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At least 577 records · Page 32

Rapid detection of mexX in Pseudomonas aeruginosa based on CRISPR-Cas13a coupled with recombinase polymerase amplification

The principal pathogen responsible for chronic urinary tract infections, immunocompromised hosts, and cystic fibrosis patients is Pseudomonas aeruginosa , which is difficult to eradicate. Due to the extensive use of antibiotics, multidrug-resistant P. aeruginosa has evolved, complicating clinical therapy. Therefore, a rapid and efficient approach for detecting P. aeruginosa strains and their resistance genes is necessary for early clinical diagnosis and appropriate treatment. This study combines recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats-association protein 13a (CRISPR-Cas13a) to establish a one-tube and two-step reaction systems for detecting the mexX gene in P. aeruginosa . The test times for one-tube and two-step RPA-Cas13a methods were 5 and 40 min (including a 30 min RPA amplification reaction), respectively. Both methods outperform Quantitative Real-time Polymerase Chain Reactions (qRT-PCR) and traditional PCR. The limit of detection (LoD) of P. aeruginosa genome in one-tube and two-step RPA-Cas13a is 10 aM and 1 aM, respectively. Meanwhile, the designed primers have a high specificity for P. aeruginosa mexX gene. These two methods were also verified with actual samples isolated from industrial settings and demonstrated great accuracy. Furthermore, the results of the two-step RPA-Cas13a assay could also be visualized using a commercial lateral flow dipstick with a LoD of 10 fM, which is a useful adjunt to the gold-standard qRT-PCR assay in field detection. Taken together, the procedure developed in this study using RPA and CRISPR-Cas13a provides a simple and fast way for detecting resistance genes.

Zhu, Xiao-Xuan↗

A Rapid Compression Machine Study of 2-Phenylethanol Autoignition at Low-To-Intermediate Temperatures

To meet the increasing anti-knocking quality demand of boosted spark-ignition engines, fuel additives are considered an effective approach to tailor fuel properties for satisfying the performance requirements. Thus, screening/developing bio-derived fuel additives that are best-suited for advanced spark-ignition engines has become a significant task. 2-Phenylethanol (2-PE) is an attractive candidate that features high research octane number, high octane sensitivity, low vapor pressure, and high energy density. Recognizing that the low temperature autoignition chemistry of 2-PE is not well understood and the need for fundamental experimental data at engine-relevant conditions, rapid compression machine (RCM) experiments are therefore conducted herein to measure ignition delay times (IDTs) of 2-PE in air over a wide range of conditions to fill this fundamental void. These newly acquired IDT data at low-to-intermediated temperatures, equivalence ratios of 0.35–1.5, and compressed pressures of 10–40 bar are then used to validate the 2-PE model developed by Shankar et al. (2017). It is found that this literature model greatly overpredicts the current RCM data. The comparison of experimental and simulated results also provides insights into 2-PE autoignition behaviors at varying conditions. Further chemical kinetic analyses demonstrate that the absence of the O2-addition pathway of β-R. radical in the 2-PE model of Shankar et al. (2017) could account for the model discrepancies observed at low-to-intermediated temperatures.

Fang, Ruozhou (ORCID:0000000348315100)↗

Phenothiazines Rapidly Induce Laccase Expression and Lignin-Degrading Properties in the White-Rot Fungus Phlebia radiata

Phlebia radiata is a widespread white-rot basidiomycete fungus with significance in diverse biotechnological applications due to its ability to degrade aromatic compounds, xenobiotics, and lignin using an assortment of oxidative enzymes including laccase. In this work, a chemical screen with 480 conditions was conducted to identify chemical inducers of laccase expression in P. radiata. Among the chemicals tested, phenothiazines were observed to induce laccase activity in P. radiata, with promethazine being the strongest laccase inducer of the phenothiazine-derived compounds examined. Secretomes produced by promethazine-treated P. radiata exhibited increased laccase protein abundance, increased enzymatic activity, and an enhanced ability to degrade phenolic model lignin compounds. Transcriptomics analyses revealed that promethazine rapidly induced the expression of genes encoding lignin-degrading enzymes, including laccase and various oxidoreductases, showing that the increased laccase activity was due to increased laccase gene expression. Finally, the generality of promethazine as an inducer of laccases in fungi was demonstrated by showing that promethazine treatment also increased laccase activity in other relevant fungal species with known lignin conversion capabilities including Trametes versicolor and Pleurotus ostreatus.

59 BASIC BIOLOGICAL SCIENCES↗

Simple and Effective Squash-PCR for Rapid Genotyping of Industrial Microalgae

Microalgae are recognized for their versatility in providing renewable energy, biopharmaceuticals, and nutraceuticals, attributed to their sustainable, renewable, and cost-effective nature. Genetic engineering has proven highly effective in enhancing microalgae production. PCR-based genotyping is the primary method for screening genetically transformed microalgae cells. Recently, we developed a novel PCR method, namely Squash-PCR, and employed it for the molecular analysis of industrially important fungi and yeasts. In this study, we successfully implemented the Squash-PCR technique in 12 industrially significant algae species. This approach offers a quick and reliable means of obtaining DNA templates directly from squashed algal cells, eliminating the need for time-consuming and labor-intensive cultivation and genomic DNA extraction steps. Our results demonstrate the effectiveness of Squash-PCR in detecting and characterizing target genes of interest in 12 different algae species. Overall, this study establishes the Squash-PCR method as a valuable tool for molecular studies in algae, enabling researchers to rapidly screen and manipulate genetic traits in diverse algal species.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid Assessment of Sulfate Resistance in Mortar and Concrete

Extensive research has been conducted on the sulfate attack of concrete structures; however, the need to adopt the use of more sustainable materials is driving a need for a quicker test method to assess sulfate resistance. This work presents accelerated methods that can reduce the time required for assessing the sulfate resistance of mixtures by 70%. Class F fly ash has historically been used in concrete mixtures to improve sulfate resistance. However, environmental considerations and the evolving energy industry have decreased its availability, requiring the identification of economically viable and environmentally friendly alternatives to fly ash. Another challenge in addressing sulfate attack durability issues in concrete is that the standard sulfate attack test (ASTM C1012) is time-consuming and designed for only standard mortars (not concrete mixtures). To expedite the testing process, accelerated testing methods for both mortar and concrete mixtures were adopted from previous work to further the development of the accelerated tests and to assess the feasibility of testing the sulfate resistance of mortar and concrete mixtures rapidly. This study also established criteria for interpreting sulfate resistance for each of the test methods used in this work. A total of 14 mortar mixtures and four concrete mixtures using two types of Portland cement (Type I and Type I/II) and various supplementary cementitious materials (SCMs) were evaluated in this study. The accelerated testing methods significantly reduced the evaluation time from 12 months to 21 days for mortar mixtures and from 6 months to 56 days for concrete mixtures. The proposed interpretation method for mortar accelerated test results showed acceptable consistency with the ACI 318-19 interpretations for ASTM C1012 results. The interpretation methods proposed for the two concrete sulfate attack tests demonstrated excellent consistency with the ASTM C1012 results from mortar mixtures with the same cementitious materials combinations. Metakaolin was shown to improve sulfate resistance for both mortar and concrete mixtures, while silica fume and natural pozzolan had a limited impact. Using 15% metakaolin in mortar or concrete mixtures with Type I/II cement provided the best sulfate resistance.

Chemistry↗

Stamping Nanoparticles onto the Electrode for Rapid Electrochemical Analysis in Microfluidics

Electrochemical analysis is an efficient way to study various materials. However, nanoparticles are challenging due to the difficulty in fabricating a uniform electrode containing nanoparticles. We developed novel approaches to incorporate nanoparticles as a working electrode (WE) in a three-electrode microfluidic electrochemical cell. Specifically, conductive epoxy was used as a medium for direct application of nanoparticles onto the electrode surface. Three approaches in this work were illustrated, including sequence stamping, mix stamping, and droplet stamping. Shadow masking was used to form the conductive structure in the WE surface on a thin silicon nitride (SiN) membrane. Two types of nanomaterials, namely cerium oxide (CeO2) and graphite, were chosen as representative nanoparticles. The as-fabricated electrodes with attached particles were characterized using atomic force microscopy (AFM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Electrochemical analysis was performed to verify the feasibility of these nanoparticles as electrodes. Nanomaterials can be quickly assessed for their electrochemical properties using these new electrode fabrication methods in a microfluidic cell, offering a passport for rapid nanomaterial electrochemical analysis in the future.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Propidium Monoazide (PMAxx)-Recombinase Polymerase Amplification Exo (RPA Exo) Assay for Rapid Detection of Burkholderia cepacia Complex in Chlorhexidine Gluconate (CHX) and Benzalkonium Chloride (BZK) Solutions

Both sterile and non-sterile pharmaceutical products, which include antiseptics, have been recalled due to Burkholderia cepacia complex (BCC) contamination. Therefore, minimizing the frequency of outbreaks may be conducive to the development of a quick and sensitive approach that can distinguish between live and dead loads of BCC. We have assessed an exo probe-based recombinase polymerase amplification (RPA) with 10 µM propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in various concentrations of antiseptics (i.e., chlorhexidine gluconate (CHX) and benzalkonium chloride (BZK) solutions) after 24 h. The optimized assay conducted using a set of primer–probes targeting gbpT was performed at 40 °C for 20 min and shows a detection limit of 10 pg/µL of genomic DNA from B. cenocepacia J2315, equivalent to 10 4 colony-forming units (CFU/mL). The specificity of a newly designed primer and probe was 80% (20 negatives out of 25). The readings for total cells (i.e., without PMAxx) from 200 µg/mL CHX using PMAxx-RPA exo assay was 310 relative fluorescence units (RFU), compared to 129 RFU with PMAxx (i.e., live cells). Furthermore, in 50–500 µg/mL BZK-treated cells, a difference in the detection rate was observed between the PMAxx-RPA exo assay in live cells (130.4–459.3 RFU) and total cells (207.82–684.5 RFU). This study shows that the PMAxx-RPA exo assay appears to be a valid tool for the simple, rapid and presumptive detection of live BCC cells in antiseptics, thereby ensuring the quality and safety of pharmaceutical products.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid and Ultrasensitive Short-Chain PFAS (GenX) Detection in Water via Surface-Enhanced Raman Spectroscopy with a Hierarchical Nanofibrous Substrate

GenX, the trade name of hexafluoropropylene oxide dimer acid (HFPO-DA) and its ammonium salt, is a short-chain PFAS that has emerged as a substitute for the legacy PFAS perfluorooctanoic acid (PFOA). However, GenX has turned out to be more toxic than people originally thought. In order to monitor and regulate water quality according to recently issued drinking water standards for GenX, rapid and ultrasensitive detection of GenX is urgently needed. For the first time, this study reports ultrasensitive (as low as 1 part per billion (ppb)) and fast detection (in minutes) of GenX in water via surface-enhanced Raman spectroscopy (SERS) using a hierarchical nanofibrous SERS substrate, which was prepared by assembling ~60 nm Ag nanoparticles on electrospun nylon-6 nanofibers through a “hot start” method. The findings in this research highlight the potential of the engineered hierarchical nanofibrous SERS substrate for enhanced detection of short-chain PFASs in water, contributing to the improvement of environmental monitoring and management strategies for PFASs.

Ismail, Ali K. (ORCID:0009000005987973)↗

Inactivation of Human Coronavirus by FATHHOME’s Dry Sanitizer Device: Rapid and Eco-Friendly Ozone-Based Disinfection of SARS-CoV-2

The pandemic of SARS-CoV-2/COVID-19 was reported in December 2019 in Wuhan, China. Pertaining to its high transmissibility and wide host adaptability, this unique human coronavirus spread across the planet inflicting 115 million people and causing 2.5 million deaths (as of March 3rd, 2021). Limited or negligible pre-existing immunity to multiple SARS-CoV-2 variants has resulted in severe morbidity and mortality worldwide, as well as a record-breaking surge in the use of medical-surgical supplies and personal protective equipment. In response to the global need for effective sterilization techniques, this study evaluated the virucidal efficacy of FATHHOME’s self-contained, ozone-based dry-sanitizing device, by dose and time response assessment. We tested inactivation of human coronavirus, HCoV-OC43, a close genetic model of SARS-CoV-2, on porous (N95 filtering facepiece respirator/FFR) and nonporous (glass) surfaces. We started our assays with 20 ppm-10 min ozone exposure, and effectively reduced 99.8% and 99.9% of virus from glass and N95 FFR surfaces, respectively. Importantly, the virus was completely inactivated, below the detection limit (over 6-log10 reduction) with 25 ppm-15 min ozone exposure on both tested surfaces. As expected, a higher ozone exposure (50 ppm-10 min) resulted in faster inactivation of HCoV-OC43 with 100% inactivation from both the surfaces, with no residual ozone present after completion of the 5-min post exposure recapture cycle and no measurable increase in ambient ozone levels. These results confirmed that FATHHOME’s device is suitable for rapid decontamination of SARS-CoV-2- from worn items, frequently touched items, and PPE including N95 FFRs, face shields, and other personal items. View Full-Text

59 BASIC BIOLOGICAL SCIENCES↗

Rapid Spaceborne Mapping of Wildfire Retardant Drops for Active Wildfire Management

Aerial application of fire retardant is a critical tool for managing wildland fire spread. Retardant applications are carefully planned to maximize fire line effectiveness, improve firefighter safety, protect high-value resources and assets, and limit environmental impact. However, topography, wind, visibility, and aircraft orientation can lead to differences between planned drop locations and the actual placement of the retardant. Information on the precise placement and areal extent of the dropped retardant can provide wildland fire managers with key information to (1) adaptively manage event resources, (2) assess the effectiveness of retardant slowing or stopping fire spread, (3) document location in relation to ecologically sensitive areas; and perform or validate cost-accounting for drop services. This study uses Sentinel-2 satellite data and commonly used machine learning classifiers to test an automated approach for detecting and mapping retardant application. We show that a multiclass model (retardant, burned, unburned, and cloud artifact classes) outperforms a single-class retardant model and that image differencing (post-application minus pre-application) outperforms single-image models. Compared to the random forest and support vector machine, the gradient boosting model performed the best with an overall accuracy of 0.88 and an F1 Score of 0.76 for fire retardant, though results were comparable for all three models. Our approach maps the full areal extent of the dropped retardant within minutes of image availability, rather than linear representations currently mapped by aerial GPS surveys. The development of this capability allows for the rapid assessment of retardant effectiveness and documentation of placement in relation to sensitive environments.

54 ENVIRONMENTAL SCIENCES↗

Machine Learning Using Rapidity-Mass Matrices for Event Classification Problems in HEP

In this work, supervised artificial neural networks (ANN) with rapidity–mass matrix (RMM) inputs are studied using several Monte Carlo event samples for various pp collision processes. The study shows the usability of this approach for general event classification problems. The proposed standardization of the ANN feature space can simplify searches for signatures of new physics at the Large Hadron Collider (LHC) when using machine learning techniques. In particular, we illustrate how to improve signal-over-background ratios in the search for new physics, how to filter out Standard Model events for model-agnostic searches, and how to separate gluon and quark jets for Standard Model measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measurements of J/ ψ Production vs. Event Multiplicity in Forward Rapidity in p + p Collisions in the PHENIX Experiment

J / Ψ, a charmonium bound state made of a charm and an anti-charm quark, was discovered in the 1970s and confirmed the quark model. Because the mass of charm quarks is significantly above the quantum chromodynamics (QCD) scale Λ QCD , charmonia are considered excellent probes to test perturbative quantum chromodynamics (pQCD) calculations. In recent decades, they have been studied extensively at different high-energy colliders. However, their production mechanisms, which involve multiple scales, are still not very well understood. Recently, in high-multiplicity p + p collisions at RHIC and at the LHC, a significant enhancement of J / Ψ production yield has been observed, which suggests a strong contribution of multi-parton interaction (MPI). This is different from the traditional pQCD picture, where charm quark pairs are produced from a single hard scattering between partons in p + p collisions. In this work, we will report the J / Ψ normalized production yield as a function of normalized charged particle multiplicity over a board range of rapidity and event multiplicity in the J / Ψ → μ + μ – channel with PHENIX Run 15 p + p data at $\sqrt s$ =200 GeV. The results are compared with PYTHIA 8 simulations with the MPI option turned on and off. Finally, the outlooks of J / Ψ in p + Au and Au + p collisions, along with color glass condensate (CGC) predictions and the multiplicity-dependent Ψ(2S) /J / Ψ ratio in p + p data, will be briefly discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns

Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM (“intrahost SARS-CoV-2 k-mer identification method”) to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.

60 APPLIED LIFE SCIENCES↗

Optimization of barrier height in InGaN quantum wells for rapid interwell carrier transport and low nonradiative recombination

Rapid interwell carrier transport is a key process for a uniform carrier distribution and reduced Auger recombination in multiple quantum well (MQW) light emitting devices. In this work, the interwell transport has been studied by time-resolved photoluminescence in In 0.12 Ga 0.88 N MQWs with In x Ga 1–x N (x = 0 - 0.06) and Al 0.065 Ga 0.935 N barriers. Only for the InGaN barriers the transport is efficient. Furthermore, introduction of In into the barriers is accompanied by an increase of the nonradiative recombination at QW interfaces. Still, even with the increased Shockley–Read–Hall recombination, structures with InGaN barriers might be advantageous for high power devices because of the reduced Auger recombination.

36 MATERIALS SCIENCE↗

A Comparison of Properties of Quasars with and without Rapid Broad Absorption Line Variability

We investigate the correlation between rest-frame UV flux variability of broad absorption line (BAL) quasars and their variability in BAL equivalent widths (EWs) in a various timescale from <10 days to a few years in the quasar rest frame. We use the data sets of BAL EWs taken by the Sloan Digital Sky Survey Reverberation Mapping project and photometric data taken by the intermediate Palomar Transient Factory in the g and R bands and the Panoramic Survey Telescope and Rapid Response System in grizy bands. Our results are summarized as follows: (1) the distributions of flux variability versus BAL variability show weak, moderate, or a strong positive correlation; (2) there is no significant difference in flux variability amplitudes between BAL quasars with significant short timescale EW variability (called class S1) and without (class S2); (3) in all timescales considered in this paper, the class S1 quasars show systematically larger BAL variability amplitudes than those of the class S2 quasars; and (4) there are possible correlations between BAL variability and physical parameters of the quasars such as black hole masses (moderate positive), Eddington ratios, and accretion disk temperature (strong negative) in the class S2 quasars. These results indicate that the BAL variability requires changing in the ionizing continuum and an ancillary mechanism such as variability in X-ray shielding gas located at the innermost region of an accretion disk.

79 ASTRONOMY AND ASTROPHYSICS↗

TOI 540 b: A Planet Smaller than Earth Orbiting a Nearby Rapidly Rotating Low-mass Star

We present the discovery of TOI 540 b, a hot planet slightly smaller than Earth orbiting the low-mass star 2MASS J05051443-4756154. The planet has an orbital period of P = 1.239149 days (±170 ms) and a radius of r=0.903±0.052R{sub ⊕}, and is likely terrestrial based on the observed mass–radius distribution of small exoplanets at similar insolations. The star is 14.008 pc away and we estimate its mass and radius to be M=0.159±0.014 M{sub ⊙} and R=0.1895±0.0079R{sub ⊙}, respectively. The star is distinctive in its very short rotational period of P{sub rot}=17.4264±0.0094 hr and correspondingly small Rossby number of 0.007 as well as its high X-ray-to-bolometric luminosity ratio of L{sub X}/L{sub bol}=0.0028 based on a serendipitous XMM-Newton detection during a slew operation. This is consistent with the X-ray emission being observed at a maximum value of L{sub X}/L{sub bol}≃10{sup −3} as predicted for the most rapidly rotating M dwarfs. TOI 540 b may be an alluring target to study atmospheric erosion due to the strong stellar X-ray emission. It is also among the most accessible targets for transmission and emission spectroscopy and eclipse photometry with the James Webb Space Telescope, and may permit Doppler tomography with high-resolution spectroscopy during transit. This discovery is based on precise photometric data from the Transiting Exoplanet Survey Satellite and ground-based follow-up observations by the MEarth team.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Hydro-particle-mesh Code for Efficient and Rapid Simulations of the Intracluster Medium

We introduce the cosmological HYPER code based on an innovative hydro-particle-mesh (HPM) algorithm for efficient and rapid simulations of gas and dark matter. For the HPM algorithm, we update the approach of Gnedin & Hui to expand the scope of its application from the lower-density intergalactic medium (IGM) to the higher-density intracluster medium (ICM). While the original algorithm tracks only one effective particle species, the updated version separately tracks the gas and dark matter particles, as they do not exactly trace each other on small scales. For the approximate hydrodynamics solver, the pressure term in the gas equations of motion is calculated using robust physical models. In particular, we use a dark matter halo model, ICM pressure profile, and IGM temperature–density relation, all of which can be systematically varied for parameter-space studies. We show that the HYPER simulation results are in good agreement with the halo model expectations for the density, temperature, and pressure radial profiles. Simulated galaxy cluster scaling relations for Sunyaev–Zel’dovich (SZ) and X-ray observables are also in good agreement with mean predictions, with scatter comparable to that found in hydrodynamic simulations. HYPER also produces lightcone catalogs of dark matter halos and full-sky tomographic maps of the lensing convergence, SZ effect, and X-ray emission. These simulation products are useful for testing data analysis pipelines, generating training data for machine learning, understanding selection and systematic effects, and for interpreting astrophysical and cosmological constraints.

79 ASTRONOMY AND ASTROPHYSICS↗

The Rapid X-Ray and UV Evolution of ASASSN-14ko

Abstract ASASSN-14ko is a recently discovered periodically flaring transient at the center of the active galactic nucleus (AGN) ESO 253−G003 with a slowly decreasing period. Here, we show that the flares originate from the northern, brighter nucleus in this dual-AGN, post-merger system. The light curves for the two flares that occurred in 2020 May and September are nearly identical over all wavelengths. For both events, Swift observations showed that the UV and optical wavelengths brightened in unison. The effective temperature of the UV/optical emission rises and falls with the increase and subsequent decline in the luminosity. The X-ray flux, by contrast, first rapidly drops over ∼2.6 days, rises for ∼5.8 days, drops again over ∼4.3 days, and then recovers. The X-ray spectral evolution of the two flares differ, however. During the 2020 May peak the spectrum softened with increases in the X-ray luminosity, while we observed the reverse for the 2020 September peak. We found a small change in the period derivative, which seems to indicate that the system does not have a static period derivative and there is some stochasticity in its evolution.

79 ASTRONOMY AND ASTROPHYSICS↗