In vivo screening for toxicity-modulating drug interactions identifies antagonism that protects against ototoxicity in zebrafish.

Introduction: Ototoxicity is a debilitating side effect of over 150 medications with diverse mechanisms of action, many of which could be taken concurrently to treat multiple conditions. Approaches for preclinical evaluation of drug-drug interactions that might impact ototoxicity would facilitate design of safer multi-drug regimens and mitigate unsafe polypharmacy by flagging combinations that potentially cause adverse interactions for monitoring. They may also identify protective agents that antagonize ototoxic injury. Methods: To address this need, we have developed a novel workflow that we call Parallelized Evaluation of Protection and Injury for Toxicity Assessment (PEPITA), which empowers high-throughput, semi-automated quantification of ototoxicity and otoprotection in zebrafish larvae via microscopy. We used PEPITA and confocal microscopy to characterize in vivo the consequences of drug-drug interactions on ototoxic drug uptake and cellular damage of zebrafish lateral line hair cells. Results and discussion: By applying PEPITA to measure ototoxic drug interaction outcomes, we discovered antagonistic interactions between macrolide and aminoglycoside antibiotics that confer protection against aminoglycoside-induced damage to lateral line hair cells in zebrafish larvae. Co-administration of either azithromycin or erythromycin in zebrafish protected against damage from a broad panel of aminoglycosides, at least in part via inhibiting drug uptake into hair cells via a mechanism independent from hair cell mechanotransduction. Conversely, combining macrolides with aminoglycosides in bacterial inhibition assays does not show antagonism of antimicrobial efficacy. The proof-of-concept otoprotective antagonism suggests that combinatorial interventions can potentially be developed to protect against other forms of toxicity without hindering on-target drug efficacy.

Ten simple rules for managing laboratory information.

Information is the cornerstone of research, from experimental (meta)data and computational processes to complex inventories of reagents and equipment. These 10 simple rules discuss best practices for leveraging laboratory information management systems to transform this large information load into useful scientific findings.

In vivo screening for toxicity-modulating drug interactions identifies antagonism that protects against ototoxicity in zebrafish.

Ototoxicity is a debilitating side effect of over 150 medications with diverse mechanisms of action, many of which could be taken concurrently to treat multiple conditions. Approaches for preclinical evaluation of drug interactions that might impact ototoxicity would facilitate design of safer multi-drug regimens and mitigate unsafe polypharmacy by flagging combinations that potentially cause adverse interactions for monitoring. They may also identify protective agents that antagonize ototoxic injury. To address this need, we have developed a novel workflow that we call Parallelized Evaluation of Protection and Injury for Toxicity Assessment (PEPITA), which empowers high-throughput, semi-automated quantification of ototoxicity and otoprotection in zebrafish larvae. By applying PEPITA to characterize ototoxic drug interaction outcomes, we have discovered antagonistic interactions between macrolide and aminoglycoside antibiotics that confer protection against aminoglycoside-induced damage to lateral line hair cells in zebrafish larvae. Co-administration of either azithromycin or erythromycin in zebrafish protected against damage from a broad panel of aminoglycosides, at least in part via inhibiting drug uptake into hair cells via a mechanism independent from hair cell mechanotransduction. Conversely, combining macrolides with aminoglycosides in bacterial inhibition assays does not show antagonism of antimicrobial efficacy. The proof-of-concept otoprotective antagonism suggests that combinatorial interventions can potentially be developed to protect against other forms of toxicity without hindering on-target drug efficacy.

Unveiling the underestimated direct emissions of nitrous acid (HONO).

Gaseous nitrous acid (HONO) is a critical source of hydroxyl radicals (OH) in the troposphere. While both direct and secondary sources contribute to atmospheric HONO, direct emissions have traditionally been considered minor contributors. In this study, we developed δ15N and δ18O isotopic fingerprints to identify six direct HONO emission sources and conducted a 1-y case study on the isotopic composition of atmospheric HONO at rural and urban sites. Interestingly, we identified that livestock farming is a previously overlooked direct source of HONO and determined its HONO to ammonia (NH3) emission ratio. Additionally, our results revealed that spatial and temporal variations in atmospheric HONO isotopic composition can be partially attributed to direct emissions. Through a detailed HONO budget analysis incorporating agricultural sources, we found that direct HONO emissions accounted for 39~45% of HONO production in rural areas across different seasons. The findings were further confirmed by chemistry transport model simulations, highlighting the significance of direct HONO emissions and their impact on air quality in the North China Plain. These findings provide compelling evidence that direct HONO emissions play a more substantial role in contributing to atmospheric HONO than previously believed. Moreover, the δ15N and δ18O isotopic fingerprints developed in this study may serve as a valuable tool for further research on the atmospheric chemistry of reactive nitrogen gases.

A review on guided-ultrasonic-wave-based structural health monitoring: From fundamental theory to machine learning techniques.

The development of structural health monitoring (SHM) techniques is of great importance to improve the structural efficiency and safety. With advantages of long propagation distances, high damage sensitivity, and economic feasibility, guided-ultrasonic-wave-based SHM is recognized as one of the most promising technologies for large-scale engineering structures. However, the propagation characteristics of guided ultrasonic waves in in-service engineering structures are highly complex, which results in difficulties in developing precise and efficient signal feature mining methods. The damage identification efficiency and reliability of existing guided ultrasonic wave methods cannot meet engineering requirements. With the development of machine learning (ML), numerous researchers have proposed improved ML methods that can be incorporated into guided ultrasonic wave diagnostic techniques for SHM of actual engineering structures. To highlight their contributions, this paper provides a state-of-the-art overview of the guided-wave-based SHM techniques enabled by ML methods. Accordingly, multiple stages required for ML-based guided ultrasonic wave techniques are discussed, including guided ultrasonic wave propagation modeling, guided ultrasonic wave data acquisition, wave signal pre-processing, guided wave data-based ML modeling, and physics-based ML modeling. By placing ML methods in the context of the guided-wave-based SHM for actual engineering structures, this paper also provides insights into future prospects and research strategies.

The Mycobacterium tuberculosis protein O-phosphorylation landscape.

Bacterial phosphosignalling has been synonymous with two-component systems and their histidine kinases, but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignalling enzymes in eukaryotes but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria is untested. Here we explored the global signalling capacity of the STPKs in Mtb using a panel of STPK loss-of-function and overexpression strains combined with mass spectrometry-based phosphoproteomics. A deep phosphoproteome with >14,000 unique phosphosites shows that O-phosphorylation in Mtb is a vastly underexplored protein modification that affects >80% of the proteome and extensively interfaces with the transcriptional machinery. Mtb O-phosphorylation gives rise to an expansive, distributed and cooperative network of a complexity that has not previously been seen in bacteria and that is on par with eukaryotic phosphosignalling networks. A resource of >3,700 high-confidence direct substrate-STPK interactions and their transcriptional effects provides signalling context for >80% of Mtb proteins and allows the prediction and assembly of signalling pathways for mycobacterial physiology.

CsPbBr3-Based Nanostructures for Room-Temperature Sensing of Volatile Organic Compounds.

All-inorganic halide perovskites, as a dominant member of the perovskite family, have been proven to be excellent semiconductors due to the great successes for solar cells, light-emitting diodes, photodetectors, and nanocrystal photocatalysts. Despite the remarkable advances in those fields, there are few research studies focusing on gas and humidity-sensing performances, especially for pure CsPbBr3 and heterogeneous CsPbBr3@MoS2 composites. Here, we first report a valuable CsPbBr3 sensor prepared by electrospinning, and the excellent gas sensing performances are investigated. The CsPbBr3 sensor can quickly and effectively detect ethanolamine at room temperature. The response time is only 16 s, and the response to 100 ppm ethanolamine is as high as 29.87, besides the excellent repeatability and good stability. The theoretical detection limit is estimated to be 21 ppb. Furthermore, considering the irreplaceable role of heterostructures in regulating the electronic structure and supporting rich reaction boundaries, we also actively explored the EA sensitivity of inorganic CsPbBr3-based heterogeneous composites CsPbBr3@MoS2. At the same time, the roles of the critical capping agents OA and OAm are systematically investigated. This work demonstrates the great potential of all-inorganic halide perovskites in promising volatile organic compound detection.

Early alveolar macrophage response and IL-1R-dependent T cell priming determine transmissibility of Mycobacterium tuberculosis strains.

Mechanisms underlying variability in transmission of Mycobacterium tuberculosis strains remain undefined. By characterizing high and low transmission strains of M.tuberculosis in mice, we show here that high transmission M.tuberculosis strain induce rapid IL-1R-dependent alveolar macrophage migration from the alveolar space into the interstitium and that this action is key to subsequent temporal events of early dissemination of bacteria to the lymph nodes, Th1 priming, granulomatous response and bacterial control. In contrast, IL-1R-dependent alveolar macrophage migration and early dissemination of bacteria to lymph nodes is significantly impeded in infection with low transmission M.tuberculosis strain; these events promote the development of Th17 immunity, fostering neutrophilic inflammation and increased bacterial replication. Our results suggest that by inducing granulomas with the potential to develop into cavitary lesions that aids bacterial escape into the airways, high transmission M.tuberculosis strain is poised for greater transmissibility. These findings implicate bacterial heterogeneity as an important modifier of TB disease manifestations and transmission.

Multi-Mode Ultrasonic Guided Waves Based Damage Detection in L-Bars with Asymmetric Cross-Section with Sum of Multiple Signals Method.

Bars are significant load-carrying components in engineering structures. In particular, L-bars are typical structural components commonly used in truss structures and have typical irregular asymmetric cross-sections. To ensure the safety of load-carrying bars, much research has been done for non-destructive testing (NDT). Ultrasonic guided waves have been widely applied in various NDT techniques for bars as a result of the long-range propagation, low attenuation, and high sensitivity to damages. Though good for inspection of ultrasonic guided waves in symmetric cross-section bar-like structures, the application in asymmetric ones lacks further research. Moreover, traditional damage detection in bars using ultrasonic guided waves usually depends on a single-mode at a lower frequency with lower sensitivity and accuracy. To make full use of all frequencies and modes, a multi-mode characteristic-based damage detection method is presented with the sum of multiple signals (SoM) strategy for L-bars with asymmetric cross-section. To control the desired mode in multi-mode ultrasonic guided waves, excitation optimization and weighted gathering are carried out by the analysis of the semi-analytical finite element (SAFE) method and the normal mode expansion (NME) method. An L-bar example with the asymmetric cross-section of 35 mm × 20 mm × 3 mm is used to specialize the proposed method, and some finite element (FE) models have been simulated to validate the mode control. In addition, one PZT is applied as a contrast in order to validate the multielement mode control. Then, more FE simulations experiments for damage detection have been performed to validate the damage detection method and verify the improvement in detection accuracy and damage sensitivity.

Experimental and Computational Workflow for RNA Sequencing in Mycobacterium tuberculosis : From Total RNA to Differentially Expressed Genes.

RNA sequencing (RNAseq) in bacteria has become a transformative tool for many applications, including the identification of mechanisms that contribute to pathogenesis, environmental adaptation, and drug response. The kinds of analysis outputs achievable from RNA-seq depend heavily on several key technical parameters during the sample preparation, sequencing, and data processing steps. In this chapter, we will describe the process of preparing Mycobacterium tuberculosis samples into sequencing libraries, selecting the appropriate sequencing platform, and performing data processing compatible with gene expression quantification. We will also discuss how each parameter could affect outcomes. The protocols described below produce consistently high yields. This chapter should inform on the technical considerations that impact sequencing output and enable the reader to decide on the best parameters to implement based on their own experimental goals.

Whole-Genome Sequence of a Strain of Brucella melitensis Isolated from a Patient with Swelling of the Right Testicle in Inner Mongolia, China.

This report describes the isolation, sequencing, and annotation of Ws20160810, which was isolated from a blood sample from a brucellosis patient suffering from swelling of the right testicle in the Inner Mongolia Autonomous Region, China. The genome size was 3,244,234 bp with a 57.23% GC content, 3,294 coding DNA sequences (CDSs), 55 tRNAs, 5 rRNAs (5S [n = 2], 16S [n = 1], and 23S [n = 2]), and 3 small RNAs (sRNAs).

Multishelled NiO/NiCo2O4 hollow microspheres derived from bimetal-organic frameworks as high-performance sensing material for acetone detection.

Recently, tremendous research interest was stimulated to obtain advanced function materials with hierarchical structure and tailored chemical composition from metal-organic frameworks (MOFs) based precursors. Herein, Bimetal-organic frameworks of Ni-Co-BTC solid microspheres synthesized through hydrothermal method were acted as template to induce multishelled NiO/NiCo2O4 hollow microspheres by annealing treatment. When evaluated as gas sensing material, the optimal hybrid of NiO/NiCo2O4 (the molar ration of NiCo=1.5) multishelled hollow microspheres endowed a high sensitivity (17.86) to 100 ppm acetone with rapid response/recovery time (11/13 s) under low working temperature (160 °C) and the low detection limit reached 25 ppb. The enhanced mechanism was originated from the following aspects: the multishelled hollow architecture provided efficient diffusion path for gas molecules and sufficient active site for gas sensing reaction; the nanoscale p-p heterojunction created at NiO and NiCo2O4 nanoparticles interface amplified the resistance variation by tuning the potential barrier; the potent combination of the "chemical catalytic" effect of NiO and the "electrical catalytic" effect of NiCo2O4 improved the selective acetone detection.

Transcriptional regulator-induced phenotype screen reveals drug potentiators in Mycobacterium tuberculosis.

Transposon-based strategies provide a powerful and unbiased way to study the bacterial stress response1-8, but these approaches cannot fully capture the complexities of network-based behaviour. Here, we present a network-based genetic screening approach: the transcriptional regulator-induced phenotype (TRIP) screen, which we used to identify previously uncharacterized network adaptations of Mycobacterium tuberculosis to the first-line anti-tuberculosis drug isoniazid (INH). We found regulators that alter INH susceptibility when induced, several of which could not be identified by standard gene disruption approaches. We then focused on a specific regulator, mce3R, which potentiated INH activity when induced. We compared mce3R-regulated genes with baseline INH transcriptional responses and implicated the gene ctpD (Rv1469) as a putative INH effector. Evaluating a ctpD disruption mutant demonstrated a previously unknown role for this gene in INH susceptibility. Integrating TRIP screening with network information can uncover sophisticated molecular response programs.

Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease.

Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, Mycobacterium tuberculosis, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of M. tuberculosis isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.

Molecular epidemiology of Brucella abortus strains from cattle in Inner Mongolia, China.

Although the prevalence of brucellosis in Inner Mongolia Autonomous Region currently remains high, data available on the epidemiological of circulating Brucella abortus strains were limited. A total of 75 isolates obtained from cattle, sheep, and humans were analysed using both the classical method and multiple locus variable-number tandem repeat analysis (MLVA). There are at least three B. abortus biovars (1, 3 and 6) in this region, and B. abortus biovar 3 is the predominant one. Ten known MLVA-11 genotypes were identified, of which five genotypes (72, 75, 78, 82 and 210) were shared among strains from this study and others previously collected in two to seven different nations, suggesting that this population has multiple geographic origins. An MLVA-16 assay sorted the 75 B. abortus strains into two groups (I and II), 5 clusters (A-E) and 44 genotypes (GT1-44), with 26 unique genotypes represented by single isolates, indicating that these B. abortus brucellosis cases were not directly epidemiologically related. The remaining 18 shared genotypes (among a total of 47 isolates) were represented by two to eight isolates, suggesting that there were epidemiologically related pathogens from each shared genotype among the cases. Importantly, the cluster B1 branch including 22 cluster isolates with identical or similar genotypes confirmed the occurrence of a concentrated outbreak epidemic in the eastern region during 1988-1995. This work will contribute to better understanding of B. abortus brucellosis epidemiology in Inner Mongolia.

Containing the spread of coronavirus disease 2019 (COVID-19): Meteorological factors and control strategies.

The novel coronavirus disease 2019 (COVID-19) has spread globally and the meteorological factors vary greatly across the world. Understanding the effect of meteorological factors and control strategies on COVID-19 transmission is critical to contain the epidemic. Using individual-level data in mainland China, Hong Kong, and Singapore, and the number of confirmed cases in other regions, we explore the effect of temperature, relative humidity, and control measures on the spread of COVID-19. We find that high temperature mitigates the transmission of the disease. High relative humidity promotes COVID-19 transmission when temperature is low, but tends to reduce transmission when temperature is high. Implementing classical control measures can dramatically slow the spread of the disease. However, due to the occurrence of pre-symptomatic infections, the effect of the measures to shorten treatment time is markedly reduced and the importance of contact quarantine and social distancing increases.

Brucella melitensis, a latent "travel bacterium," continual spread and expansion from Northern to Southern China and its relationship to worldwide lineages.

Brucellosis caused by Brucella melitensis is considered to be one of the most important zoonotic diseases in China. In this study, Conventional bio-typing, MLVA (multiple locus variable-number tandem repeat analysis), and WGS (whole-genome sequencing)-SNP (single nucleotide polymorphism) were used to study the genetic similarity of B. melitensis in northern and southern China and analyze its relationship with worldwide lineages. Currently, the distribution of species/biovars of B. melitensis has obviously changed, and B. melitensis has become the dominant species in southern regions of China. Strains from the southern had a common geographic origin with strains from the northern. Many MLVA-16 events were shared in the genotypes of the southern and northern strains, suggest that genotypic movement occurred from north to south. Based on WGS-SNP analysis, strains from different provinces were closely related and may have descended from one common ancestor, suggests that the southern strains originated from northern China. These data indicate that B. melitensis is a latent "travel bacterium" that spread and expanded from North China to South China. Moreover, B. melitensis strains from China are also genetically related to strains from other Asian regions (Kazakhstan, Russia, Mongolia, and India). The movement of infected sheep and their products requires control.

Rapidly Correcting Frameshift Mutations in the Mycobacterium tuberculosis orn Gene Produce Reversible Ethambutol Resistance and Small-Colony-Variant Morphology.

We have identified a previously unknown mechanism of reversible high-level ethambutol (EMB) resistance in Mycobacterium tuberculosis that is caused by a reversible frameshift mutation in the M. tuberculosisorn gene. A frameshift mutation in orn produces the small-colony-variant (SCV) phenotype, but this mutation does not change the MICs of any drug for wild-type M. tuberculosis However, the same orn mutation in a low-level EMB-resistant double embB-aftA mutant (MIC = 8 µg/ml) produces an SCV with an EMB MIC of 32 µg/ml. Reversible resistance is indistinguishable from a drug-persistent phenotype, because further culture of these orn-embB-aftA SCV mutants results in rapid reversion of the orn frameshifts, reestablishing the correct orn open reading frame, returning the culture to normal colony size, and reversing the EMB MIC back to that (8 µg/ml) of the parental strain. Transcriptomic analysis of orn-embB-aftA mutants compared to wild-type M. tuberculosis identified a 27-fold relative increase in the expression of embC, which is a cellular target for EMB. Expression of embC in orn-embB-aftA mutants was also increased 5-fold compared to that in the parental embB-aftA mutant, whereas large-colony orn frameshift revertants of the orn-embB-aftA mutant had levels of embC expression similar to that of the parental embB-aftA strain. Reversible frameshift mutants may contribute to a reversible form of microbiological drug resistance in human tuberculosis.

Investigation of thermo-acoustoelastic guided waves by semi-analytical finite element method.

Guided waves are sensitive to variations in propagation environments. Many recent studies have focused on the uniform thermal effect on Lamb waves. However, there is little research on the thermal effect in a more complex situation, such as a nonuniform thermal effect and wave propagation in an arbitrary cross-section. In this study, a thermo-acoustoelastic theory combined with the semi-analytical finite element (TAE-SAFE) method is proposed to investigate both uniform and nonuniform thermal effects on acoustoelastic guided wave propagation. In the TAE-SAFE method, effective thermo-acoustoelastic constants including third-order elastic constants are employed. Then, an acoustoelastic wave equation of the thermal effect is formulated by Hamilton's principle and computed by the semi-analytical finite element (SAFE) method. The phase velocity, group velocity, velocity thermal sensitivity, and displacement mode shape shift can be extracted by the proposed method. To validate this method, numerical results of Lamb waves in an aluminum plate subjected to a uniform thermal effect are compared with the results of a previous theoretical analysis. The results show computational veracity and validity. Two typical cases are investigated: (1) an isotropic aluminum plate under a linear temperature gradient condition; (2) a uniform temperature case in a rail track with a constant irregular cross-section. This study provides an effective numerical method to analyze thermo-acoustoelastic guided wave propagation.