Simultaneous Quantification of Multiple Bacteria by the BactoChip Microarray Designed to Target Species-Specific Marker Genes

Bacteria are ubiquitous throughout the environment, the most abundant inhabitants of the healthy human microbiome, and causal pathogens in a variety of diseases. Their identification in disease is often an essential step in rapid diagnosis and targeted intervention, particularly in clinical settings. At present, clinical bacterial detection and discrimination is primarily culture-based, requiring both time and microbiological expertise, especially for bacteria that are not easily cultivated. Higher-throughput molecular methods based on PCR amplification or, recently, microarrays are reaching the clinic as well. However, these methods are currently restricted to a small set of microbes or based on conserved phylogenetic markers such as the 16S rRNA gene, which are difficult to resolve at the species or strain levels. Here, we designed and experimentally validated the BactoChip, an oligonucleotide microarray for bacterial detection and quantification. The chip allows the culture-independent identification of bacterial species, also determining their relative abundances in complex communities as occur in the commensal microbiota or in clinical settings. The microarray successfully distinguished among bacterial species from 21 different genera using 60-mer probes targeting a novel set of in silico identified high-resolution marker genes. The BactoChip additionally proved accurate in determining species-level relative abundances over a 100-fold dynamic range in complex bacterial communities and with a low limit of detection (0.1%). In combination with the continually increasing number of sequenced bacterial genomes, future iterations of the technology could enable to highly accurate clinically-oriented tools for rapid assessment of bacterial community composition and relative abundances

Metagenomic microbial community profiling using unique clade-specific marker genes

Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large datasets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches. We validated MetaPhlAn on terabases of short reads and provide the largest metagenomic profiling to date of the human gu

Room temperature polariton condensation from Whispering gallery modes in CsPbBr3 microplatelets

Room temperature (RT) polariton condensate holds exceptional promise for revolutionizing various fields of science and technology, encompassing optoelectronics devices to quantum information processing. Using perovskite materials like all-inorganic CsPbBr3 single crystal provides additional advantages, such as ease of synthesis, cost-effectiveness, and compatibility with existing semiconductor technologies. In this work, we show the formation of whispering gallery modes (WGM) in CsPbBr3 single crystals with controlled geometry, synthesized using a lowcost and efficient capillary bridge method. Through the implementation of microplatelets geometry, we achieve enhanced optical properties and performance thanks to the presence of sharp edges and a uniform surface, effectively avoiding non-radiative scattering losses caused by defects. This allows us not only to observe strong light matter coupling and formation of whispering gallery polaritons, but also to demonstrate the onset of polariton condensation at RT. This investigation not only contributes to the advancement of our knowledge concerning the exceptional optical properties of perovskite-based polariton systems, but also unveils prospects for the exploration of WGM polariton condensation within the framework of a 3D perovskite-based platform, working at RT. The unique characteristics of polariton condensate, including low excitation thresholds and ultrafast dynamics, open up unique opportunities for advancements in photonics and optoelectronics devices

Engineering Dion-Jacobson Perovskites in Polariton Waveguides

Hybrid two-dimensional perovskites hold considerable promise as semiconductors for a wide range of optoelectronic applications. Many efforts are addressed to exploit the potential of these materials by tailoring their characteristics. In this work, the optical properties and electronic band structure in three new Dion-Jacobson (DJ) perovskites (PVKs) are engineered by modulating their structural distortion. Two different interlayer cations: 1-6, Hexamethylendiammonium, HE, and 3-(Dimethylamino)-1-propylammonium, DMPA, have been selected to investigate the role of the cation length and the ammonium binding group on the crystalline structure. This study provides new insights into the understanding of the structure-property relationship in DJ perovskites and demonstrates that exciton characteristics can be easily modulated with the judicious design of the organic cations. DJ PVKs developed in this work were also grown as size-controlled single crystal microwires through a microfluidic-assisted synthesis technique and integrated in a nanophotonic device. The DJ PVK microwire acts as a waveguide exhibiting strong light-matter coupling between the crystal optical modes and DJ PVK exciton. Through the investigation of these polariton waveguides, the nature of the double peak emission, which is often observed in these materials and whose nature is largely debated in the literature, is demonstrated originating from the hybrid polariton state

Oxaliplatin-induced peripheral neurotoxicity: morphological characterization in different mouse strains

Oxaliplatin is one of the most effective anticancer drug, particularly employed in the treatment of colorectal cancer, but one of the major limitation in its use is peripheral neurotoxicity. Oxaliplatin induced peripheral neurotoxicity (OIPN) has a high incidence and is frequently long lasting or permanent. Neuropathy is characterized by distal sensory impairment initially in the legs, then extending to the arms. A prominent manifestation of sensitive damage is ataxia. Besides chronic neurotoxicity, many patients experience an acute, rapidly developing cold-induced sensory neuropathy, usually resolving within one week. OIPN clinical manifestations reflect the involvement of dorsal root ganglia (DRG) as primary target of the drug toxicity. Although this assumption is largely accepted and some pathogenetic hypothesis have been proposed, mechanisms at the basis of OIPN need to be clearly defined. OIPN may vary in frequency and severity among different cancer patients despite equal treatment schedules. A genetic susceptibility for more severe oxaliplatin-induced peripheral neurotoxicity (OIPN) has been suggested but never confirmed. Therefore we designed a study to assess the phenotypic differences induced by oxaliplatin treatment in six different mice strains (Balb c, AJ, C57Bl6, FVB, DBA, CD1) aiming at identifying the more and less severely affected. Animals were treated with OHP 3.5 mg/Kg/iv twice weekly x 4 weeks and evaluated before and after treatment. In all strains we performed a multimodal characterization of its neurotoxicity through morphological and morphometrical assessment in caudal nerve and DRG at light and electron microscopy, intra-epidermal nerve fibers density quantification, evaluation of mechanical and cold allodynia/hypoaesteshesia, caudal and digital nerve conduction velocity, activity of wide dynamic range (WDR) neurons of the spinal dorsal horn. Our preliminary data suggest that all the strains show signs of OIPN but not the same modifications in the parameters examined. We will show these results with particular attention to morphological data. This study suggests that genetic variability might have a role in the type and severity of OHP-induced peripheral damage

Wedge-shaped fracturing in the pull out of FRP stiffeners from quasi-brittle substrates

Fiber-Reinforced-Polymer (FRP) strips can be glued to the surface of concrete or masonry structures to improve their strength. Pull-out tests on FRP bonds have shown a progressive failure of the adhesive joint involving early-stage cracking parallel to the axis of the FRP stiffener, and an inclined crack initiating at the free end of the stiffener and extending into the quasi-brittle substrate in the latest stage. The subsurface crack produces a characteristic wedge-shaped spall. There is no consensus on the reasons for the transition from cracking along the bond to cracking within the substrate. Therefore a Linear Elastic Fracture Mechanics model problem is presented here that accounts for and provides improved understanding of the formation of the subsurface crack. The boundary value problem is solved analytically using the distributed dislocation technique. Competition between crack extension along the adhesive joint and into the substrate is quantified using a quantized crack propagation criterion, whereby the crack does not advance in infinitesimal continuous increments, but instead in finite steps of length comparable to the characteristic dimensions of the material microstructure. The model predicts results that are in good agreement with experimental evidence

Molecular typing and epidemiological investigation of clinical populations of <it>Pseudomonas aeruginosa</it> using an oligonucleotide-microarray

Abstract Background Pseudomonas aeruginosa is an opportunistic pathogen which has the potential to become extremely harmful in the nosocomial environment, especially for cystic fibrosis (CF) patients, who are easily affected by chronic lung infections. For epidemiological purposes, discriminating P.aeruginosa isolates is a critical step, to define distribution of clones among hospital departments, to predict occurring microevolution events and to correlate clones to their source. A collection of 182 P. aeruginosa clinical strains isolated within Italian hospitals from patients with chronic infections, i.e. cystic fibrosis (CF) patients, and with acute infections were genotyped. Molecular typing was performed with the ArrayTube (AT) multimarker microarray (Alere Technologies GmbH, Jena, Germany), a cost-effective, time-saving and standardized method, which addresses genes from both the core and accessory P.aeruginosa genome. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were employed as reference genotyping techniques to estimate the ArrayTube resolution power. Results 41 AT-genotypes were identified within our collection, among which 14 were novel and 27 had been previously described in publicly available AT-databases. Almost 30% of the genotypes belonged to a main cluster of clones. 4B9A, EC2A, 3C2A were mostly associated to CF-patients whereas F469, 2C1A, 6C22 to non CF. An investigation on co-infections events revealed that almost 40% of CF patients were colonized by more than one genotype, whereas less than 4% were observed in non CF patients. The presence of the exoU gene correlated with non-CF patients within the intensive care unit (ICU) whereas the pKLC102-like island appeared to be prevalent in the CF centre. The congruence between the ArrayTube typing and PFGE or MLST was 0.077 and 0.559 (Adjusted Rand coefficient), respectively. AT typing of this Italian collection could be easily integrated with the global P. aeruginosa AT-typed population, uncovering that most AT-genotypes identified (> 80%) belonged to two large clonal clusters, and included 12 among the most abundant clones of the global population. Conclusions The ArrayTube (AT) multimarker array represented a robust and portable alternative to reference techniques for performing P. aeruginosa molecular typing, and allowed us to draw conclusions especially suitable for epidemiologists on an Italian clinical collection from chronic and acute infections.</p

Quantification of the relative abundances of multiple species from the same genus contained within a single sample.

<p>True versus detected relative abundances for each of 6 <i>Staphylococcus</i> species are shown in blue (gold standard) and red (inferred), respectively. Even DNA relative abundances were targeted, with true experimental abundances of cell copy numbers varying due to differences in genome size. Mean Squared Error (MSE) of relative abundance over all predictions was below 0.0019.</p

Design of the BactoChip and its application for microbial species identification and quantification.

<p>(A) Schematic overview of computational design and its output. (A1) Complete genomes from 186 bacterial species were retrieved from the National Centre for Biotechnology Information microbial database. (A2) Gene sequences core to each target species were defined on the basis of sequence conservation within each clade. Red dots represent the distribution of core genes shared by strains within and outside a target clade. (A3) Core genes unique to each target species were selected by sequence alignment against all available archaeal and bacterial sequences. (A4) Oligonucleotide probes were designed for up to 10 identified unique genes for each target bacterial species. Each probe color represents specificity to a defined bacterial species. (B) Experimental design and example data. (B1) DNA from microbial communities was tested on the BactoChip. Green dots represent Cy3 bound to genomic DNA fragments from a sample hybridized to the chip. (B2) Species relative abundances are finally inferred by normalization of the fluorescence signal for each probe and species.</p