Dynamic Pathways for Viral Capsid Assembly

We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive assembly. For some ranges of parameters, assembly is facile, while for others, assembly is dynamically frustrated by kinetic traps corresponding to malformed or incompletely formed capsids. Our simulations sample many independent trajectories at various capsomer concentrations, allowing for statistically meaningful conclusions. Depending on subunit (i.e., capsomer) geometries, successful assembly proceeds by several mechanisms involving binding of intermediates of various sizes. We discuss the relationship between these mechanisms and experimental evaluations of capsid assembly processes.Comment: 13 pages, 13 figures. Submitted to Biophys.

The effect of differential growth rates across plants on spectral predictions of physiological parameters.

Leaves of various ages and positions in a plant's canopy can present distinct physiological, morphological and anatomical characteristics, leading to complexities in selecting a single leaf for spectral representation of an entire plant. A fortiori, as growth rates between canopies differ, spectral-based comparisons across multiple plants--often based on leaves' position but not age--becomes an even more challenging mission. This study explores the effect of differential growth rates on the reflectance variability between leaves of different canopies, and its implication on physiological predictions made by widely-used spectral indices. Two distinct irrigation treatments were applied for one month, in order to trigger the formation of different growth rates between two groups of grapevines. Throughout the experiment, the plants were physiologically and morphologically monitored, while leaves from every part of their canopies were spectrally and histologically sampled. As the control vines were constantly developing new leaves, the water deficit plants were experiencing growth inhibition, resulting in leaves of different age at similar nodal position across the treatments. This modification of the age-position correlation was characterized by a near infrared reflectance difference between younger and older leaves, which was found to be exponentially correlated (R(2) = 0.98) to the age-dependent area of intercellular air spaces within the spongy parenchyma. Overall, the foliage of the control plant became more spectrally variable, creating complications for intra- and inter-treatment leaf-based comparisons. Of the derived indices, the Structure-Insensitive Pigment Index (SIPI) was found indifferent to the age-position effect, allowing the treatments to be compared at any nodal position, while a Normalized Difference Vegetation Index (NDVI)-based stomatal conductance prediction was substantially affected by differential growth rates. As various biotic and abiotic factors may form distinctions in growth, future precision agriculture studies should consider its spectral effect on physiological predictions

Combining leaf physiology, hyperspectral imaging and partial least squares-regression (PLS-R) for grapevine water status assessment

Physiological measurements are considered to be the most accurate way of assessing plant water status, but they might also be time-consuming, costly and intrusive. Since visible (VIS)-to-shortwave infrared (SWIR) imaging spectrometers are able to monitor various bio-chemical alterations in the leaf, such narrow-band instruments may offer a faster, less expensive and non-destructive alternative. This requires an intelligent downsizing of broad and noisy hyperspectra into the few most physiologically-sensitive wavelengths. In the current study, hyperspectral signatures of water-stressed grapevine leaves (Vitis vinifera L. cv. Cabernet Sauvignon) were correlated to values of midday leaf water potential (Wl), stomatal conductance (gs) and non-photochemical quenching (NPQ) under controlled conditions, using the partial least squares-regression (PLS-R) technique. It was found that opposite reflectance trends at 530\u2013550 nm and around 1500 nm \u2013 associated with independent changes in photoprotective pigment contents and water availability, respectively \u2013 were indicative of stress-induced alterations in Wl, gs and NPQ. Furthermore, combining the spectral responses at these VIS and SWIR regions yielded three normalized water balance indices (WABIs), which were superior to various widely-used reflectance models in predicting physiological values at both the leaf and canopy levels. The potential of the novel WABI formulations also under field conditions demonstrates their applicability for water status monitoring and irrigation scheduling

Volumetric water content (A; VWC), stomatal conductance (B; g_s) and net assimilation rate (C; A_N) throughout the experiment.

<p>Excluding day 1, values of the two groups were significantly different for every measuring date. Vertical bars represent means ± standard deviations (n = 10).</p

Percentage of mesophyll void areas within leaves along the control (C) and water deficit (WD) canopies at day 29.

<p>CM =  Column mesophyll; SM =  Spongy mesophyll. Data represents means ± standard deviations (n = 5). Upper-case letters indicate significance of differences.</p

Summary of all measurement types that were taken during the experiment.

<p>Measurements were taken on days of experiment (DOE) that are signified by X.</p

Near infrared reflectance of leaves as a function of their nodal position at day 29.

<p>Significant differences in the means of near infrared reflectance (750–1250 nm) were found between control and stressed leaves of the same nodal position down until the 16th node. The reflectance values in the upper 15 and 11 nodes of the control and water deficit groups, respectively, were significantly different from those in the rest of the nodes, and thus were not representative for most of the plant. Vertical bars represent means ± standard deviations (n = 10). Lower-case letters indicate significance of differences.</p

Thickness of strata in leaves along the control (C) and water deficit (WD) canopies at day 29.

<p>UC =  Upper cuticle; UE =  Upper epidermis; CM =  Column mesophyll; SM =  Spongy mesophyll; LE =  Lower epidermis; LC =  Lower cuticle; WL =  Whole leaf. Data represents means ± standard deviations (n = 5). Upper-case letters indicate significance of differences.</p

Reflectance of leaves from different nodal positions as a function of wavelength throughout the experiment.

<p>The reflectance signatures presented are of the 7^th, 14^th, and 29^th days of measuring for the control (A, C, and E, respectively) and water deficit (B, D, and F, respectively) groups. Each reflectance signature was averaged out of 10 leaf samples.</p

Stomatal conductance (g_s) as a function of the Normalized Difference Vegetation Index (NDVI) throughout the experiment.

<p>The diamonds represent values of the youngest, fully-matured leaves of both treatments from all time points, and were used to create a linear regression. The filled square and circle are the 29^th day's mean values of leaves from the whole control and water deficit canopies, respectively. The unfilled square and circle are the 29^th day's mean values from only the representative portion of the control and water deficit canopies (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088930#pone-0088930-t002" target="_blank">Table 2</a>), respectively.</p