Reply to: “Comment on root orientation can affect detection accuracy of ground-penetrating radar”

Introduction

We showed that root orientation affected a parameter of ground penetrating radar (GPR), amplitude area (A) (Tanikawa et al. Plant Soil 373:317–327, 2013). The aims of this reply to Wu et al. (2014) are (i) to correct the two inaccuracies in Tanikawa et al. (2013) and (ii) to improve our method of estimating A(90°) using A(x) of root angle x.

Methods

Measured A values of Tanikawa et al. (2013) were analyzed with the modified equations.

Results

The first inaccuracy was the use of incorrect units for the coefficient b (the phase shift) in the sinusoidal waveform of A(x). The units should have been radians instead of degrees. The second inaccuracy was the mis-derivation of A(x) into A(x?+?90°). In the modified method, A(90°) was estimated by A(x) from two orthogonally intersecting transect lines and a transect line at a diagonal to them.

Conclusions

The two inaccuracies did not affect the previous main conclusions that the parameter T was suitable for estimating root diameter and that grid transects are likely to identify clear hyperbolas reflecting roots in radar profiles (Tanikawa et al. 2013). By the improved method, we could accurately estimate root diameter by scanning using three transect lines intersecting at angles of x, x?+?45°, and x?+?90°.     

Comment on “numerical treatment of two-center overlap integrals”

The subject paper by H. Safouhi (J Mol Model 12:213–220, 2006) presents a scheme based on a nonlinear convergence acceleration transformation for the numerical evaluation of two-center overlap integrals of Slater-type orbitals. In this comment we argue that there is no reason to adopt such an approach, as well-known methods for these integrals are substantially superior both in speed and in accuracy.     

Forward simulation of root’s ground penetrating radar signal: simulator development and validation

Background and aims

It remains unclear how the limiting factors (e.g., root size, root water content, spacing between roots, and soil water content) affect root investigation using ground penetrating radar (GPR). The objective of this study is to develop a theoretical forward simulation protocol of synthesizing root’s GPR signal and test the feasibility of our proposed simulation protocol in evaluating the impacts of limiting factors on GPR-based root detection and quantification.

Methods

The proposed forward simulation protocol was developed by integrating several existing numerical models, such as the Root Composition Model, the Root Dielectric Constant Model, the Root Electrical Conductivity Model, the Soil Dielectric Constant Model, the Soil Electrical Conductivity Model, and a newly-established model (Root Length-Biomass Model). Resolution and GPR index obtained from both field collected radargrams and corresponding simulations were compared to validate the accuracy of simulation.

Results

Simulated radargrams exhibit similar resolution with that of the in situ collected. The same trends of root radar signals against different levels of root size, root water content, interval between roots, root depth, and antenna frequency were observed on both in situ radargrams and simulated radargrams. Strong correlations (correlation coefficients ranging from 0.87 to 0.96) were found between GPR indices extracted from the simulated data and those from the field collected data.

Conclusions

Our proposed forward simulation is effective for assessing the impacts of limiting factors on root detection and quantification using GPR. This forward simulation protocol can be used to provide guidance for in situ GPR root investigation and can predict the accuracy of GPR-based root quantification under site-specific conditions.     

Comment on “allomothering in Hanuman langurs”

It is argued that “alloparental” care may represent behavior favored by selection to maximize individual reproductive success where aggressive costs are high. The relative pattern of results reported by Scollay and DeBold are consistent with the rare dominance hierarchy observed in Hanuman langurs and mantled howler monkeys, both folivorous primates in which infants wear a “natal” coat. It is suggested that the variability of results obtained by Scollay and DeBold is a function of captive conditions in which environmental stress is minimized.     

Comment on: “neutron imaging reveals internal plant water dynamics”

Introduction

In a recent paper, Warren et al. (2013) illustrated the potential of neutron radiography to visualize water dynamics in soil and plants.

Methods

After injection of deuterated water (D₂O) in soil, the authors could monitor the changes of D₂O concentration in roots.

Results

Based on the radiographs, the authors concluded that D₂O was transported from roots growing in a wet soil region to roots in a dry region, proving hydraulic redistribution between roots. However, this interpretation depends on the correct estimation of D₂O concentration in soil.

Conclusions

The experiments of Warren et al. (2013) could also be explained by diffusion of D₂O from soil to roots, without hydraulic redistribution within the root system.     

Statistical analysis of structural compensatory growth: how can we reduce the rate of false detection?

Compensatory growth (CG) is a key issue in work aiming at a full understanding of the adaptive significance of growth plasticity and its carryover effects on life-history. The number of studies addressing evolutionary explanations for CG has increased rapidly during the last few years, but there has not been a parallel gain in our understanding of the methodological difficulties associated with the analysis of CG. We point out two features of growth that can have serious consequences for detecting CG: (1) size dependence of growth rates, which causes nonlinearity of growth trajectories, and; (2) temporal overlapping of structural growth and replenishment of energy reserves after a period of famine. We show that the currently used methods can be prone to spurious detection of CG (Type I error) under conditions of nonlinear growth, and therefore lead to the accumulation of a significant amount of false “empirical support.” True and simulated growth data provided consistent results suggesting that a substantial fraction of the existing evidence for CG may be spurious. A small curvature in the growth trajectory can lead to spurious “detection” of CG when control and manipulated trajectories are compared over the same time interval (the “simultaneous” approach). We present a novel, robust method (the “asynchronous” approach) based on the accurate selection of control trajectories and comparison of control and treatment growth rates at different times. This method enables a reliable test to be performed for compensation under asymptotic growth. While the general results of our simulations do not support the application of conventional methods to the general case of nonlinear growth trajectories under the simultaneous approach, simple methods may prove valid if the experimental design allows for asynchronous comparisons. We advocate an alternative approach to deal with “safe” detection of CG that overcomes the problems associated with the occurrence of nonlinear and asymptotic growth, and provide recommendations for improving CG study designs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Localization of aluminium in the maize root apex: can morin detect cell wall-bound aluminium?

Morin is a fluorochrome which forms a fluorescent complex with aluminium (Al) and is thus used to localize Al in plant tissues. However, reports about the cellular distribution of Al-apoplastic versus symplastic-based on morin staining are often conflicting. The objective of this work was to investigate whether Al localization with morin staining can show the proper cellular distribution of Al. Fresh root cross-sections were made from root apices of maize (cv. Lixis) treated with 25 muM Al for 6 h and stained with morin. Fluorescence microscopic investigation showed Al-morin fluorescence in the cytosol, but not in the cell wall. This is in contrast to the growing evidence which shows that Al mainly accumulates in the cell wall, especially bound to the pectin matrix. Therefore, in vitro analyses were carried out to study whether morin can form a fluorescent complex with Al, which is bound to pectin, cell wall, and other Al-binding ligands such as phosphate, galacturonate, DNA, and ATP. Compared with the control treatment without Al-binding ligands, fluorescence intensity was reduced by about 10-fold in the presence of pectin and isolated cell walls, but fairly unaffected in the presence of phosphate and galacturonate. Al associated with DNA and ATP also formed a fluorescent complex with morin. This implies that, although Al is mainly accumulated in the cell wall, it cannot be detected with morin as it is tightly bound to cell-wall pectin. Thus, morin staining should not be used to study the distribution of Al between cell compartments.     

How well can the accuracy of comparative protein structure models be predicted?

Comparative structure models are available for two orders of magnitude more protein sequences than are experimentally determined structures. These models, however, suffer from two limitations that experimentally determined structures do not: They frequently contain significant errors, and their accuracy cannot be readily assessed. We have addressed the latter limitation by developing a protocol optimized specifically for predicting the Calpha root-mean-squared deviation (RMSD) and native overlap (NO3.5A) errors of a model in the absence of its native structure. In contrast to most traditional assessment scores that merely predict one model is more accurate than others, this approach quantifies the error in an absolute sense, thus helping to determine whether or not the model is suitable for intended applications. The assessment relies on a model-specific scoring function constructed by a support vector machine. This regression optimizes the weights of up to nine features, including various sequence similarity measures and statistical potentials, extracted from a tailored training set of models unique to the model being assessed: If possible, we use similarly sized models with the same fold; otherwise, we use similarly sized models with the same secondary structure composition. This protocol predicts the RMSD and NO3.5A errors for a diverse set of 580,317 comparative models of 6174 sequences with correlation coefficients (r) of 0.84 and 0.86, respectively, to the actual errors. This scoring function achieves the best correlation compared to 13 other tested assessment criteria that achieved correlations ranging from 0.35 to 0.71.     

Sharing a predator: can an invasive alien pest affect the predation on a local pest?

Invasive species can strongly affect biotic interactions in ecosystems, interacting both directly and indirectly with local species. In European tomato greenhouses, the invasive alien pest Tuta absoluta may impact the population dynamics of other pests like whiteflies. Besides inducing damages to the host plant and competing for resources with local pests, this alien species may exert a predator-mediated interaction on local pests sharing common natural enemies. Biocontrol agents usually used against whiteflies may also prey upon T. absoluta and this could alter the dynamics of local pest populations. We evaluated possible resource competition and predator-mediated interactions in a system involving one mirid predator Macrolophus pygmaeus and two pests, T. absoluta and a local whitefly, Bemisia tabaci, on greenhouse tomatoes. Results showed that both resource competition and predator-mediated interactions occurred simultaneously. In the presence of the shared predator, there was a short-term positive effect of T. absoluta on B. tabaci [up to 5.9-fold increase of B. tabaci juveniles (egg + larvae) after four weeks]. However, in the long-term there was a negative predator-mediated interaction of T. absoluta on B. tabaci, i.e., after ten weeks the density of B. tabaci was 7.3-fold lower in the presence of the invasive pest. We emphasize the critical role of generalist predators in managing both local and invasive alien pest populations and that the strength and direction of predator-mediated indirect interactions can depend on the time scale considered.     

Comment on Altaba (2015): a case of species misidentification?

Previously in this journal, Altaba (2015) presented an original hypothesis on the dispersal of small wetland snails in Central Europe after the Last Glacial Maximum, based on the discovery of rare species of the genus Vallonia at the foot of the Devín Hill (Slovakia). On the basis of the evidence available to us, it is our opinion that the existence of Vallonia declivis, Vallonia suevica, Vallonia enniensis, and Vallonia tenuilabris at Devín Gate has not been established, and that the hypothesis advanced in Altaba (2015) is therefore unsubstantiated by hard evidence.     

Contact-force monitoring increases accuracy of right ventricular voltage mapping avoiding “false scar” detection in patients with no evidence of structural heart disease

PurposeElectroanatomical mapping (EAM) could increase cardiac magnetic resonance imaging (CMR) sensitivity in detecting ventricular scar. Possible bias may be scar over-estimation due to inadequate tissue contact. Aim of the study is to evaluate contact-force monitoring influence during EAM, in patients with idiopathic right ventricular arrhythmias.Methods20 pts (13 M; 43 ± 12 y) with idiopathic right ventricular outflow tract (RVOT) arrhythmias and no structural abnormalities were submitted to Smarttouch catheter Carto3 EAM. Native maps included points collected without considering contact-force. EAM scar was defined as area ≥1 cm² including at least 3 adjacent points with signal amplitude (bipolar <0.5 mV, unipolar 3,5 mV), surrounded by low-voltage border zone. EAM were re-evaluated offline, removing points collected with contact force <5 g. Finally, contact force-corrected maps were compared to the native ones.ResultsAn EAM was created for each patient (345 ± 85 points). After removing poor contact points, a mean of 149 ± 60 points was collected. The percentage of false scar, collected during contact force blinded mapping compared to total volume, was 6.0 ± 5.2% for bipolar scar and 7.1 ± 5.9% for unipolar scar, respectively. No EAM scar was present after poor contact points removal. Right ventricular areas analysis revealed a greater number of points with contact force < 5 g acquired in free wall, where reduced mean bipolar and unipolar voltage were recorded.ConclusionsTo date this is the first work conducted on structurally normal hearts in which contact-force significantly increases EAM accuracy, avoiding “false scar” related to non-adequate contact between catheter and tissue.     

Metal ion-induced assembly of dipeptide-attached perylenediimide for fluorometric “turn on” detection of biologically important small molecule

A dipeptide-appended perylenediimide (PDI-CFF) fluorescent molecule was designed, synthesized, and characterized. Though the molecule does not dissolve in any individual solvent, it dissolves well in an organic/water mixed solvent system such as tetrahydrofuran/water. This new fluorescent molecule was self-assembled in a tetrahydrofuran/water mixture to form both nanofibrous network structures and a nano ring structure. It has shown nanofibril morphology by the interactions with ferric ions (PDI-CFF/Fe³⁺ system) with diminishing fluorescent property. Interestingly, L-ascorbic acid (LAA) interacts with the PDI-CFF/Fe³⁺ system, showing turn-on fluorescence. Another interesting feature is that the minimum detection limits for Fe³⁺ ions and LAA are at the submicromolar levels of 6.2 × 10⁻⁸ and 3 × 10⁻⁸ M, respectively. Moreover, the fluorescent (10 μM) signals can be monitored by the naked eye under handheld UV lamp irradiation at 365 nm, and this is very convenient for the real application. In this study, the molecule offers the opportunity for processing these sequential fluorescence responses in order to fabricate a implication logic gate that includes NOT, AND, and OR simple logic gates using chemical stimuli (ferric ions and LAA) as inputs and fluorescence emission at 536 nm as output. The detailed mechanism of interactions of Fe³⁺ with PDI-CFF and LAA with the PDI-CFF/Fe³⁺ system is vividly studied by using Fourier transform infrared (FT-IR) analysis and fluorescence. Moreover, this new molecule was reusable for several times without significant loss of its activity. The construction of logic gates using biologically important molecules/ions holds future promise for the design and development of new bio-logic gates.     

“Round Up the Usual Suspects”: A Comment on Nonexistent Plant G Protein-Coupled Receptors

An evolutionary argument supports the conclusion that plants do not have G protein coupled receptors.In the classic 1942 movie Casablanca, Vichy Police Captain Louis Renault obfuscated the truth by commanding his lieutenants to “round up the usual suspects,” knowing well that the culprit with the gun stood in plain view. Something similar has happened in the plant G protein field. This Scientific Correspondence was written to shed light on the source of misunderstanding and to preempt further confusion. Plant heterotrimeric G proteins are self-activating and therefore do not need and do not utilize G protein-coupled receptors (GPCRs). This conclusion was reached previously from biochemical analyses of plant G proteins (Johnston et al., 2007a; Urano et al., 2012); here, we buttress this point of view using an evolutionary argument. Proteins suspected as plant GPCRs were “rounded up” because they have the predicted topology of animal GPCRs and/or have been misannotated as such; however, these proteins are highly conserved in organisms that lack heterotrimeric G proteins. Therefore, they have functions unrelated to G-coupled signaling. Instead, the culprit protein standing in plain view is a receptor GTPase-accelerating protein (GAP), a receptor GAP called AtRGS1 (for regulator of G signaling).