context of brood site size and availability. We demonstrate that in addition to direct resource competition and predator-prey (host-parasitoid) interactions, these communities display exploitative or apparent competition and trait-mediated indirect interactions. Inflorescence size and plant reproductive phenology impacted plant-herbivore and plant-parasitoid associations. These plant traits also influenced herbivore-herbivore and herbivore-parasitoid relationships via indirect effects. Most importantly, we found a reciprocal effect between within-tree reproductive asynchrony and fig wasp progeny abundances per syconium that drives a positive feedback cycle within the system. The impact of a multitrophic feedback cycle within a community built around a mutualistic core highlights the need for a holistic view of plant-herbivore-parasitoid interactions in the community ecology of mutualisms.