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.

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.

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.

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.

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.

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.

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.

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.

Rinosinusitis micótica alérgica con destrucción de base de cráneo / Allergic fungal rhinosinusitis with skull base destruction

La sinusitis micótica alérgica es una enfermedad inflamatoria de la mucosa rinosinusal producida por hongos que pueden aislarse de la cavidad de nasal de individuos sanos. Se produce indirectamente por los hongos que actúan como antígeno y desencadenan una reacción inmunológica mediada por IgE que origina pólipos y una secreción mucosa espesa con detritus e hifas denominada mucina. Su presentación clínica más frecuente es una sinusitis crónica unilateral o bilateral con pólipos. Con menos frecuencia, las sustancias originadas por la desgranulación de los eosinófilos producen remodelación o destrucción ósea y la sinusitis puede simular una neoplasia. Se describe el caso clínico de un paciente que padeció una sinusitis micótica alérgica con destrucción ósea masiva de la base del cráneo y que tuvo extensión intracraneal extradural e intraorbitaria de la enfermedad. Fue tratado con éxito mediante cirugía y corticoides. (AU)

Allergic fungal sinusitis is an inflammatory disease of the rhinosinusal mucosa caused by fungi that can be isolated from the nasal cavity of healthy individuals. The pathology is produced indirectly by the fungus that acts as an antigen and triggers an IgE-mediated allergic reaction that causes polyps and a thick mucous discharge with detritus and hyphae called mucin. Its most common clinical presentation is unilateral or bilateral chronic sinusitis with polyps. Less commonly, substances originated by the degranulation of eosinophils cause bone remodeling or destruction, and sinusitis can simulate a neoplasia. We describe the clinical case of a patient who suffered from allergic fungal sinusitis with massive bone destruction of the skull base and who had intracranial, extradural and intraorbital extension of the disease. He was successfully treated with surgery and corticosteroids.Key words: allergic fungal sinusitis, intracranial extension, endoscopic surgery, transorbital transpalpebral approach. (AU)

Social motility of biofilm-like microcolonies in a gliding bacterium.

Bacterial biofilms are aggregates of surface-associated cells embedded in an extracellular polysaccharide (EPS) matrix, and are typically stationary. Studies of bacterial collective movement have largely focused on swarming motility mediated by flagella or pili, in the absence of a biofilm. Here, we describe a unique mode of collective movement by a self-propelled, surface-associated biofilm-like multicellular structure. Flavobacterium johnsoniae cells, which move by gliding motility, self-assemble into spherical microcolonies with EPS cores when observed by an under-oil open microfluidic system. Small microcolonies merge, creating larger ones. Microscopic analysis and computer simulation indicate that microcolonies move by cells at the base of the structure, attached to the surface by one pole of the cell. Biochemical and mutant analyses show that an active process drives microcolony self-assembly and motility, which depend on the bacterial gliding apparatus. We hypothesize that this mode of collective bacterial movement on solid surfaces may play potential roles in biofilm dynamics, bacterial cargo transport, or microbial adaptation. However, whether this collective motility occurs on plant roots or soil particles, the native environment for F. johnsoniae, is unknown.

One-reactor vacuum and plasma synthesis of transparent conducting oxide nanotubes and nanotrees: from single wire conductivity to ultra-broadband perfect absorbers in the NIR.

The eventual exploitation of one-dimensional nanomaterials needs the development of scalable, high yield, homogeneous and environmentally friendly methods capable of meeting the requirements for fabrication of functional nanomaterials with properties on demand. In this article, we demonstrate a vacuum and plasma one-reactor approach for the synthesis of fundamental common elements in solar energy and optoelectronics, i.e. the transparent conducting electrode but in the form of nanotube and nanotree architectures. Although the process is generic and can be used for a variety of TCOs and wide-bandgap semiconductors, we focus herein on indium doped tin oxide (ITO) as the most previously researched in previous applications. This protocol combines widely applied deposition techniques such as thermal evaporation for the formation of organic nanowires serving as 1D and 3D soft templates, deposition of polycrystalline layers by magnetron sputtering, and removal of the templates by simply annealing under mild vacuum conditions. The process variables are tuned to control the stoichiometry, morphology, and alignment of the ITO nanotubes and nanotrees. Four-probe characterization reveals the improved lateral connectivity of the ITO nanotrees and applied on individual nanotubes shows resistivities as low as 3.5 ± 0.9 × 10-4Ω cm, a value comparable to that of single-crystalline counterparts. The assessment of diffuse reflectance and transmittance in the UV-Vis range confirms the viability of the supported ITO nanotubes as random optical media working as strong scattering layers. Their further ability to form ITO nanotrees opens a path for practical applications as ultra-broadband absorbers in the NIR. The demonstrated low resistivity and optical properties of these ITO nanostructures open a way for their use in LEDs, IR shields, energy harvesting, nanosensors, and photoelectrochemical applications.

Highly Versatile Upconverting Oxyfluoride-Based Nanophosphor Films.

Fluoride-based compounds doped with rare-earth cations are the preferred choice of materials to achieve efficient upconversion, of interest for a plethora of applications ranging from bioimaging to energy harvesting. Herein, we demonstrate a simple route to fabricate bright upconverting films that are transparent, self-standing, flexible, and emit different colors. Starting from the solvothermal synthesis of uniform and colloidally stable yttrium fluoride nanoparticles doped with Yb3+ and Er3+, Ho3+, or Tm3+, we find the experimental conditions to process the nanophosphors as optical quality films of controlled thickness between few hundreds of nanometers and several micrometers. A thorough analysis of both structural and photophysical properties of films annealed at different temperatures reveals a tradeoff between the oxidation of the matrix, which transitions through an oxyfluoride crystal phase, and the efficiency of the upconversion photoluminescence process. It represents a significant step forward in the understanding of the fundamental properties of upconverting materials and can be leveraged for the optimization of upconversion systems in general. We prove bright multicolor upconversion photoluminescence in oxyfluoride-based phosphor transparent films upon excitation with a 980 nm laser for both rigid and flexible versions of the layers, being possible to use the latter to coat surfaces of arbitrary shape. Our results pave the way toward the development of upconverting coatings that can be conveniently integrated in applications that demand a large degree of versatility.

Worker Injuries in Southern California's Warehousing Industry: How to Better Protect Workers in This Burgeoning Industry?

Dangerous conditions and worker injuries in the rapidly growing warehousing industry have gained attention in recent years, with accounts typically drawing on worker reports and investigative journalism. We analyzed workers' compensation injury claims and California Division of Occupational Safety and Health (Cal/OSHA) citations in Southern California's large warehousing sector. Claims increased from 2014 to 2018, with a majority of injuries caused by repetitive motion, lifting and other ergonomic risk factors. Cal/OSHA cited employers for violating standards to protect workers from unsafe vehicle operations, dangerous machinery and equipment, and falls; and for failing to implement injury prevention programs. These citations address the causes of some worker injuries; however, no Cal/OSHA citations were issued for violating the state's Repetitive Motion Injuries prevention standard. Nor do enforcement activities address the underlying causes highlighted by workers-high production quotas and a relentless work pace-that characterize the industry. We discuss the value and limitations of our approach and the implications of our results.

Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery.

The world faces two seemingly unrelated challenges-a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.

A Chemical Counterpunch: Chromobacterium violaceum ATCC 31532 Produces Violacein in Response to Translation-Inhibiting Antibiotics.

Antibiotics produced by bacteria play important roles in microbial interactions and competition Antibiosis can induce resistance mechanisms in target organisms, and at sublethal doses, antibiotics have been shown to globally alter gene expression patterns. Here, we show that hygromycin A from Streptomyces sp. strain 2AW. induces Chromobacterium violaceum ATCC 31532 to produce the purple antibiotic violacein. Sublethal doses of other antibiotics that similarly target the polypeptide elongation step of translation likewise induced violacein production, unlike antibiotics with different targets. C. violaceum biofilm formation and virulence against Drosophila melanogaster were also induced by translation-inhibiting antibiotics, and we identified an antibiotic-induced response (air) two-component regulatory system that is required for these responses. Genetic analyses indicated a connection between the Air system, quorum-dependent signaling, and the negative regulator VioS, leading us to propose a model for induction of violacein production. This work suggests a novel mechanism of interspecies interaction in which a bacterium produces an antibiotic in response to inhibition by another bacterium and supports the role of antibiotics as signal molecules.IMPORTANCE Secondary metabolites play important roles in microbial communities, but their natural functions are often unknown and may be more complex than appreciated. While compounds with antibiotic activity are often assumed to underlie microbial competition, they may alternatively act as signal molecules. In either scenario, microorganisms might evolve responses to sublethal concentrations of these metabolites, either to protect themselves from inhibition or to change certain behaviors in response to the local abundance of another species. Here, we report that violacein production by C. violaceum ATCC 31532 is induced in response to hygromycin A from Streptomyces sp. 2AW, and we show that this response is dependent on inhibition of translational polypeptide elongation and a previously uncharacterized two-component regulatory system. The breadth of the transcriptional response beyond violacein induction suggests a surprisingly complex metabolite-mediated microbe-microbe interaction and supports the hypothesis that antibiotics evolved as signal molecules. These novel insights will inform predictive models of soil community dynamics and the unintended effects of clinical antibiotic administration.

Optical Responses of Localized and Extended Modes in a Mesoporous Layer on Plasmonic Array to Isopropanol Vapor.

Mesoporous silica features open and accessible pores that can intake substances from the outside. The combination of mesoporous silica with plasmonic nanostructures represents an interesting platform for an optical sensor based on the dependence of plasmonic modes on the refractive index of the medium in which metallic nanoparticles are embedded. However, so far only a limited number of plasmonic nanostructures are combined with mesoporous silica, including random dispersion of metallic nanoparticles and flat metallic thin films. In this study, we make a mesoporous silica layer on an aluminum nanocylinder array. Such plasmonic arrangements support both localized surface plasmon resonances (LSPRs) and extended modes which are the result of the hybridization of LSPRs and photonic modes extending into the mesoporous layer. We investigate in situ optical reflectance of this system under controlled pressure of isopropanol vapor. Upon exposure, the capillary condensation in the mesopores results in a gradual spectral shift of the reflectance. Our analysis demonstrates that such shifts depend largely on the nature of the modes; that is, the extended modes show larger shifts compared to localized ones. Our materials represent a useful platform for the field of environmental sensing.

Design and validation of a transposon that promotes expression of genes in episomal DNA.

Functional metagenomics, or the cloning and expression of DNA isolated directly from environmental samples, represents a source of novel compounds with biotechnological potential. However, attempts to identify such compounds in metagenomic libraries are generally inefficient in part due to lack of expression of heterologous DNA. In this research, the TnC_T7 transposon was developed to supply transcriptional machinery during functional analysis of metagenomic libraries. TnC_T7 contains bidirectional T7 promoters, the gene encoding the T7 RNA polymerase (T7RNAP), and a kanamycin resistance gene. The T7 RNA polymerase gene is regulated by the inducible arabinose promoter (PBAD), thereby facilitating inducible expression of genes adjacent to the randomly integrating transposon. The high processivity of T7RNAP should make this tool particularly useful for obtaining gene expression in long inserts. TnC_T7 functionality was validated by conducting in vitro transposition of pKR-C12 or fosmid pF076_GFPmut3*, carrying metagenomic DNA from soil. We identified transposon insertions that enhanced GFP expression in both vectors, including insertions in which the promoter delivered by the transposon was located as far as 8.7 kb from the GFP gene, indicating the power of the high processivity of the T7 polymerase. The results gathered in this research demonstrate the potential of TnC_T7 to enhance gene expression in functional metagenomic studies.