Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations.

Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding-upon-binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict the three-dimensional structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine the structures of peptide-protein complexes. Here, we use the MELD (Modeling Employing Limited Data) technique applied to polypeptide complexes formed with the extraterminal domain (ET) of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can adopt different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only protein receptor backbone chemical shift data, in excellent agreement with experimentally determined structures for moderately tight (Kd ∼100 nM) binders. The hybrid MELD + NMR approach required additional peptide ligand chemical shift data for weaker (Kd ∼250 µM) peptide binding partners. AlphaFold also successfully predicts the structures of some of these peptide-protein complexes. However, whereas AlphaFold can provide qualitative peptide rankings, MELD can directly estimate relative binding affinities. The hybrid MELD + NMR approach offers a powerful new tool for structural analysis of protein-polypeptide complexes involving disorder-to-order transitions upon complex formation, which are not successfully modeled with most other complex prediction methods, providing both the 3D structures of peptide-protein complexes and their relative binding affinities.

In-phase sub-Nyquist lenslet arrays encoded onto spatial light modulators.

When encoding diffractive lenses onto a spatial light modulator (SLM), there is a Nyquist limit to the smallest focal length that can be formed. When this limit is surpassed, a two-dimensional array of lenslets is formed. There have been very few discussions on the performance of these lenslets. In this work, we focus on the phase distribution of these lenses in the array. We show that, for certain values of the focal length, the lenslets are all in perfect phase. We show that this situation happens for a total number of N/4 different discrete equidistant sub-Nyquist focal lengths, where N×N is the number of pixels in the SLM. We find other distances in between where the array is composed of two sets of lenslets with a relative π phase among them. Finally, we illustrate these phase distributions in the application to generate an array of vortex producing lenses. We expect that these results might be useful for high-accuracy interferometric or multiple imaging where this phase must be exactly the same for each replica.

Optimal triplicator design applied to a geometric phase vortex grating.

In this work, a geometric phase liquid-crystal diffraction grating based on the optimal triplicator design is realized, i.e., a phase-only profile that generates three diffraction orders with equal intensity and maximum diffraction efficiency. We analyze the polarization properties of this special diffraction grating and then use embedded spiral phases to design geometric phase vortex diffraction gratings. Finally, the fabrication of a two-dimensional version of such a design using a micro-patterned half-wave retarder is demonstrated, where the phase distribution is encoded as the orientation of the fast axis of the retarder. This proof-of-concept element is made of liquid crystal on BK7 substrate where the orientation of the LC is controlled via photoalignment, using a commercially available fabrication facility. Experimental results demonstrate the parallel generation of vortex beams with different topological charge and different states of polarization.

Gouy phase effects on propagation of pure and hybrid vector beams.

The robustness of the polarization spatial distribution of vector beams upon propagation is crucial for a number of applications, including optical communications and materials processing. This study has been commonly centered on Gouy phase effects on focused vector beams. In this work, we present a theoretical and experimental analysis of the Gouy phase's effects on the propagation of pure and hybrid vector beams. Experimental results at various axial planes, before and past the focus, are obtained by using a simplified liquid-crystal spatial light modulator-based optical system that allows the easy generation of these beams. Furthermore, a new alternative optical set-up that is devoid of moving elements is demonstrated, which simplifies this study. We experimentally verify the differences between pure and hybrid vector beams upon propagation. While the first ones remain stable, hybrid vector beams show Gouy phase effects that demonstrate an optical activity where the local polarization states rotate by an angle that depends on the propagation distance. Experimental results agree with the theory.

Specificity of plant-plant communication for Baccharis salicifolia sexes but not genotypes.

Plants are able to adjust their anti-herbivore defenses in response to the volatile organic compounds (VOCs) emitted by herbivore-damaged neighbors, and some of these changes increase resistance against subsequent herbivory. This phenomenon of plant-plant communication is thought to be widespread, but recent investigations have cautioned that it can be context dependent, including variation in the strength of communication based on the identity of plants and their associated herbivores. Here, we performed three greenhouse experiments using multiple male and female genotypes of the dioecious woody shrub Baccharis salicifolia and its specialist aphid Uroleucon macolai to test for specificity of plant-plant communication with respect to plant sex and genotype. Moreover, we evaluated plant sexual dimorphism and genotypic variation in VOC emissions (i.e., the "speaking" side of the interaction) and response of plants to VOC exposure (i.e., the "listening" side of the interaction) in order to identify the chemical mechanisms underlying such specificity. We did not find genotypic specificity of communication; emitter plants damaged by U. macolai significantly reduced subsequent U. macolai performance on receivers, but these effects were indistinguishable for communication within vs. among genotypes. In contrast, we found sex specificity of communication; male emitter plants reduced subsequent U. macolai performance on male and female receiver plants equally, while female emitter plants only did so for female receivers. We found sexual (but not genotypic) dimorphism in speaking but not listening; of the seven compounds induced by U. macolai feeding (speaking), pinocarvone was approximately fivefold greater in female than in male plants, while exposure of plants to pinocarvone emissions (listening) reduced U. macolai performance equally in both male and female plants. Together, our study demonstrates novel evidence for sexually dimorphic specificity of plant-plant communication and the chemical mechanism underlying this effect.

Achromatic linear retarder with tunable retardance.

We present a universal design and proof-of-concept of a tunable linear retarder of uniform wavelength response in a broad spectral range. It consists of two half-wave retarders (HWR) between two quarter-wave retarders (QWRs), where the uniform retardance can be tuned continuously by simply rotating one of the HWRs. A proof-of-concept of this design is built by using commercially available Fresnel rhomb retarders that provide retardation with almost wavelength uniformity in the visible and near infrared from 450 to 1550 nm. The design is universal, since other achromatic QWRs and HWRs could also be employed. The system is experimentally demonstrated to control the state of polarization of a supercontinuum laser.

Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees.

Three isolates obtained from symptomatic nectarine trees (Prunus persica var. nectarina) cultivated in Murcia, Spain, which showed yellow and mucoid colonies similar to Xanthomonas arboricola pv. pruni, were negative after serological and real-time PCR analyses for this pathogen. For that reason, these isolates were characterized following a polyphasic approach that included both phenotypic and genomic methods. By sequence analysis of the 16S rRNA gene, these novel strains were identified as members of the genus Xanthomonas, and by multilocus sequence analysis (MLSA) they were clustered together in a distinct group that showed similarity values below 95 % with the rest of the species of this genus. Whole-genome comparisons of the average nucleotide identity (ANI) of genomes of the strains showed less than 91 % average nucleotide identity with all other species of the genus Xanthomonas. Additionally, phenotypic characterization based on API 20 NE, API 50 CH and BIOLOG tests differentiated the strains from the species of the genus Xanthomonas described previously. Moreover, the three strains were confirmed to be pathogenic on peach (Prunus persica), causing necrotic lesions on leaves. On the basis of these results, the novel strains represent a novel species of the genus Xanthomonas, for which the name Xanthomonas prunicola is proposed. The type strain is CFBP 8353 (=CECT 9404=IVIA 3287.1).

Relative effects of genetic variation sensu lato and sexual dimorphism on plant traits and associated arthropod communities.

Intraspecific plant trait variation can have cascading effects on plant-associated biotic communities. Sexual dimorphism is an important axis of genetic variation in dioecious plants, but the strength of such effects and the underlying mechanisms relative to genetic variation are unknown. We established a common garden with 39 genotypes of Baccharis salicifolia sampled from a single population that included male and female genotypes and measured plant traits and quantified associated arthropod communities. Genetic variation sensu lato (genotypic variation) had strong effects on most plant traits (flower number, relative growth rate, specific leaf area, percent water content, carbon-nitrogen ratio, monoterpene but not sesquiterpene concentrations) and on herbivore and predator density, and on arthropod community composition (relative abundance of 14 orders). In contrast, sexual dimorphism had weaker effects on only a few plant traits (flower number and relative growth rate), on predator density, and on arthropod community composition, but had no effect on herbivore density. Variation in flower number drove genetic variation sensu lato and sex dimorphism in predator density and arthropod community composition. There was unique genetic variation sensu lato in herbivore density (positively) associated with monoterpene concentration and in arthropod community composition associated with specific leaf area and carbon-nitrogen ratio. There was unique sexual dimorphism in arthropod community composition associated with plant relative growth rate. Together, these results demonstrate that genetic variation sensu lato and sexual dimorphism can shape plant-associated arthropod communities via both parallel and unique mechanisms, with greater overall effects of the former.

Q-plates with a nonlinear azimuthal distribution of the principal axis: application to encoding binary data.

We encode q-plates where the angular orientation of the principal axis is varied spatially with a nonstandard distribution. In the usual q-plate design, the orientation of the optical axis depends linearly on the azimuthal angle. In this work, we examine cases where this azimuthal dependence is nonlinear. We consider two cases: first, where the principal axis distribution is like an inverse-tangent function of the azimuth; and second, where it displays linear and flat segments. This last case is proposed as a new method for encoding binary data into the azimuthal lobes of the vector beam. We encode these patterns using a spatial light modulator system that allows new and exotic q-plate designs without the difficulty of fabricating individual plates. Experimental results are presented.

Dual polarization split lenses.

We report the realization of polarization sensitive split lens configurations. While split lenses can be used to easily generate different types of controlled structured light patterns, their realization has been limited so far to scalar beams. Here we propose and experimentally demonstrate their generalization to vectorial split lenses, leading to light patterns with customized intensity and state of polarization. We demonstrate how these polarization split lenses can be experimentally implemented by means of an optical system using two liquid crystal spatial light modulators, each one phase modulating one orthogonal polarization component. As a result, we demonstrate the experimental generation of vectorial beams with different shapes generated with these dual polarization split lenses. Excellent experimental results are provided in each case. The proposed technique is a simple method to generate structured light beams with polarization diversity, with potential applications in polarimetry, customized illuminators or quantum optics.

Arithmetic with q-plates.

In this work we show the capability to form various q-plate equivalent systems using combinations of commercially available q-plates. We show operations like changing the sign of the q-value, or the addition and subtraction of q-plates. These operations only require simple combinations of q-plates and half-wave plates. Experimental results are presented in all cases. Following this procedure, experimental testing of higher and negative q-valued devices can be carried out using commonly available q-valued devices.

Diffraction gratings generating orders with selective states of polarization.

We propose specially designed double anisotropic polarization diffraction gratings capable of producing a selective number of diffraction orders and with selective different states of polarization. Different polarization diffraction gratings are demonstrated, including linear polarization with horizontal, vertical and ± 45° orientations, and circular R and L polarization outputs. When illuminated with an arbitrary state of polarization, the system acts as a complete polarimeter where the intensities of the diffraction orders allow measurement of the Stokes parameters with a single shot. Experimental proof-of-concept is presented using a parallel-aligned liquid crystal display operating in a double pass architecture.

Nondiffracting vector beams where the charge and the polarization state vary with propagation distance.

We generate nondiffracting vector beams where the charge and the polarization state vary with the propagation distance. We use reflective geometry where a parallel-aligned spatial light modulator is used to spatially modulate two orthogonal linear polarizations. We encode spiral phases with equal charge but with opposite signs onto the two polarization directions to encode a vector beam and add two axicon phases. Both the charge and the phase shift between the two axicons can be varied along the focus line. We provide experimental results that demonstrate both features.

Generation of integer and fractional vector beams with q-plates encoded onto a spatial light modulator.

We generate programmable vector beams with arbitrary q-plates encoded using a spatial light modulator system. Consequently, we can analyze new and exotic q-plate designs without the difficulty of fabricating individual plates. We show experimental results for positive and negative integer and new fractional vector beam values.

Performance of a q-plate tunable retarder in reflection for the switchable generation of both first- and second-order vector beams.

We examine the performance of a tunable liquid crystal q-plate in a reflective geometry. When the device is tuned to a half-wave retardance, it operates as a q-plate with twice the value (2q) by adding a quarter-wave retarder between the mirror and the q-plate. However, when the device is tuned to a quarter-wave retardance, it acts as the original q-plate without the retarder. Experimental results are shown. Using an input tunable polarization state generator, the system allows the switchable production of all states on both the first- and second-order Poincaré spheres.

Nondiffracting Bessel beams with polarization state that varies with propagation distance.

We generate nondiffracting Bessel beams whose polarization state varies with propagation distance. We use a reflective geometry where a single parallel-aligned spatial light modulator device is used to spatially modulate two orthogonal linear polarizations with two axicon phase profiles. Then, by adding an extra phase retardation radial profile between these linear states, we are able to modulate the state of polarization along the line focus of the axicon. We provide experimental results that demonstrate the polarization axial control with zero-order and higher order Bessel beams.

Analysis of a segmented q-plate tunable retarder for the generation of first-order vector beams.

In this work we study a prototype q-plate segmented tunable liquid crystal retarder device. It shows a large modulation range (5π rad for a wavelength of 633 nm and near 2π for 1550 nm) and a large clear aperture of one inch diameter. We analyze the operation of the q-plate in terms of Jones matrices and provide different matrix decompositions useful for its analysis, including the polarization transformations, the effect of the tunable phase shift, and the effect of quantization levels (the device is segmented in 12 angular sectors). We also show a very simple and robust optical system capable of generating all polarization states on the first-order Poincaré sphere. An optical polarization rotator and a linear retarder are used in a geometry that allows the generation of all states in the zero-order Poincaré sphere simply by tuning two retardance parameters. We then use this system with the q-plate device to directly map an input arbitrary state of polarization to a corresponding first-order vectorial beam. This optical system would be more practical for high speed and programmable generation of vector beams than other systems reported so far. Experimental results are presented.

Pathogenic serum amyloid A 1.1 shows a long oligomer-rich fibrillation lag phase contrary to the highly amyloidogenic non-pathogenic SAA2.2.

Serum amyloid A (SAA) is best known for being the main component of amyloid in the inflammation-related disease amyloid A (AA) amyloidosis. Despite the high sequence identity among different SAA isoforms, not all SAA proteins are pathogenic. In most mouse strains, the AA deposits mostly consist of SAA1.1. Conversely, the CE/J type mouse expresses a single non-pathogenic SAA2.2 protein that is 94% identical to SAA1.1. Here we show that SAA1.1 and SAA2.2 differ in their quaternary structure, fibrillation kinetics, prefibrillar oligomers, and fibril morphology. At 37 °C and inflammation-related SAA concentrations, SAA1.1 exhibits an oligomer-rich fibrillation lag phase of a few days, whereas SAA2.2 shows virtually no lag phase and forms small fibrils within a few hours. Deep UV resonance Raman, far UV-circular dichroism, atomic force microscopy, and fibrillation cross-seeding experiments suggest that SAA1.1 and SAA2.2 fibrils possess different morphology. Both the long-lived oligomers of pathogenic SAA1.1 and the fleeting prefibrillar oligomers of non-pathogenic SAA2.2, but not their respective amyloid fibrils, permeabilized synthetic bilayer membranes in vitro. This study represents the first comprehensive comparison between the biophysical properties of SAA isoforms with distinct pathogenicities, and the results suggest that structural and kinetic differences in the oligomerization-fibrillation of SAA1.1 and SAA2.2, more than their intrinsic amyloidogenicity, may contribute to their diverse pathogenicity.

Conventional and real-time PCRs for detection of Erwinia piriflorinigrans allow its distinction from the fire blight pathogen, Erwinia amylovora.

Erwinia piriflorinigrans is a new pathogenic species of the bacterial genus Erwinia that has been described recently in Spain. Accurate detection and identification of E. piriflorinigrans are challenging because its symptoms on pear blossoms are similar to those caused by Erwinia amylovora, the causal agent of fire blight. Moreover, these two species share phenotypic and molecular characteristics. Two specific and sensitive conventional and real-time PCR protocols were developed to identify and detect E. piriflorinigrans and to differentiate it from E. amylovora and other species of this genus. These protocols were based on sequences from plasmid pEPIR37, which is present in all strains of E. piriflorinigrans analyzed. After the stability of the plasmid was demonstrated, the specificities of the protocols were confirmed by the amplification of all E. piriflorinigrans strains tested, whereas 304 closely related pathogenic and nonpathogenic Erwinia strains and microbiota from pear trees were not amplified. In sensitivity assays, 10(3) cells/ml extract were detected in spiked plant material by conventional or real-time PCR, and 10(2) cells/ml were detected in DNA extracted from spiked plant material by real-time PCR. The protocols developed here succeeded in detecting E. piriflorinigrans in 102 out of 564 symptomatic and asymptomatic naturally infected pear samples (flowers, cortex stem tissue, leaves, shoots, and fruitlets), in necrotic Pyracantha sp. blossoms, and in necrotic pear and apple tissues infected with both E. amylovora and E. piriflorinigrans. Therefore, these new tools can be used in epidemiological studies that will enhance our understanding of the life cycle of E. piriflorinigrans in different hosts and plant tissues and its interaction with E. amylovora.

Optical retarder system with programmable spectral retardance.

An optical system that works as a retarder waveplate with programmable spectral retardance is proposed. The system is based on a pixelated liquid crystal on silicon (LCoS) spatial light modulator (SLM). The input light beam is spectrally dispersed and different spectral components are projected onto different pixels of the LCoS-SLM. A different retardance is then addressed for each pixel, adapted to the incoming wavelength. Light reflected from the SLM is then recombined by the same setup. In this way a programmable polarization spectrum can be encoded. We illustrate the broadband characterization that is required for proper use of the system. Then several examples are shown, including spectral compensation to yield retarders with constant retardance, retarders with abrupt changes in the spectral retardance function, or bandpass variable retarder filters. The system is also demonstrated to provide programmable light spectrum generation.