Limited Humoral and Specific T-Cell Responses After SARS-CoV-2 Vaccination in PWH With Poor Immune Reconstitution.

BACKGROUND: We analyzed humoral and cellular immune responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) messenger RNA (mRNA) vaccines in people with human immunodeficiency virus (HIV; PWH) who had CD4+ T-cell counts <200/µL (HIV<200 group). METHODS: This prospective cohort study included 58 PWH in the HIV<200 group, 36 with CD4+ T-cell counts >500/µL (HIV>500 group), and 33 HIV-1-negative controls (control group). Antibodies against the SARS-CoV-2 spike protein (anti-S immunoglobulin [Ig] G) and the receptor-binding domain (anti-RBD IgG) were quantified before and 4 weeks after the first and the second doses of BNT162b2 or mRNA-1273 (at week 8). Viral neutralization activity and T-cell responses were also determined. RESULTS: At week 8, anti-S/anti-RBD IgG responses increased in all groups (P < .001). Median (interquartile range) anti-S and anti-RBD IgG levels at week 8 were 153.6 (26.4-654.9) and 171.9 (61.8-425.8) binding antibody units (BAU)/mL, respectively, in the HIV<200 group, compared with 245.6 (145-824) and 555.8 (166.4-1751) BAU/mL in the HIV>500 group and 274.7 (193.7-680.4) and 281.6 (181-831.8) BAU/mL in controls (P < .05). Neutralizing capacity and specific T-cell immune responses were absent or reduced in 33% of those in the HIV<200 group, compared with 3.7% in the HIV>500 group (P < .01). CONCLUSIONS: One-third of PWH with CD4+ T-cell counts <200/µL show low anti-S/anti-RBD IgG levels, reduced in vitro neutralization activity against SARS-CoV-2, and no vaccine-induced T cells after receiving coronavirus disease 2019 mRNA vaccines.

Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System.

Plants expend significant resources to select and maintain rhizosphere communities that benefit their growth and protect them from pathogens. A better understanding of assembly and function of rhizosphere microbial communities will provide new avenues for improving crop production. Secretion of antibiotics is one means by which bacteria interact with neighboring microbes and sometimes change community composition. In our analysis of a taxonomically diverse consortium from the soybean rhizosphere, we found that Pseudomonas koreensis selectively inhibits growth of Flavobacterium johnsoniae and other members of the Bacteroidetes grown in soybean root exudate. A genetic screen in P. koreensis identified a previously uncharacterized biosynthetic gene cluster responsible for the inhibitory activity. Metabolites were isolated based on biological activity and were characterized using tandem mass spectrometry, multidimensional nuclear magnetic resonance, and Mosher ester analysis, leading to the discovery of a new family of bacterial tetrahydropyridine alkaloids, koreenceine A to D (metabolites 1 to 4). Three of these metabolites are analogs of the plant alkaloid γ-coniceine. Comparative analysis of the koreenceine cluster with the γ-coniceine pathway revealed distinct polyketide synthase routes to the defining tetrahydropyridine scaffold, suggesting convergent evolution. Koreenceine-type pathways are widely distributed among Pseudomonas species, and koreenceine C was detected in another Pseudomonas species from a distantly related cluster. This work suggests that Pseudomonas and plants convergently evolved the ability to produce similar alkaloid metabolites that can mediate interbacterial competition in the rhizosphere.IMPORTANCE The microbiomes of plants are critical to host physiology and development. Microbes are attracted to the rhizosphere due to massive secretion of plant photosynthates from roots. Microorganisms that successfully join the rhizosphere community from bulk soil have access to more abundant and diverse molecules, producing a highly competitive and selective environment. In the rhizosphere, as in other microbiomes, little is known about the genetic basis for individual species' behaviors within the community. In this study, we characterized competition between Pseudomonas koreensis and Flavobacterium johnsoniae, two common rhizosphere inhabitants. We identified a widespread gene cluster in several Pseudomonas spp. that is necessary for the production of a novel family of tetrahydropyridine alkaloids that are structural analogs of plant alkaloids. We expand the known repertoire of antibiotics produced by Pseudomonas in the rhizosphere and demonstrate the role of the metabolites in interactions with other rhizosphere bacteria.

Dipole reorientation and local density of optical states influence the emission of light-emitting electrochemical cells.

Herein, we analyze the temporal evolution of the electroluminescence of light-emitting electrochemical cells (LECs), a thin-film light-emitting device, in order to maximize the luminous power radiated by these devices. A careful analysis of the spectral and angular distribution of the emission of LECs fabricated under the same experimental conditions allows describing the dynamics of the spatial region from which LECs emit, i.e. the generation zone, as bias is applied. This effect is mediated by dipole reorientation within such an emissive region and its optical environment, since its spatial drift yields a different interplay between the intrinsic emission of the emitters and the local density of optical states of the system. Our results demonstrate that engineering the optical environment in thin-film light-emitting devices is key to maximize their brightness.

Highly efficient perovskite solar cells with tunable structural color.

The performance of perovskite solar cells has been progressing over the past few years and efficiency is likely to continue to increase. However, a negative aspect for the integration of perovskite solar cells in the built environment is that the color gamut available in these materials is very limited and does not cover the green-to-blue region of the visible spectrum, which has been a big selling point for organic photovoltaics. Here, we integrate a porous photonic crystal (PC) scaffold within the photoactive layer of an opaque perovskite solar cell following a bottom-up approach employing inexpensive and scalable liquid processing techniques. The photovoltaic devices presented herein show high efficiency with tunable color across the visible spectrum. This now imbues the perovskite solar cells with highly desirable properties for cladding in the built environment and encourages design of sustainable colorful buildings and iridescent electric vehicles as future power generation sources.

Comprehensive biometric, biochemical and histopathological assessment of nutrient deficiencies in gilthead sea bream fed semi-purified diets.

Seven isoproteic and isolipidic semi-purified diets were formulated to assess specific nutrient deficiencies in sulphur amino acids (SAA), n-3 long-chain PUFA (n-3 LC-PUFA), phospholipids (PL), P, minerals (Min) and vitamins (Vit). The control diet (CTRL) contained these essential nutrients in adequate amounts. Each diet was allocated to triplicate groups of juvenile gilthead sea bream fed to satiety over an 11-week feeding trial period. Weight gain of n-3 LC-PUFA, P-Vit and PL-Min-SAA groups was 50, 60-75 and 80-85 % of the CTRL group, respectively. Fat retention was decreased by all nutrient deficiencies except by the Min diet. Strong effects on N retention were found in n-3 LC-PUFA and P fish. Combined anaemia and increased blood respiratory burst were observed in n-3 LC-PUFA fish. Hypoproteinaemia was found in SAA, n-3 LC-PUFA, PL and Vit fish. Derangements of lipid metabolism were also a common disorder, but the lipodystrophic phenotype of P fish was different from that of other groups. Changes in plasma levels of electrolytes (Ca, phosphate), metabolites (creatinine, choline) and enzyme activities (alkaline phosphatase) were related to specific nutrient deficiencies in PL, P, Min or Vit fish, whereas changes in circulating levels of growth hormone and insulin-like growth factor I primarily reflected the intensity of the nutritional stressor. Histopathological scoring of the liver and intestine segments showed specific nutrient-mediated changes in lipid cell vacuolisation, inflammation of intestinal submucosa, as well as the distribution and number of intestinal goblet and rodlet cells. These results contribute to define the normal range of variation for selected biometric, biochemical, haematological and histochemical markers.

Design and realization of transparent solar modules based on luminescent solar concentrators integrating nanostructured photonic crystals.

Herein, we present a prototype of a photovoltaic module that combines a luminescent solar concentrator integrating one-dimensional photonic crystals and in-plane CuInGaSe2 (CIGS) solar cells. Highly uniform and wide-area nanostructured multilayers with photonic crystal properties were deposited by a cost-efficient and scalable liquid processing amenable to large-scale fabrication. Their role is to both maximize light absorption in the targeted spectral range, determined by the fluorophore employed, and minimize losses caused by emission at angles within the escape cone of the planar concentrator. From a structural perspective, the porous nature of the layers facilitates the integration with the thermoplastic polymers typically used to encapsulate and seal these modules. Judicious design of the module geometry, as well as of the optical properties of the dielectric mirrors employed, allows optimizing light guiding and hence photovoltaic performance while preserving a great deal of transparency. Optimized in-plane designs like the one herein proposed are of relevance for building integrated photovoltaics, as ease of fabrication, long-term stability and improved performance are simultaneously achieved. © 2015 The Authors. Progress in Photovoltaics: Research and Applications published by John Wiley & Sons Ltd.

Metabolic and transcriptional responses of gilthead sea bream (Sparus aurata L.) to environmental stress: new insights in fish mitochondrial phenotyping.

The aim of the current study was to phenotype fish metabolism and the transcriptionally-mediated response of hepatic mitochondria of gilthead sea bream to intermittent and repetitive environmental stressors: (i) changes in water temperature (T-ST), (ii) changes in water level and chasing (C-ST) and (iii) multiple sensory perception stressors (M-ST). Gene expression profiling was done using a quantitative PCR array of 60 mitochondria-related genes, selected as markers of transcriptional regulation, oxidative metabolism, respiration uncoupling, antioxidant defense, protein import/folding/assembly, and mitochondrial dynamics and apoptosis. The mitochondrial phenotype mirrored changes in fish performance, haematology and lactate production. T-ST especially up-regulated transcriptional factors (PGC1α, NRF1, NRF2), rate limiting enzymes of fatty acid ß-oxidation (CPT1A) and tricarboxylic acid cycle (CS), membrane translocases (Tim/TOM complex) and molecular chaperones (mtHsp10, mtHsp60, mtHsp70) to improve the oxidative capacity in a milieu of a reduced feed intake and impaired haematology. The lack of mitochondrial response, increased production of lactate and negligible effects on growth performance in C-ST fish were mostly considered as a switch from aerobic to anaerobic metabolism. A strong down-regulation of PGC1α, NRF1, NRF2, CPT1A, CS and markers of mitochondrial dynamics and apoptosis (BAX, BCLX, MFN2, MIRO2) occurred in M-ST fish in association with the greatest circulating cortisol concentration and a reduced lactate production and feed efficiency, which represents a metabolic condition with the highest allostatic load score. These findings evidence a high mitochondrial plasticity against stress stimuli, providing new insights to define the threshold level of stress condition in fish.

Massively parallel mutant selection identifies genetic determinants of Pseudomonas aeruginosa colonization of Drosophila melanogaster.

Pseudomonas aeruginosa is recognized for its ability to colonize diverse habitats and cause disease in a variety of hosts, including plants, invertebrates, and mammals. Understanding how this bacterium is able to occupy wide-ranging niches is important for deciphering its ecology. We used transposon sequencing [Tn-Seq, also known as insertion sequencing (INSeq)] to identify genes in P. aeruginosa that contribute to fitness during the colonization of Drosophila melanogaster. Our results reveal a suite of critical factors, including those that contribute to polysaccharide production, DNA repair, metabolism, and respiration. Comparison of candidate genes with fitness determinants discovered in previous studies on P. aeruginosa identified several genes required for colonization and virulence determinants that are conserved across hosts and tissues. This analysis provides evidence for both the conservation of function of several genes across systems, as well as host-specific functions. These findings, which represent the first use of transposon sequencing of a gut pathogen in Drosophila, demonstrate the power of Tn-Seq in the fly model system and advance the existing knowledge of intestinal pathogenesis by D. melanogaster, revealing bacterial colonization determinants that contribute to a comprehensive portrait of P. aeruginosa lifestyles across habitats.IMPORTANCEDrosophila melanogaster is a powerful model for understanding host-pathogen interactions. Research with this system has yielded notable insights into mechanisms of host immunity and defense, many of which emerged from the analysis of bacterial mutants defective for well-characterized virulence factors. These foundational studies-and advances in high-throughput sequencing of transposon mutants-support unbiased screens of bacterial mutants in the fly. To investigate mechanisms of host-pathogen interplay and exploit the tractability of this model host, we used a high-throughput, genome-wide mutant analysis to find genes that enable the pathogen P. aeruginosa to colonize the fly. Our analysis reveals critical mediators of P. aeruginosa establishment in its host, some of which are required across fly and mouse systems. These findings demonstrate the utility of massively parallel mutant analysis and provide a platform for aligning the fly toolkit with comprehensive bacterial genomics.

Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts.

BACKGROUND: The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of gilthead sea bream sequences derived from public repositories of mRNA and collections of expressed sequence tags together with new high-quality reads from five cDNA 454 normalized libraries of skeletal muscle (1), intestine (1), head kidney (2) and blood (1). RESULTS: Sequencing of the new 454 normalized libraries produced 2,945,914 high-quality reads and the de novo global assembly yielded 125,263 unique sequences with an average length of 727 nt. Blast analysis directed to protein and nucleotide databases annotated 63,880 sequences encoding for 21,384 gene descriptions, that were curated for redundancies and frameshifting at the homopolymer regions of open reading frames, and hosted at http://www.nutrigroup-iats.org/seabreamdb. Among the annotated gene descriptions, 16,177 were mapped in the Ingenuity Pathway Analysis (IPA) database, and 10,899 were eligible for functional analysis with a representation in 341 out of 372 IPA canonical pathways. The high representation of randomly selected stickleback transcripts by Blast search in the nucleotide gilthead sea bream database evidenced its high coverage of protein-coding transcripts. CONCLUSIONS: The newly assembled gilthead sea bream transcriptome represents a progress in genomic resources for this species, as it probably contains more than 75% of actively transcribed genes, constituting a valuable tool to assist studies on functional genomics and future genome projects.

Effect of ration size on fillet fatty acid composition, phospholipid allostasis and mRNA expression patterns of lipid regulatory genes in gilthead sea bream (Sparus aurata).

The effect of ration size on muscle fatty acid (FA) composition and mRNA expression levels of key regulatory enzymes of lipid and lipoprotein metabolism have been addressed in juveniles of gilthead sea bream fed a practical diet over the course of an 11-week trial. The experimental setup included three feeding levels: (i) full ration until visual satiety, (ii) 70 % of satiation and (iii) 70 % of satiation with the last 2 weeks at the maintenance ration. Feed restriction reduced lipid content of whole body by 30 % and that of fillet by 50 %. In this scenario, the FA composition of fillet TAG was not altered by ration size, whereas that of phospholipids was largely modified with a higher retention of arachidonic acid and DHA. The mRNA transcript levels of lysophosphatidylcholine acyltransferases, phosphatidylethanolamine N-methyltransferase and FA desaturase 2 were not regulated by ration size in the present experimental model. In contrast, mRNA levels of stearoyl-CoA desaturases were markedly down-regulated by feed restriction. An opposite trend was found for a muscle-specific lipoprotein lipase, which is exclusive of fish lineage. Several upstream regulatory transcriptions were also assessed, although nutritionally mediated changes in mRNA transcripts were almost reduced to PPARα and ß, which might act in a counter-regulatory way on lipolysis and lipogenic pathways. This gene expression pattern contributes to the construction of a panel of biomarkers to direct marine fish production towards muscle lean phenotypes with increased retentions of long-chain PUFA.

Determination of the optical constants of ligand-free organic lead halide perovskite quantum dots.

Precise knowledge of the optical constants of perovskite lead halide quantum dots (QDs) is required to both understand their interaction with light and to rationally design and optimize the devices based on them. However, their determination from colloidal nanocrystal suspensions, or films made out of them, remains elusive, as a result of the difficulty in disentangling the optical constants of the organic capping ligands and those of the semiconductor itself. In this work, we extract the refractive index and extinction coefficient of ligand-free methylammonium lead iodide (MAPbI3) and bromide (MAPbBr3) nanocrystals. In order to prevent the use of organic ligands in the preparation, we follow a scaffold assisted synthetic procedure, which yields a composite film of high optical quality that can be independently and precisely characterized and modelled. In this way, the contribution of the guest nanocrystals can be successfully discriminated from that of the host matrix. Using a Kramers-Kronig consistent dispersion model along with an effective medium approximation, it is possible to derive the optical constants of the QDs by fitting the spectral dependence of light transmitted and reflected at different angles and polarizations. Our results indicate a strong dependence of the optical constants on the QD size. Small nanocrystals show remarkably large values of the extinction coefficient compared to their bulk counterparts. This analysis opens the door to the rigorous modelling of solar cells and light-emitting diodes with active layers based on perovskite QDs.

Effect of the effective refractive index on the radiative decay rate in nanoparticle thin films.

In this work, we theoretically and experimentally study the influence of the optical environment on the radiative decay rate of rare-earth transitions in luminescent nanoparticles forming a thin film. We use electric dipole sources in finite-difference time-domain simulations to analyze the effect of modifying the effective refractive index of transparent layers made of phosphor nanocrystals doped with rare earth cations, and propose a correction to previously reported analytical models for calculating the radiative decay rate. Our predictions are tested against an experimental realization of such luminescent films, in which we manage to vary the effective refractive index in a gradual and controllable manner. Our model accurately accounts for the measurements attained, allows us to discriminate the radiative and non-radiative contributions to the time-resolved photoluminescence, and provides a way to rationally tune the spontaneous decay rate and hence the photoluminescence quantum yield in an ensemble of luminescent nanoparticles.

Collective plasmonic resonances enhance the photoluminescence of rare-earth nanocrystal films processed by ultrafast annealing.

Herein, we demonstrate that rapid thermal annealing allows achieving close-to-one photoluminescence quantum yield while preserving the transparency of rare-earth nanocrystal films, which further enables their integration with nanophotonics. The combination with periodic arrays of aluminum nanodisks that support collective plasmonic resonances leads to enhanced directional emission.

Massively parallel mutant selection identifies genetic determinants of Pseudomonas aeruginosa colonization of Drosophila melanogaster.

Pseudomonas aeruginosa is recognized for its ability to colonize diverse habitats and cause disease in a variety of hosts, including plants, invertebrates, and mammals. Understanding how this bacterium is able to occupy wide-ranging niches is important for deciphering its ecology. We used transposon sequencing (Tn-Seq, also known as INSeq) to identify genes in P. aeruginosa that contribute to fitness during colonization of Drosophila melanogaster. Our results reveal a suite of critical factors, including those that contribute to polysaccharide production, DNA repair, metabolism, and respiration. Comparison of candidate genes with fitness determinants discovered in previous studies of P. aeruginosa identified several genes required for colonization and virulence determinants that are conserved across hosts and tissues. This analysis provides evidence for both the conservation of function of several genes across systems, as well as host-specific functions. These findings, which represent the first use of transposon sequencing of a gut pathogen in Drosophila, demonstrate the power of Tn-Seq in the fly model system and advance existing knowledge of intestinal pathogenesis by D. melanogaster, revealing bacterial colonization determinants that contribute to a comprehensive portrait of P. aeruginosa lifestyles across habitats.

Enhancement of upconversion photoluminescence in phosphor nanoparticle thin films using metallic nanoantennas fabricated by colloidal lithography.

Lanthanide-doped upconversion nanoparticles (UCNPs), as multifunctional light sources, are finding utility in diverse applications ranging from biotechnology to light harvesting. However, the main challenge in realizing their full potential lies in achieving bright and efficient photon upconversion (UC). In this study, we present a novel approach to fabricate an array of gold nanoantennas arranged in a hexagonal lattice using a simple and inexpensive colloidal lithography technique, and demonstrate a significant enhancement of UC photoluminescence (UCPL) by up to 35-fold through plasmon-enhanced photoexcitation and emission. To elucidate the underlying physical mechanisms responsible for the observed UCPL enhancement, we provide a comprehensive theoretical and experimental characterization, including a detailed photophysical description and numerical simulations of the spatial electric field distribution. Our results shed light on the fundamental principles governing the enhanced UCNPs and pave the way for their potential applications in photonic devices.

Characterization of mesoporous thin films by specular reflectance porosimetry.

The pore size distribution of mesoporous thin films is herein investigated through a reliable and versatile technique coined specular reflectance porosimetry. This method is based on the analysis of the gradual shift of the optical response of a porous slab measured in quasi-normal reflection mode that occurs as the vapor pressure of a volatile liquid varies in a closed chamber. The fitting of the spectra collected at each vapor pressure is employed to calculate the volume of solvent contained in the interstitial sites and thus to obtain adsorption-desorption isotherms from which the pore size distribution and internal and external specific surface areas are extracted. This technique requires only a microscope operating in the visible range attached to a spectrophotometre. Its suitability to analyze films deposited onto arbitrary substrates, one of the main limitations of currently employed ellipsometric porosimetry and quartz balance techniques, is demonstrated. Two standard mesoporous materials, supramolecularly templated mesostructured films and packed nanoparticle layers, are employed to prove the concept proposed herein.

Enhanced up-conversion photoluminescence in fluoride-oxyfluoride nanophosphor films by embedding gold nanoparticles.

Owing to their unique non-linear optical character, lanthanide-based up-converting materials are potentially interesting for a wide variety of fields ranging from biomedicine to light harvesting. However, their poor luminescent efficiency challenges the development of technological applications. In this context, localized surface plasmon resonances (LSPRs) have been demonstrated as a valuable strategy to improve light conversion. Herein, we utilize LSPR induced by gold nanoparticles (NPs) to enhance up-conversion photoluminescence (UCPL) in transparent, i.e. scattering-free, films made of nanophosphors formed by fluoride-oxyfluoride host matrix that feature high thermal stability. Transparency allows excitation by an external source without extinction losses caused by unwanted diffuse reflection. We provide a simple method to embed gold NPs in films made of YF/YOF:Yb3+,Er3+ UC nanophosphors, via preparation of a viscous paste composed of both UC nanophosphors and colloidal gold NPs, reducing complexity in sample fabrication. The dimensions of gold NPs are such that their associated LSPR matches spectrally with the green emission band of the Er3+ doped nanophosphors. In order to demonstrate the benefits of plasmonic nanoparticles for UCPL in nanophosphor films, we provide a careful analysis of the structural properties of the composite thin films along with precise characterization of the impact of the gold NPs on the photophysical properties of UC nanophosphors.

Nanoantennas Patterned by Colloidal Lithography for Enhanced Nanophosphor Light Emission.

Transparent coatings made of rare-earth doped nanocrystals, also known as nanophosphors, feature efficient photoluminescence and excellent thermal and optical stability. Herein, we demonstrate that the optical antennas prepared by colloidal lithography render thin nanophosphor films with a brighter emission. In particular, we fabricate gold nanostructures in the proximity of GdVO4:Eu3+ nanophosphors by metal evaporation using a mask made of a monolayer of polymer beads arranged in a triangular lattice. Optical modes supported by the antennas can be controlled by tuning the diameter of the polymer spheres in the colloidal mask, which determines the shape of the gold nanostructure, as confirmed by numerical simulations. Confocal microscopy reveals that metallic antennas induce brighter photoluminescence at specific spatial regions of the nanophosphor film at targeted frequencies as a result of the coupling between gold nanostructures and nanophosphors. Patterning of nanophosphor thin layers with arrays of metallic antennas offers an inexpensive nanophotonic solution to develop bright emitting coatings of interest for color conversion, labeling, or anti-counterfeiting.

Understanding signatures of positive natural selection in human zinc transporter genes.

Zinc is an essential micronutrient with a tightly regulated systemic and cellular homeostasis. In humans, some zinc transporter genes (ZTGs) have been previously reported as candidates for strong geographically restricted selective sweeps. However, since zinc homeostasis is maintained by the joint action of 24 ZTGs, other more subtle modes of selection could have also facilitated human adaptation to zinc availability. Here, we studied whether the complete set of ZTGs are enriched for signals of positive selection in worldwide populations and population groups from South Asia. ZTGs showed higher levels of genetic differentiation between African and non-African populations than would be randomly expected, as well as other signals of polygenic selection outside Africa. Moreover, in several South Asian population groups, ZTGs were significantly enriched for SNPs with unusually extended haplotypes and displayed SNP genotype-environmental correlations when considering zinc deficiency levels in soil in that geographical area. Our study replicated some well-characterized targets for positive selection in East Asia and sub-Saharan Africa, and proposes new candidates for follow-up in South Asia (SLC39A5) and Africa (SLC39A7). Finally, we identified candidate variants for adaptation in ZTGs that could contribute to different disease susceptibilities and zinc-related human health traits.