The NanoFlow Repository.

MOTIVATION: Extracellular particles (EPs) are the focus of a rapidly growing area of exploration due to the widespread interest in understanding their roles in health and disease. However, despite the general need for EP data sharing and established community standards for data reporting, no standard repository for EP flow cytometry data captures rigor and minimum reporting standards such as those defined by MIFlowCyt-EV (https://doi.org/10.1080/20013078.2020.1713526). We sought to address this unmet need by developing the NanoFlow Repository. RESULTS: We have developed The NanoFlow Repository to provide the first implementation of the MIFlowCyt-EV framework. AVAILABILITY AND IMPLEMENTATION: The NanoFlow Repository is freely available and accessible online at https://genboree.org/nano-ui/. Public datasets can be explored and downloaded at https://genboree.org/nano-ui/ld/datasets. The NanoFlow Repository's backend is built using the Genboree software stack that powers the ClinGen Resource, specifically the Linked Data Hub (LDH), a REST API framework written in Node.js, developed initially to aggregate data within ClinGen (https://ldh.clinicalgenome.org/ldh/ui/about). NanoFlow's LDH (NanoAPI) is available at https://genboree.org/nano-api/srvc. NanoAPI is supported by a Node.js Genboree authentication and authorization service (GbAuth), a graph database called ArangoDB, and an Apache Pulsar message queue (NanoMQ) to manage data inflows into NanoAPI. The website for NanoFlow Repository is built with Vue.js and Node.js (NanoUI) and supports all major browsers.

Extracellular Vesicle Refractive Index Derivation Utilizing Orthogonal Characterization.

The analysis of small particles, including extracellular vesicles and viruses, is contingent on their ability to scatter sufficient light to be detected. These detection methods include flow cytometry, nanoparticle tracking analysis, and single particle reflective image sensing. To standardize measurements and enable orthogonal comparisons between platforms, a quantifiable limit of detection is required. The main parameters that dictate the amount of light scattered by particles include size, morphology, and refractive index. To date, there has been a lack of accessible techniques for measuring the refractive index of nanoparticles at a single-particle level. Here, we demonstrate two methods of deriving a small particle refractive index using orthogonal measurements with commercially available platforms. These methods can be applied at either a single-particle or population level, enabling the integration of diameter and scattering cross section values to derive the refractive index using Mie theory.

Identification of second-generation P2X3 antagonists for treatment of pain.

A second-generation small molecule P2X3 receptor antagonist has been developed. The lead optimization strategy to address shortcomings of the first-generation preclinical lead compound is described herein. These studies were directed towards the identification and amelioration of preclinical hepatobiliary findings, reducing potential for drug-drug interactions, and decreasing the projected human dose of the first-generation lead.

Quantitative flow cytometry enables end-to-end optimization of cross-platform extracellular vesicle studies.

Flow cytometry (FCM) is a common method for characterizing extracellular particles (EPs), including viruses and extracellular vesicles (EVs). Frameworks such as MIFlowCyt-EV exist to provide reporting guidelines for metadata, controls, and data reporting. However, tools to optimize FCM for EP analysis in a systematic and quantitative way are lacking. Here, we demonstrate a cohesive set of methods and software tools that optimize FCM settings and facilitate cross-platform comparisons for EP studies. We introduce an automated small-particle optimization (SPOT) pipeline to optimize FCM fluorescence and light scatter detector settings for EP analysis and leverage quantitative FCM (qFCM) as a tool to further enable FCM optimization of fluorophore panel selection, laser power, pulse statistics, and window extensions. Finally, we demonstrate the value of qFCM to facilitate standardized cross-platform comparisons, irrespective of instrument configuration, settings, and sensitivity, in a cross-platform standardization study utilizing a commercially available EV reference material.

Viral Immune signatures from cerebrospinal fluid extracellular vesicles and particles in HAM and other chronic neurological diseases.

Background and objectives: Extracellular vesicles and particles (EVPs) are released from virtually all cell types, and may package many inflammatory factors and, in the case of infection, viral components. As such, EVPs can play not only a direct role in the development and progression of disease but can also be used as biomarkers. Here, we characterized immune signatures of EVPs from the cerebrospinal fluid (CSF) of individuals with HTLV-1-associated myelopathy (HAM), other chronic neurologic diseases, and healthy volunteers (HVs) to determine potential indicators of viral involvement and mechanisms of disease. Methods: We analyzed the EVPs from the CSF of HVs, individuals with HAM, HTLV-1-infected asymptomatic carriers (ACs), and from patients with a variety of chronic neurologic diseases of both known viral and non-viral etiologies to investigate the surface repertoires of CSF EVPs during disease. Results: Significant increases in CD8+ and CD2+ EVPs were found in HAM patient CSF samples compared to other clinical groups (p = 0.0002 and p = 0.0003 compared to HVs, respectively, and p = 0.001 and p = 0.0228 compared to MS, respectively), consistent with the immunopathologically-mediated disease associated with CD8+ T-cells in the central nervous system (CNS) of HAM patients. Furthermore, CD8+ (p < 0.0001), CD2+ (p < 0.0001), CD44+ (p = 0.0176), and CD40+ (p = 0.0413) EVP signals were significantly increased in the CSF from individuals with viral infections compared to those without. Discussion: These data suggest that CD8+ and CD2+ CSF EVPs may be important as: 1) potential biomarkers and indicators of disease pathways for viral-mediated neurological diseases, particularly HAM, and 2) as possible meditators of the disease process in infected individuals.

MPAPASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays.

Extracellular vesicles (EVs) of various types are released or shed from all cells. EVs carry proteins and contain additional protein and nucleic acid cargo that relates to their biogenesis and cell of origin. EV cargo in liquid biopsies is of widespread interest owing to its ability to provide a retrospective snapshot of cell state at the time of EV release. For the purposes of EV cargo analysis and repertoire profiling, multiplex assays are an essential tool in multiparametric analyte studies but are still being developed for high-parameter EV protein detection. Although bead-based EV multiplex analyses offer EV profiling capabilities with conventional flow cytometers, the utilization of EV multiplex assays has been limited by the lack of software analysis tools for such assays. To facilitate robust EV repertoire studies, we developed multiplex analysis post-acquisition analysis (MPAPASS) open-source software for stitched multiplex analysis, EV database-compatible reporting, and visualization of EV repertoires.

A point mutation at F1737 of the human Nav1.7 sodium channel decreases inhibition by local anesthetics.

Voltage-gated sodium channels (VGSC) contribute to the initiation and propagation of action potentials within the nervous system. These channels are important targets for inhibition by several classes of drugs, including antiarrhythmics and local anesthetics. Structural and pharmacological studies have localized the binding of these drugs to a common site near the channel's intracellular pore region. Point mutations within this region disrupt local anesthetic inhibition of cardiac, CNS, and skeletal muscle VGSC subtypes. This study was designed to test whether a similar structural requirement for drug binding exists on the peripheral neuronal VGSC subtype; Na(v)1.7. In support of this hypothesis, an alanine substitution for phenylalanine at position 1737 (F1737A) in the pore lining S6 segment of domain IV in human Na(v)1.7 reduced both use- and state- dependent inhibition of the local anesthetics, lidocaine and tetracaine, by 8-21-fold. We also saw a 2-3-fold reduction in tonic inhibition with the F1737A mutant. The voltage dependence of both activation and inactivation were unaffected by the F1737A mutation, however, fast inactivation kinetics were impaired, such that a significant portion of inward current remained at the end of a 20-ms depolarization. These data suggest that F1737 forms a part of the high affinity binding of local anesthetics as well as mediating inactivation processes of neuronal Na(v)1.7 channels.

Identification of non-amidine inhibitors of acid-sensing ion channel-3 (ASIC3).

A series of benzothiophene methyl amines were examined in an effort to identify non-amidine chemotypes with reduced polypharmacology from existing leads with the goal of finding potent ASIC3 channel blockers to advance the therapeutic evaluation of ASIC3 inhibition.

High concentration electrophysiology-based fragment screen: discovery of novel acid-sensing ion channel 3 (ASIC3) inhibitors.

The Merck Fragment Library was screened versus acid-sensing ion channel 3 (ASIC3), a novel target for the treatment of pain. Fragment hits were optimized using two strategies, and potency was improved from 0.7 mM to 3 µM with retention of good ligand efficiency and incorporation of reasonable physical properties, off-target profile, and rat pharmacokinetics.

Amiloride derived inhibitors of acid-sensing ion channel-3 (ASIC3).

A series of amiloride derivatives modified at the 5-position of the pyrazine ring were evaluated as inhibitors of acid-sensing ion channel-3 (ASIC3), a novel target for the treatment of chronic pain.

Amidine derived inhibitors of acid-sensing ion channel-3 (ASIC3).

A series of indole amidines modified at the 2-position of the indole ring were evaluated as inhibitors of Acid-Sensing Ion Channel-3 (ASIC3), a novel target for the treatment of chronic pain.

In vitro evaluation of cytotoxicity of engineered metal oxide nanoparticles.

The recent advances in nanotechnology and the corresponding popular usage of nanomaterials have resulted in uncertainties regarding their environmental impacts. In this study, we used a systematic approach to study and compare the in vitro cytotoxicity of selected engineered metal oxide nanoparticles to the test organisms--E. coli. Among the seven test nano-sized metal oxides, ZnO, CuO, Al2O3, La2O3, Fe2O3, SnO2 and TiO2, ZnO showed the lowest LD(50) of 21.1 mg/L and TiO2 had the highest LD(50) of 1104.8 mg/L. Data of 14C-glucose mineralization test paralleled the results of bacteria viability test. After regression calculation, the cytotoxicity was found to be correlated with cation charges (R(2) = 0.9785). The higher the cation charge is, the lower the cytotoxicity of the nano-sized metal oxide becomes. To the best of our knowledge, this finding is the first report in nanotoxicology.

Single-Step Synthesis of Atmospheric CO2 Sorbents through Radiation-Induced Graft Polymerization on Commercial-Grade Fabrics.

Primary amines form a key component of a well-studied mechanism for capturing carbon dioxide (CO2) from the atmosphere. This study comprises a single-step synthesis of a novel sorbent for CO2 by grafting monomers rich in primary amines to three commercial-grade fabrics: polyethylene terephthalate, high-density polyethylene and nylon 6. An initial evaluation of the sorbency of the chosen monomers, allylamine and butenylamine, qualitatively confirmed their ability to extract CO2 from the atmosphere. Six novel copolymers, comprised of each of the three fabrics grafted with one of each monomer, were synthesized using radiation-induced graft copolymerization through electron beam irradiation. All fabrics achieved greater grafting with butenylamine compared to allylamine, likely given the closer proximity of the primary amine to the radical on the latter's structure. Primary amines can stabilize radicals, preventing copolymerization reactions. Characterization of sorbency revealed that the majority of the grafted amines likely reacted to adsorb CO2. Therefore, the amount of amine grafted comprises the primary limiting factor on the sorbents' CO2 capacity.

Botulinum toxin type A inhibits sensory neuropeptide release in rat bladder models of acute injury and chronic inflammation.

OBJECTIVE: To determine the effect of botulinum toxin type A (BTX-A) on the release of the neuropeptides substance P (SP) and calcitonin gene-related peptide (CGRP) from isolated bladder preparations after acute injury with HCl and the induction of cyclophosphamide (CYP)-induced cystitis, as neurogenic inflammation has been increasingly identified in urological disorders such as interstitial cystitis. MATERIALS AND METHODS: Adult rats had either an intraperitoneal injection with CYP or saline over a 10-day period to induce chronic bladder inflammation, after which the bladder was harvested, or normal bladder explants were injured acutely with incubation (20 s) in HCl (0.4 m). To measure the effect of BTX-A on the release of neurotransmitters, harvested bladders were incubated in an organ bath containing BTX-A (10 U) or vehicle. Bladders were transferred to a subsequent bath (physiological saline) and incubated for 15 min, and the bathing medium analysed to measure neurotransmitter release, as determined by radioimmunoassay. Bladder specimens from sham treatment, controls and experimental rats were compared histologically. RESULTS: Acute injury with HCl caused a significantly greater release of both CGRP and SP release (1235 and 1655 pg/g, respectively) than in controls (183 and 449 pg/g, respectively; P < 0.001). This increase in neurotransmitter release was partly inhibited by exposure to BTX-A (870 and 1033 pg/g (P < 0.05 and <0.01). CYP-induced chronic inflammation caused significantly greater release of SP than in the controls (1060 and 605 pg/g, respectively; P < 0.005). Exposure to BTX-A partly inhibited the release of SP after CYP-induced cystitis (709 pg/g, P < 0.05). CONCLUSIONS: The application of BTX-A inhibits the release of sensory neurotransmitters from isolated bladder preparations in rat bladder models of both acute injury and chronic inflammation, suggesting a potential clinical benefit of BTX-A in the treatment of neurogenic inflammation.

Dental caries experience and association to risk indicators of remote rural populations.

BACKGROUND: Dental caries continues to be the most common infectious disease of childhood; however, it is no longer pandemic, but endemic in specific sectors of populations. Therefore, it is important to identify and target patients at risk of developing caries in order to develop specific preventive measures. AIM: This study aims to test dental caries risk indicators for significant associations with caries severity. DESIGN: Five separate, small, isolated rural villages in Mexico with varying degrees of caries prevalence were selected for this observational study. A total of 248 children were examined. Risk indicators were assessed via questionnaire and water and salt fluoride analysis. Caries severity was measured by the International Caries Detection and Assessment System (ICDAS-I). RESULTS: Prevalence of caries ranged from 95% to 100% for the five villages. Mean total DMFS (decayed, missing, or filled surfaces-permanent teeth) and dmfs (decayed, missing, or filled surfaces-primary teeth) scores ranged from 2.5 to 5.0 and from 11.3 to 16.9, respectively. Multivariable models showed age and drinking soda between meals to be significantly associated with DMFS, and drinking juice and being female were significantly associated with dmfs. CONCLUSION: DMFS and dmfs were high in each village, significantly different between villages, and associated with specific risk indicators.

Ertapenem-Induced Encephalopathy in a Patient With Normal Renal Function.

Drug-induced neurotoxicity is a rare adverse reaction associated with ertapenem. Encephalopathy is a type of neurotoxicity that is defined as a diffuse disease of the brain that alters brain function or structure. We report a patient with normal renal function who developed ertapenem-induced encephalopathy manifesting as altered mental status, hallucinations, and dystonic symptoms. The patient's symptoms improved dramatically following ertapenem discontinuation, consistent with case reports describing ertapenem neurotoxicity in renal dysfunction. Since clinical evidence strongly suggested ertapenem causality, we utilized the Naranjo Scale to estimate the probability of an adverse drug reaction to ertapenem. Our patient received a Naranjo Scale score of 7, suggesting a probable adverse drug reaction, with a reasonable temporal sequence to support our conclusion.

Use-dependent inhibition of P2X3 receptors by nanomolar agonist.

P2X3 receptors desensitize within 100 ms of channel activation, yet recovery from desensitization requires several minutes. The molecular basis for this slow rate of recovery is unknown. We designed experiments to test the hypothesis that this slow recovery is attributable to the high affinity (< 1 nM) of desensitized P2X3 receptors for agonist. We found that agonist binding to the desensitized state provided a mechanism for potent inhibition of P2X3 current. Sustained applications of 0.5 nM ATP inhibited > 50% of current to repetitive applications of P2X3 agonist. Inhibition occurred at 1000-fold lower agonist concentrations than required for channel activation and showed strong use dependence. No inhibition occurred without previous activation and desensitization. Our data are consistent with a model whereby inhibition of P2X3 by nanomolar [agonist] occurs by the rebinding of agonist to desensitized channels before recovery from desensitization. For several ATP analogs, the concentration required to inhibit P2X3 current inversely correlated with the rate of recovery from desensitization. This indicates that the affinity of the desensitized state and recovery rate primarily depend on the rate of agonist unbinding. Consistent with this hypothesis, unbinding of [32P]ATP from desensitized P2X3 receptors mirrored the rate of recovery from desensitization. As expected, disruption of agonist binding by site-directed mutagenesis increased the IC50 for inhibition and increased the rate of recovery.

Cause of death in HIV-infected patients in South Carolina (2005-2013).

The life span of persons with HIV has been greatly extended over the past 30 years due to novel therapies. In the developed world and urban settings, this results in a lifespan rivaling the lifespan of a person without HIV. A retrospective study was conducted on 459 patients of an urban, academic medical center who died between 2005 and 2013 in a medium-sized US city. Using the established Cause of Death Project (CoDe) protocol, we measured multiple factors including comorbidities, risk behaviours, contributing and underlying causes of death. This study is one of the few US-based studies using this validated protocol. Among the deaths, 25.9% were sudden and 15.2% were unexpected. Almost one-fifth were related to AIDS-related infections; 47.5% related to non-AIDS causes; with the remainder unknown. Statistically significant increases in CD4 counts and decreasing viral loads were observed over the study period. There were no statistically significant differences observed by HIV risk behaviour, race, gender, age at death, or on antiretrovirals at death. In support of the existing literature, improved HIV management appears to reduce the AIDS-related attributable death among patients observed in this study.

Kinetic Analysis of Membrane Potential Dye Response to NaV1.7 Channel Activation Identifies Antagonists with Pharmacological Selectivity against NaV1.5.

The NaV1.7 voltage-gated sodium channel is a highly valued target for the treatment of neuropathic pain due to its expression in pain-sensing neurons and human genetic mutations in the gene encoding NaV1.7, resulting in either loss-of-function (e.g., congenital analgesia) or gain-of-function (e.g., paroxysmal extreme pain disorder) pain phenotypes. We exploited existing technologies in a novel manner to identify selective antagonists of NaV1.7. A full-deck high-throughput screen was developed for both NaV1.7 and cardiac NaV1.5 channels using a cell-based membrane potential dye FLIPR assay. In assay development, known local anesthetic site inhibitors produced a decrease in maximal response; however, a subset of compounds exhibited a concentration-dependent delay in the onset of the response with little change in the peak of the response at any concentration. Therefore, two methods of analysis were employed for the screen: one to measure peak response and another to measure area under the curve, which would capture the delay-to-onset phenotype. Although a number of compounds were identified by a selective reduction in peak response in NaV1.7 relative to 1.5, the AUC measurement and a subsequent refinement of this measurement were able to differentiate compounds with NaV1.7 pharmacological selectivity over NaV1.5 as confirmed in electrophysiology.

Choosing safe dispersing media for C60 fullerenes by using cytotoxicity tests on the bacterium Escherichia coli.

Assessment of C(60) nanotoxicity requires a variety of strategies for dispersing it into biological systems. Our objective was to determine organic solvent/surfactant combinations suitable for this purpose. We used Escherichia coli (ATCC# 25254) to determine the cytotoxicity of C(60) in solvents at concentrations up to 100 ppm. In this preliminary study we hypothesized that C(60) toxicity is directly correlated with its degree of dispersion in solution and that more solubilizing solvents induce higher toxicity. Test solvent concentration (1%) and Tween 80 (0.04%) were based on E. coli viability assay. Sonication was used to further enhance C(60) dispersal. The end-point response was measured with viability (in terms of LC(50)) and general metabolic activity (in terms of IC(50)) of E. coli cultures after exposure. The ultimate goal was to select safe dispersing media and enrich the database of C(60) nanotoxicity for NanoQuantitative-Structure-Activity-Relationship (NanoQSAR) applications. LC(50) range was 30 ppm to >400 ppm. IC(50) followed the trend. Among the six solvent combinations, DMSO combined with Tween 80 was the optimum combination for defining a dose-response relationship for assessing its toxicity to E. coli. However, N,N-dimethylformamide has the greatest potential to be a safe solvent for C(60) applications based upon its biocompatibility. Solvent solubility alone could not account for the cytotoxicity observed in this study.