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Each of the three isomeric pyridyl radicals (2-, 3-, and 4-dehydropyridines) contains a lone pair and an unpaired electron. As a result, a potential two centered-three electron interaction between the radical electron and the lone pair through-space (TS) and/or through-bond (TB) can exist that may influence the stability of the radicals. Due to the change in geometrical positions relative to each other, the strength of interaction can be varied. In this study, we investigated the structural and stability aspects of pyridyl radical isomers with a major emphasis on the interaction of a nitrogen lone pair with the radical center. In order to obtain evidence for such interactions, protonated and N-oxide analogues of the corresponding isomeric pyridyl radicals have been considered in such a way to understand the consequences due to unavailability of the lone pair. Similarly, electron attachment and detachment energies at the radical center (vertical detachment energy, VDE, of corresponding anions and vertical ionization energy, VIE, of radical isomers) have been calculated to find out the interaction trend upon modification at the radical center. Different levels of theory including (U)B3LYP/cc-pVTZ, (U)M06/cc-pVTZ, CBS-QB3, single-point energy calculations at (U)CCSD(T)/cc-pVTZ, and multireference CASSCF/cc-pVTZ methods have been employed in this regard. A closer inspection of geometries, relative stability order, spin density, electrostatic potential, molecular orbitals, NBO analysis, and vibrational analysis have showed a strong and stabilizing TS interaction between the radical center and the lone pair in the case of the 2-pyridyl radical. On the other hand, the 4-pyridyl radical showed stabilizing interactions only via TB coupling, whereas the TS interaction is nonexistent. Despite the presence of both interactions in the case of the 3-pyridyl radical, their overall influence is less effective toward stability.

DFT (U)B3LYP/cc-pVTZ and (U)M06-2X/cc-pVTZ and multireference CASSCF/cc-pVTZ level of theories have been used to investigate the electronic structure of isomeric dehydrooxazole (1b-d, 3 isomers), dehydrothiazole (2b-d, 3 isomers) and dehydroimidazole (3a-d, 4 isomers) radicals. The ground state electronic structure of each radical isomer has been confirmed by predicting their doublet excited state structure and calculating the adiabatic energy difference. The stability order of the individual isomeric radicals has been estimated through the comparison of absolute energies. A hypothetical isodesmic reaction has been utilized to calculate radical stabilization energies (RSEs). The results show N-dehydro imidazole 3a as the thermodynamically most stable radical. In order to understand the structural and stability aspects of the radicals and interactions between the radical electron and the electron lone pairs, we have analysed spin densities and hybridisation changes and also performed MCSCF calculations. The reason for the higher stability of 3a has been attributed to the attainment of a π-character and subsequent delocalization, whereas, all other carbon centred radicals are found to be localized σ-radicals. Furthermore, the kinetic stability of the radicals has been investigated through unimolecular decomposition channels. All the studies showed a weak to strong coupling between the N3 and the radical centre depending on the location of the radical centre. NBO analysis suggests that through space coupling between N3 and σ* of the radical centre leads to a stabilising effect when the radical centre is adjacent to N3, whereas such interactions are absent when the radical centre is away from it. However, only a weak coupling is observed between the radical centre and X1 (O/S/NH). Particularly the interaction strength has the following trend: S < O < N-H. Indeed S, O and N-H show a stabilising effect through bond interactions with the antibonding orbitals of the alternate bonds on either side.

This paper examines the role of inhibition in generating the receptive-field properties of local edge detector (LED) ganglion cells in the rabbit retina. We confirm that the feed-forward inhibition is largely glycinergic but, contrary to a recent report, our data demonstrate that the glycinergic inhibition contributes to temporal tuning for the OFF and ON inputs to the LEDs by delaying the onset of spiking; this delay was more pronounced for the ON inputs (∼ 340 ms) than the OFF inputs (∼ 12 ms). Blocking glycinergic transmission reduced the delay to spike onset and increased the responses to flickering stimuli at high frequencies. Analysis of the synaptic conductances indicates that glycinergic amacrine cells affect temporal tuning through both postsynaptic inhibition of the LEDs and presynaptic modulation of the bipolar cells that drive the LEDs. The results also confirm that presynaptic GABAergic transmission contributes significantly to the concentric surround antagonism in LEDs; however, unlike presumed LEDs in the mouse retina, the surround is only partly generated by spiking amacrine cells.

Aim: The current work is aimed at understanding the effect of pH on the thermal stability of hen egg white lysozyme (HEWL) at high concentration (200 mg/mL)., Materials and Methods: Fourier Transform Infrared (FTIR) Spectroscopy with modified hardware and software to overcome some of the traditional challenges like water subtraction, sample evaporation, proper purging etc., are used in this study., Results: HEWL was subjected to thermal stress at pH 3.0-7.0 between 25°C and 95°C and monitored by FTIR spectroscopy. Calculated Tm values showed that the enzyme exhibited maximum thermal stability at pH 5.0. Second derivative plots constructed in the amide I region suggested that at pH 5.0 the enzyme possessed higher amount of α-helix and lower amount of aggregates, when compared to other pHs., Conclusions: Considering the fact that HEWL has attractive applications in various industries and being processed under different experimental conditions including high temperatures, our work is able to reveal the reason behind the pH dependent thermal stability of HEWL at high concentration, when subjected to heat denaturation. In future, studies should aim at using various excipients that may help to increase the stability and activity of the enzyme at this high concentration.

We investigate the linear propagation of Gaussian-apodized solutions to the paraxial wave equation in free-space and first-order optical systems. In particular, we present complex coordinate transformations that yield a very general and efficient method to apply a Gaussian apodization (possibly with initial phase curvature) to a solution of the paraxial wave equation. Moreover, we show how this method can be extended from free space to describe propagation behavior through nonimaging first-order optical systems by combining our coordinate transform approach with ray transfer matrix methods. Our framework includes several classes of interesting beams that are important in applications as special cases. Among these are, for example, the Bessel-Gauss and the Airy-Gauss beams, which are of strong interest to researchers and practitioners in various fields.

The Arabidopsis ACCELERATED CELL DEATH 2 (ACD2) protein protects cells from programmed cell death (PCD) caused by endogenous porphyrin-related molecules like red chlorophyll catabolite or exogenous protoporphyrin IX. We previously found that during bacterial infection, ACD2, a chlorophyll breakdown enzyme, localizes to both chloroplasts and mitochondria in leaves. Additionally, acd2 cells show mitochondrial dysfunction. In plants with acd2 and ACD2 (+) sectors, ACD2 functions cell autonomously, implicating a pro-death ACD2 substrate as being cell non-autonomous in promoting the spread of PCD. ACD2 targeted solely to mitochondria can reduce the accumulation of an ACD2 substrate that originates in chloroplasts, indicating that ACD2 substrate molecules are likely to be mobile within cells. Two different light-dependent reactive oxygen bursts in mitochondria play prominent and causal roles in the acd2 PCD phenotype. Finally, ACD2 can complement acd2 when targeted to mitochondria or chloroplasts, respectively, as long as it is catalytically active: the ability to bind substrate is not sufficient for ACD2 to function in vitro or in vivo. Together, the data suggest that ACD2 localizes dynamically during infection to protect cells from pro-death mobile substrate molecules, some of which may originate in chloroplasts, but have major effects on mitochondria., (© 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.)

The 15-20 physiological types of retinal ganglion cells (RGCs) can be grouped according to whether they fire to increased illumination in the receptive-field center (ON cells), decreased illumination (OFF cells), or both (ON-OFF cells). The diversity of RGCs has been best described in the rabbit retina, which has three types of ON-OFF RGCs with complex receptive-field properties: the ON-OFF direction-selective ganglion cells (DSGCs), the local edge detectors, and the uniformity detectors. Here we describe a novel type of bistratified ON-OFF RGC that has not been described in either physiological or morphological studies of rabbit RGCs. These cells stratify in the ON and OFF sublaminae of the inner plexiform layer, branching at about 30% and 60% depth, between the ON and OFF arbors of the bistratified DSGCs. Similar to the ON-OFF DSGCs, these cells respond with transient firing to both bright and dark spots flashed in the receptive field but, unlike the DSGCs, they show no directional preference for moving stimuli. We have termed these cells "transient ON-OFF" RGCs. Area-response measurements show that both the ON and the OFF spike responses have an antagonistic receptive-field organization, but with different spatial extents. Voltage-clamp recordings reveal transient excitatory inputs at light ON and light OFF; this excitation is strongly suppressed by surround stimulation, which also elicits direct inhibitory inputs to the cells at light ON and light OFF. Thus the receptive-field organization is mediated both within the presynaptic circuitry and by direct feed-forward inhibition., (Copyright © 2011 Wiley-Liss, Inc.)

We present the first quantitative measurements of shape and energy variation in non-Euclidean plates. Using environmentally responsive gel, we construct non-Euclidean disks of constant imposed Gaussian curvature, K(tar). We vary the disks' thickness t(0) and measure the dependence of configurations, surface curvature, and energy content on t(0). For K(tar)<0, configurations are of a single wavy mode and undergo a set of bifurcations that leads to their refinement with decreasing thickness. This leads to sharp increase in the amount of surface bending as t(0)→0, and to a slow decay of both bending and stretching energies. Both vary like t(0)(2), compared with t(0)(3) of the bending energy in disks with K(tar)>0.

Arabidopsis thaliana ANKYRIN REPEAT-CONTAINING PROTEIN 2A (AKR2A) interacts with peroxisomal membrane-bound ASCORBATE PEROXIDASE3 (APX3). This interaction involves the C-terminal sequence of APX3 (i.e., a transmembrane domain plus a few basic amino acid residues). The specificity of the AKR2A-APX3 interaction suggests that AKR2A may function as a molecular chaperone for APX3 because binding of AKR2A to the transmembrane domain can prevent APX3 from forming aggregates after translation. Analysis of three akr2a mutants indicates that these mutant plants have reduced steady state levels of APX3. Reduced expression of AKR2A using RNA interference also leads to reduced steady state levels of APX3 and reduced targeting of APX3 to peroxisomes in plant cells. Since AKR2A also binds specifically to the chloroplast OUTER ENVELOPE PROTEIN7 (OEP7) and is required for the biogenesis of OEP7, AKR2A may serve as a molecular chaperone for OEP7 as well. The pleiotropic phenotype of akr2a mutants indicates that AKR2A plays many important roles in plant cellular metabolism and is essential for plant growth and development.

Recently, Efron (2007) provided methods for assessing the effect of correlation on false discovery rate (FDR) in large-scale testing problems in the context of microarray data. Although FDR procedure does not require independence of the tests, existence of correlation grossly under- or overestimates the number of critical genes. Here, we briefly review Efron's method and apply it to a relatively smaller spectrometry proteomics data. We show that even here the correlation can affect the FDR values and the number of proteins declared as critical.

The molecular and electronic structure of 1,2,3-tridehydrobenzene was investigated by a variety of computational methods. The two lowest electronic states of the triradical are the (2)B(2) and (2)A(1) doublet states characterized by different interactions of the unpaired electrons. Vertically, the two states are well separated in energy-by 4.9 and 1.4 eV, respectively. However, due to different bonding patterns, their equilibrium structures are very different and, adiabatically, the two states are nearly degenerate. The adiabatic energy gap between the (2)B(2) and (2)A(1) states is estimated to be 0.7-2.1 kcal/mol, in favor of the (2)A(1) state. Harmonic vibrational frequencies and anharmonic corrections were calculated for both states. Comparison with the three experimentally observed IR transitions supports the assignment of the (2)A(1) ground state for the triradical with a weakly bonding distance of 1.67-1.69 A between the meta radical centers.

'Caged' compounds are biological molecules that are rendered inactive by a protecting (cage) group. Photocleaving of chemical bonds associated with the cage species with intense UV light results in the release of the active molecules. This technique, called flash photolysis, allows for real-time study of interacting biological molecules and typically involves the use of high intensity lasers or flash lamps to deliver the UV pulse to the biological specimen [Callaway EM, Katz LC. Photostimulation using caged glutamate reveals functional circuitry in living brain slices. Proc Natl Acad Sci USA 1993;90(16):7661-5; Parpura V, Haydon PG. "Uncaging" using optical fibers to deliver UV light directly to the sample. Croat Med J 1999;40(3):340-5; Denk W. Pulsing mercury arc lamps for uncaging and fast imaging. J Neurosci Methods 1997;72(1):39-42]. Here, we introduce compact, custom-designed semiconductor UV light-emitting diodes (LEDs) as a viable and efficient source for performing flash photolysis studies, focusing specifically on the application of these devices for uncaging neurotransmitters locally onto neurons cultured on artificial substrates. The illumination design feature incorporated in these devices allows for direct placement of the UV source in immediate proximity with the neuron of interest and provides a means for optical triggering of activity in the neuronal culture.

In vitro neuronal networks with geometrically defined features are desirable for studying long-term electrical activity within the neuron assembly and for interfacing with external microelectronic circuits. In standard cultures, the random spatial distribution and overlap of neurites makes this aim difficult; hence, many recent efforts have been made on creating patterned cellular circuits. Here, we present a novel method for creating a planar neural network that is compatible with optical devices. This method combines both topographical and chemical micropatterns onto which neurons can be cultured. Compared to other reported patterning techniques, our approach and choice of template appears to show both geometrical control over the formation of specific neurite connections at low plating density and compatibility with microelectronic circuits that stimulate and record neural activity.

Ascorbate peroxidase (APX) exists as several isoforms that are found in various compartments in plant cells. The cytosolic and chloroplast APXs appear to play important roles in antioxidation metabolism in plant cells, yet the function of peroxisomal APX is not well studied. In this study, the localization of a putative peroxisomal membrane-bound ascorbate peroxidase, APX3 from Arabidopsis, was confirmed by studying the green fluorescent protein (GFP)-APX3 fusion protein in transgenic plants. GFP-APX3 was found to co-localize with a reporter protein that was targeted to peroxisomes by the peroxisomal targeting signal 1. The function of APX3 in Arabidopsis was investigated by analysing an APX3 knockout mutant under normal and several stress conditions. It was found that loss of function in APX3 does not affect Arabidopsis growth and development, suggesting that APX3 may not be an important antioxidant enzyme in Arabidopsis, at least under the conditions that were tested, or the function of APX3 could be compensated by other antioxidant enzymes in plant cells.

We propose that a useful approach to the modeling of periodically forced extended systems is through continuum coupled map (CCM) models. CCM models are discrete time, continuous space models, mapping a continuous spatially varying field xi(n)(x) from time n to time n+1. The efficacy of CCM models is illustrated by an application to experiments of Umbanhowar, Melo, and Swinney [Nature 382, 793 (1996)] on vertically vibrated granular layers. Using a simple CCM model incorporating temporal period doubling and spatial patterning at a preferred length scale, we obtain results that bear remarkable similarities to the experimental observations. The fact that the model does not make use of physics specific to granular layers suggests that similar phenomena may be observed in other (nongranular) periodically forced, strongly dissipative systems. We also present a framework for the analysis of pattern selection in CCM models using a truncated modal expansion. Through the analysis, we predict scaling laws of various quantities, and these laws may be verifiable experimentally.

To examine the effects of unusual or atypical beta-globin gene cluster haplotypes on the hematological features and Hb F levels of sickle cell anemia, we studied African Americans who had an atypical or Cameroon haplotype chromosome in association with a typical haplotype. We identified over 20 atypical haplotypes. The distribution of 5' sub-haplotypes of the atypical chromosomes mirrored the distribution of common haplotypes in African Americans with sickle cell anemia. Neither 5' nor 3' subhaplotypes of the atypical chromosomes affected Hb F levels, packed cell volume, or mean corpuscular volume in individuals with a Benin chromosome. That the 5' subhaplotype is unaffected might be a consequence of the small numbers of Senegal 5' subhaplotypes in our sample, the need for linkage of both 5' and 3' subhaplotypes of any haplotype for an effect on Hb F to be present, or the likelihood that a normal beta-globin gene contributed the 5' subhaplotypes of some atypical haplotypes.