Colorectal Cancer Diagnosis through Breath Test Using a Portable Breath Analyzer-Preliminary Data.

Screening methods available for colorectal cancer (CRC) to date are burdened by poor reliability and low patient adherence and compliance. An altered pattern of volatile organic compounds (VOCs) in exhaled breath has been proposed as a non-invasive potential diagnostic tool for distinguishing CRC patients from healthy controls (HC). The aim of this study was to evaluate the reliability of an innovative portable device containing a micro-gas chromatograph in enabling rapid, on-site CRC diagnosis through analysis of patients' exhaled breath. In this prospective trial, breath samples were collected in a tertiary referral center of colorectal surgery, and analysis of the chromatograms was performed by the Biomedical Engineering Department. The breath of patients with CRC and HC was collected into Tedlar bags through a Nafion filter and mouthpiece with a one-way valve. The breath samples were analyzed by an automated portable gas chromatography device. Relevant volatile biomarkers and discriminant chromatographic peaks were identified through machine learning, linear discriminant analysis and principal component analysis. A total of 68 subjects, 36 patients affected by histologically proven CRC with no evidence of metastases and 32 HC with negative colonoscopies, were enrolled. After testing a training set (18 CRC and 18 HC) and a testing set (18 CRC and 14 HC), an overall specificity of 87.5%, sensitivity of 94.4% and accuracy of 91.2% in identifying CRC patients was found based on three VOCs. Breath biopsy may represent a promising non-invasive method of discriminating CRC patients from HC.

Safety, efficacy, and pharmacokinetics of nirmatrelvir and ritonavir in patients with severe COVID-19 and renal impairment: A case report.

Nirmatrelvir/ritonavir (N/r) has received emergency use authorization for mild-to-moderate COVID-19 treatment in adult and pediatric patients (aged and weighing at least 12 years and 40 kg, respectively) presenting positive direct SARS-CoV-2 viral testing results and a high risk of disease progression to severe COVID-19. However, information remains limited concerning the corresponding drug safety, efficacy, and pharmacokinetics in patients with severe renal impairment. In this study, we present the case of a 91-year-old Chinese man who, despite exhibiting recurrent positive SARS-CoV-2 results and progression to severe COVID-19, was treated with N/r. Due to severe renal impairment and concurrent administration of continuous renal replacement therapy (continuous venovenous hemofiltration) during medication, we aimed to determine the serum N/r drug concentration in the patient. Our analysis revealed Cmax values of 12.42 and 2.001 µg/mL for nirmatrelvir and ritonavir, respectively. Despite the particularly high serum N/r concentration in this patient, the clinical and laboratory test analyses confirmed that the treatment was safe and effective. Nevertheless, N/r should be used with caution and at lower doses in patients with severe renal impairment to avoid potential high N/r concentration-related adverse reactions and events.

1D-Guided Differential Rescaling of a Contour Plot in Comprehensive 2D Gas Chromatography.

A 1D-guided differential rescaling algorithm for a contour plot is developed based on our recently proposed comprehensive two-dimensional gas chromatography (GC × GC) system with a first-dimensional (1D) detector added. Chromatograms obtained from 1D and second-dimensional (2D) detectors are both incorporated during the data processing. As compared to the conventional contour plot methods using only 2D data, our algorithm can significantly improve precision and consistency of GC × GC results in terms of retention times, peak widths, and peak areas or volumes, regardless of modulation time selection, modulation phase shift fluctuations, and modulation duty cycle. The peak identification, quantification, and capacity can therefore be enhanced. Furthermore, the 1D-guided differential rescaling method is shown to better handle the coelution and missing peak issues often encountered in the conventional methods. Finally, the new method exhibits high versatility in 1D and 2D detector selection, which greatly broadens GC × GC utility. Our method can easily be adapted to other two-dimensional chromatography systems that have direct access to 1D chromatograms.

Application of Biotechniques for In Vitro Virus and Viroid Elimination in Pome Fruit Crops.

Sustainable production of pome fruit crops is dependent upon having virus-free planting materials. The production and distribution of plants derived from virus- and viroid-negative sources is necessary not only to control pome fruit viral diseases but also for sustainable breeding activities, as well as the safe movement of plant materials across borders. With variable success rates, different in vitro-based techniques, including shoot tip culture, micrografting, thermotherapy, chemotherapy, and shoot tip cryotherapy, have been employed to eliminate viruses from pome fruits. Higher pathogen eradication efficiencies have been achieved by combining two or more of these techniques. An accurate diagnosis that confirms complete viral elimination is crucial for developing effective management strategies. In recent years, considerable efforts have resulted in new reliable and efficient virus detection methods. This comprehensive review documents the development and recent advances in biotechnological methods that produce healthy pome fruit plants. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Recent advances in bimetallic nanoscale zero-valent iron composite for water decontamination: Synthesis, modification and mechanisms.

The environmental pollution of water is one of the problems that have plagued human society. The bimetallic nanoscale zero-valent iron (BnZVI) technology has increased wide attention owing to its high performance for water treatment and soil remediation. In recent years, the BnZVI technology based on the development of nZVI has been further developed. The material chemistry, synthesis methods, and immobilization or surface stabilization of bimetals are discussed. Further, the data of BnZVI (Fe/Ni, Fe/Cu, Fe/Pd) articles that have been studied more frequently in the last decade are summarized in terms of the types of contaminants and the number of research literatures on the same contaminants. Five contaminants including trichloroethylene (TCE), Decabromodi-phenyl Ether (BDE209), chromium (Cr(VI)), nitrate and 2,4-dichlorophenol (2,4-DCP) were selected for in-depth discussion on their influencing factors and removal or degradation mechanisms. Herein, comprehensive views towards mechanisms of BnZVI applications including adsorption, hydrodehalogenation and reduction are provided. Particularly, some ambiguous concepts about formation of micro progenitor cell, production of hydrogen radicals (H·) and H2 and the electron transfer are highlighted. Besides, in-depth discussion of selectivity for N2 from nitrates and co-precipitation of chromium are emphasized. The difference of BnZVI is also discussed.

Improving the multi-functionality of optical tweezers with FPGA integration.

The development of optical tweezers aims to extend their operating function and pattern. However, excessive programming can lead to a decrease in the system's operating speed and introduce bugs or data transmission delays. In this study, we present a time-shared optical tweezers system that allows for parallel operation of multiple functions. To enable efficient data transmission, we employ a queue structure and a buffer. To assess the system's performance, we utilize a biological sample in conjunction with the optical tweezers system and scanning imaging technique. We quantify the trapping parameter while concurrently running power stabilization programs. As a result, the standard deviation of the measured stiffness is reduced by 60% in the x and y directions and 30% in the z direction, indicating a significant improvement in calibration precision. Throughout the program execution, the system maintains an operating rate of 110 kHz, and the data are continuously updated in real time on the host. The system's performance demonstrates its potential for quantification and morphological reconstruction of biological samples.

Development, Validation, and Clinical Application of an Ultra-High-Performance Liquid Chromatography Coupled With Tandem Mass Spectrometry Method for the Determination of 10 Antituberculosis Drugs in Human Serum.

INTRODUCTION: Linezolid, moxifloxacin, rifapentine, rifabutin, cycloserine, clofazimine, bedaquiline, levofloxacin, prothionamide, and ethionamide are commonly used second-line antituberculosis (anti-TB) drugs. To support therapeutic drug monitoring in regular clinical practice, the authors sought to develop a method based on ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) that would allow for the simultaneous quantification of multiple second-line anti-TB drugs in human serum. METHODS: Analytes were extracted from human serum by protein precipitation. UHPLC-MS/MS was performed using a gradient at a flow rate of 0.3 mL/min, and each sample was taken for 7.5 minutes. The mass spectrometry scanning mode used was electrospray ionization with multiple reaction monitoring in the positive mode. RESULTS: Validation showed that endogenous substances in the sample did not interfere with the assay, and the relationship between X and Y was highly linear, with a coefficient of determination (R2) >0.9954 for each curve. The accuracy (85.0%-114.7%) and precision (intraday: 0.27%-9.32%; interday: 0.20%-7.66%) were less than 15.0%, and the internal standard-normalized matrix effects were consistent (coefficient of variation ≤4.40%). The analytes were stable in the final extract and human serum under various storage conditions (recovery: 87.0%-115.0%). The clinical applicability of the method was demonstrated by quantitative determination of analytes in serum samples obtained from patients with TB. Reproducibility of the drug concentrations measured in clinical samples was confirmed by incurred sample reanalysis. CONCLUSIONS: A simple and reliable analytical method was developed and validated for the simultaneous determination of 10 anti-TB drugs in human serum using UHPLC-MS/MS. Quantitation of anti-TB drugs in clinical samples confirmed that the assay is suitable for therapeutic drug monitoring in regular clinical practice.

Automated Gas Chromatography Peak Alignment: A Deep Learning Approach using Greedy Optimization and Simulation.

The clinical significance of volatile organic compounds (VOC) in detecting diseases has been established over the past decades. Gas chromatography (GC) devices enable the measurement of these VOCs. Chromatographic peak alignment is one of the important yet challenging steps in analyzing chromatogram signals. Traditional semi-automated alignment algorithms require manual intervention by an operator which is slow, expensive and inconsistent. A pipeline is proposed to train a deep-learning model from artificial chromatograms simulated from a small, annotated dataset, and a postprocessing step based on greedy optimization to align the signals.Clinical Relevance- Breath VOCs have been shown to have a significant diagnostic power for various diseases including asthma, acute respiratory distress syndrome and COVID-19. Automatic analysis of chromatograms can lead to improvements in the diagnosis and management of such diseases.

Submonolayer biolasers for ultrasensitive biomarker detection.

Biomarker detection is key to identifying health risks. However, designing sensitive and single-use biosensors for early diagnosis remains a major challenge. Here, we report submonolayer lasers on optical fibers as ultrasensitive and disposable biosensors. Telecom optical fibers serve as distributed optical microcavities with high Q-factor, great repeatability, and ultralow cost, which enables whispering-gallery laser emission to detect biomarkers. It is found that the sensing performance strongly depends on the number of gain molecules. The submonolayer lasers obtained a six-order-of-magnitude improvement in the lower limit of detection (LOD) when compared to saturated monolayer lasers. We further achieve an ultrasensitive immunoassay for a Parkinson's disease biomarker, alpha-synuclein (α-syn), with a lower LOD of 0.32 pM in serum, which is three orders of magnitude lower than the α-syn concentration in the serum of Parkinson's disease patients. Our demonstration of submonolayer biolaser offers great potentials in high-throughput clinical diagnosis with ultimate sensitivity.

WASP: Wearable Analytical Skin Probe for Dynamic Monitoring of Transepidermal Water Loss.

Early diagnosis of skin barrier dysfunction helps provide timely preventive care against diseases such as atopic dermatitis, psoriasis, food allergies, and other atopic skin disorders. Skin barrier function is commonly evaluated by measuring the transepidermal water loss (TEWL) through stratum corneum due to its noninvasive characteristics. However, existing commercial TEWL devices are significantly affected by many factors, such as ambient temperature, humidity, air flow, water accumulation, initial water contents on the skin surface, bulky sizes, high costs, and requirements for well-controlled environments. Here, we developed a wearable closed-chamber hygrometer-based TEWL device (Wearable Analytical Skin Probe, WASP) and the related algorithm for accurate and continuous monitoring of skin water vapor flux. The WASP uses short dry air purges to dry the skin surface and chamber before each water vapor flux measurement. Its design ensures a highly controlled local environment, such as consistent initial dry conditions for the skin surface and the chamber. We further applied WASP to measure the water vapor flux from six different locations of a small group of human participants. It is found that the WASP can not only measure and distinguish between insensible sweating (i.e., TEWL) and sensible sweating (i.e., thermal sweating) but also track skin dehydration-rehydration cycles. Comparisons with a commercial TEWL device, AquaFlux, show that the results obtained by both devices agree well. The WASP will be broadly applicable to clinical, cosmetic, and biomedical research.

Identification and complete genome sequence of a novel sadwavirus discovered in chrysanthemum (Chrysanthemum morifolium Ramat.).

The complete genome sequence of a putative novel member of the genus Sadwavirus was determined by high-throughput sequencing of a chrysanthemum from an orchard of the Tongxiang Agricultural Science Institute in Tongxiang, Zhejiang province. The complete genome sequence was confirmed using RT-PCR and the rapid amplification of cDNA ends (RACE) method. The predicted genome of the putative virus is composed of two RNA molecules, 7016 and 6772 nucleotides in length, excluding their poly-A tails. The new virus was tentatively named "chrysanthemum sadwavirus" (ChSV). The Pro-Pol region of RNA1 and the CP region of RNA2 of ChSV shared the highest amino acid sequence identity (53.01% and 36.40%, respectively) with the corresponding sequences of lettuce secovirus 1 (LSV-1). Phylogenetic analysis showed that ChSV clustered with members of the subgenus Stramovirus (genus Sadwavirus). Taken together, these results suggest that ChSV is a new member of the genus Sadwavirus.

Born approximation of trapping forces by acoustical Bessel and vortex fields.

Acoustic radiation forces have been used to trap various objects for fundamental studies and practical applications. Born approximation method, originally introduced to solve quantum scattering problems, is herein extended to analyze trapping forces exerted by two- and three-dimensional acoustic Bessel and vortex fields on spherical and nonspherical objects of arbitrary size. The results are compared with the conventional models like the partial wave expansion and Gorkov force potential. It is shown that for weakly scattering objects (such as common soft biological particles surrounded by fluids), the Born approximation can make predictions for the trapping forces on objects whose characteristic lengths are even up to multiple wavelengths of the sound beams. With the aid of the approximation, the Gorkov force potential is applied to analyze and gain insights into trapping forces on large objects far beyond the original Rayleigh scattering regime. The effects caused by the beam parameters, object shape, and orientation on the trapping behaviors are revealed. This work is useful for the further study of acoustic radiation forces and will guide the experiment of simplified acoustic tweezers on arbitrary-shaped particles.

Retention Time Trajectory Matching for Peak Identification in Chromatographic Analysis.

Retention time drift caused by fluctuations in physical factors such as temperature ramping rate and carrier gas flow rate is ubiquitous in chromatographic measurements. Proper peak matching and identification across different chromatograms is critical prior to any subsequent analysis but is challenging without using mass spectrometry. The purpose of this work was to describe and validate a peak matching and identification method called retention time trajectory (RTT) matching that can be used in targeted analyses free of mass spectrometry. This method uses chromatographic retention times as the only input and identifies peaks associated with any subset of a predefined set of target compounds. An RTT is a two-dimensional (2D) curve formed uniquely by the retention times of the chromatographic peaks. The RTTs obtained from the chromatogram of a sample under test and those pre-installed in a library are matched and statistically compared. The best matched pair implies identification. Unlike most existing peak-alignment methods, no mathematical warping or transformation is involved. Based on the experimentally characterized RTT, an RTT hybridization method was also developed to rapidly generate more RTTs and expand the library without performing actual time-consuming chromatographic measurements, which enables successful peak matching even for chromatograms with severe retention time drifts. Additionally, 3.15 × 105 tests using experimentally obtained gas chromatograms and 2 × 1012 tests using two publicly available fruit metabolomics datasets validated the proposed method, demonstrating real-time peak/interferent identification.

Single-cell RNA sequencing analysis of the temporomandibular joint condyle in 3 and 4-month-old human embryos.

BACKGROUND: The temporomandibular joint (TMJ) is a complex joint consisting of the condyle, the temporal articular surface, and the articular disc. Functions such as mastication, swallowing and articulation are accomplished by the movements of the TMJ. To date, the TMJ has been studied more extensively, but the types of TMJ cells, their differentiation, and their interrelationship during growth and development are still unclear and the study of the TMJ is limited. The aim of this study was to establish a molecular cellular atlas of the human embryonic temporomandibular joint condyle (TMJC) by single-cell RNA sequencing, which will contribute to understanding and solving clinical problems. RESULTS: Human embryos at 3 and 4 months of age are an important stage of TMJC development. We performed a comprehensive transcriptome analysis of TMJC tissue from human embryos at 3 and 4 months of age using single-cell RNA sequencing. A total of 16,624 cells were captured and the gene expression profiles of 15 cell clusters in human embryonic TMJC were determined, including 14 known cell types and one previously unknown cell type, "transition state cells (TSCs)". Immunofluorescence assays confirmed that TSCs are not the same cell cluster as mesenchymal stem cells (MSCs). Pseudotime trajectory and RNA velocity analysis revealed that MSCs transformed into TSCs, which further differentiated into osteoblasts, hypertrophic chondrocytes and tenocytes. In addition, chondrocytes (CYTL1high + THBS1high) from secondary cartilage were detected only in 4-month-old human embryonic TMJC. CONCLUSIONS: Our study provides an atlas of differentiation stages of human embryonic TMJC tissue cells, which will contribute to an in-depth understanding of the pathophysiology of the TMJC tissue repair process and ultimately help to solve clinical problems.

Ultrathin Silica Integration for Enhancing Reliability of Microfluidic Photoionization Detectors.

Microfluidic photoionization detectors (µPIDs) based on silicon chips can rapidly and sensitively detect volatile compounds. However, the applications of µPID are limited by the manual assembly process using glue, which may outgas and clog the fluidic channel, and by the short lifetime of the vacuum ultraviolet (VUV) lamps (especially, argon lamps). Here, we developed a gold-gold cold welding-based microfabrication process to integrate ultrathin (10 nm) silica into µPID. The silica coating enables direct bonding of the VUV window to silicon under amicable conditions and works as a moisture and plasma exposure barrier for VUV windows that are susceptible to hygroscopicity and solarization. Detailed characterization of the silica coating was conducted, showing that the 10 nm silica coating allows 40-80% VUV transmission from 8.5 to 11.5 eV. It is further shown that the silica-protected µPID maintained 90% of its original sensitivity after 2200 h of exposure to ambient (dew point = 8.0 ± 1.8 °C), compared to 39% without silica. Furthermore, argon plasma inside an argon VUV lamp was identified as the dominant degradation source for the LiF window with color centers formation in UV-vis and VUV transmission spectra. Ultrathin silica was then also demonstrated effective in protecting the LiF from argon plasma exposure. Lastly, thermal annealing was found to bleach the color centers and restore VUV transmission of degraded LiF windows effectively, which will lead to future development of a new type of VUV lamp and the corresponding µPID (and PID in general) that can be mass produced with a high yield, a longer lifetime, and better regenerability.

First report of grapevine asteroid mosaic-associated virus in grapevines in China.

Grapevine asteroid mosaic-associated virus (GAMaV), a member of the genus Marafivirus of the family Tymoviridae, was first described to infect grapevines in California (Abou Ghanem-Sabanadzovic et al. 2003). Since then, GAMaV has been reported from Greece, Japan, Canada, Uruguay, France, Hungary, Italy, Spain, Switzerland and Russia, and also in some free-living grapevines in North America (Kyriakopoulou, 1991; Morán et al., 2021; Reynard et al., 2022; Shvets et al., 2022; Thompson et al., 2021). GAMaV may be associated with grapevine asteroid mosaic disease (Martelli 2014). In August 2022, a grapevine cv. Cabernet Sauvignon exhibiting chlorotic mottling was collected in Ningxia, China. Total RNAs were extracted using RNAprep Pure Plant Plus Kit (DP441, TIANGEN BIOTECH, Beijing), and the ribosomal RNA were removed by the Epicentre Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). The ribosomal RNA-depleted RNAs were then used to construct a cDNA library using a TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA), which was sequenced on an Illumina NovaSeq 6000 platform (Biomarker Biology Technology), resulting in 39,297,567 paired-end clean reads (150 nt × 2). Reads mapping to the grapevine genome (GenBank accession no PN40024) were removed using hisat2 2.1.0 software. The 15,003,158 unmapped reads were de novo assembled into 70,512 contigs using the rnaviralSPAdes method in the SPAdes v3.15.3 software with default parameters and analyzed through BLASTn and BLASTx analysis. Five viruses and two viroids were identified: GAMaV (5 contigs), grapevine Pinot gris virus (3 contigs), grapevine berry inner necrosis virus (3 contigs) , grapevine rupestris stem pitting-associated virus (4 contigs), grapevine red globe virus (2 contigs), grapevine yellow speckle 1 viroid (4 contigs) and hop stunt viroid (3 contigs). The five contigs of GAMaV were 352 nt~2, 224 nt in length, which were assembled from 3, 308 reads and shared 85.56%~91.81% nt identity with the genome of the GAMaV isolate GV30 (KX354202) with 93.3% coverage. To further confirm the infection of GAMaV, we designed two pairs of primers, GAMaV-mel1a/1b (5'-CACCTCGCCCCCTACCTTGAC-3'/5'-AAGAGGACGCCTTTGCGGGAG-3') and GAMaV-cp1a/1b (5'-CTAGCGACGACCGCACTGATC-3'/5'-GTCGGTGTACGAGATTTGGTC-3'), which were used to amplify the 329-bp and 440-bp fragments in the helicase (Hel) domain and coat protein (CP) gene of GAMaV genome in RT-PCR, respectively. The amplified PCR products were cloned and sequenced and the two sequences (OQ676951 and OQ676958) showed 91.2% and 93.4% nt identity with the isolate GV30, respectively. Furthermore, 429 grapevine samples of 71 cultivars were collected from 21 provinces and tested by RT-PCR using the above primer pairs. The results showed that 1.4% (6/429) of the samples tested positive, including one 'Autumn seedless' grapevine (Liaoning province), two 'Dawuhezi' (Liaoning), one 'Cabernet Gernischt' (Liaoning) and two 'Cabernet Sauvignon' (Tianjing and Shandong respectively). The partial sequences of the Hel domain (OQ676952-57) and CP gene (OQ676959-61) obtained from the positive samples by sequencing showed 89.1% to 84.5% and 93.6% to 93.9% nt identity with the isolate GV30, respectively. Because these GAMaV-positive grapevines did not show distinct symptoms, GAMaV pathogenicity remains challenging to confirm. This is the first report of GAMaV in grapevines in China, extending the information on its geographical distribution.

Assessment of the impacts of climat change on water supply system pipe failures.

Climate change is projected to have profound impacts on the resilience and sustainability of built infrastructure. This study aims to understand the impacts of climate change on water supply systems and to facilitate adaptive actions. A premium database maintained by the Cleveland Water Division, Cleveland, Ohio, USA is analyzed. It contains 29,621 pipe failure records of 51,832 pipes over the past 30 years, representing one of the largest dataset in current literature. From the database, pipe failure rate models have been developed for water pipes made of different types of materials at different ages. The influence of climate (temperature and precipitation) on fragility of water pipes are obtained. Based on the developed climate-fragility failure rate models, the impacts of climate change on the water systems located in different geographic regions are evaluated by predicting the failure rate and number of failures in the water systems in the next 80 years (2020 to 2100). Climate models are used to predict weather under different climate change scenarios. The results demonstrate that the impacts of climate change on water supply system are likely complicated and are dependent upon factors such as the geographic location, pipe material, pipe age, and maintenance strategies. Water pipes in the cold regions may experience fewer number breaks due to the warmer weather and less severe winter, whereas those located in the hot regions may experience more failures associated with more corrosion. Different pipe replacement strategies are compared, which demonstrate the importance of considering the aging of water supply system in future maintenance decisions. This study enriches current understandings on the impacts of climate change on the water systems. The results will help water utilities to design climate change adaptation strategies.

Genomic characterization of a novel torradovirus infecting Arctium lappa L. in China.

Burdock (Arctium lappa L.) is not only a popular vegetable crop but also an important medicinal plant. In burdock plants with symptoms of leaf mosaic, a novel torradovirus tentatively named "burdock mosaic virus" (BdMV) was identified by high-throughput sequencing. The complete genomic sequence of BdMV was further determined using RT-PCR and the rapid amplification of cDNA ends (RACE) method. The genome is composed of two positive-sense single-stranded RNAs. RNA1 (6991 nt) encodes a polyprotein of 2186 aa, and RNA2 (4700 nt) encodes a protein of 201 aa and a polyprotein of 1212 aa that is predicted to be processed into one movement protein (MP) and three coat proteins (CPs). The Pro-Pol region of RNA1 and the CP region of RNA2 shared the highest amino acid sequence identity of 74.0% and 70.6%, respectively, with the corresponding sequences of lettuce necrotic leaf curl virus (LNLCV) isolate JG3. Phylogenetic analysis based on the amino acid sequences of the Pro-Pol and CP regions showed that BdMV clustered with other non-tomato-infecting torradoviruses. Taken together, these results suggest that BdMV is a new member of the genus Torradovirus.

Portable Breath-Based Volatile Organic Compound Monitoring for the Detection of COVID-19 During the Circulation of the SARS-CoV-2 Delta Variant and the Transition to the SARS-CoV-2 Omicron Variant.

Importance: Breath analysis has been explored as a noninvasive means to detect COVID-19. However, the impact of emerging variants of SARS-CoV-2, such as Omicron, on the exhaled breath profile and diagnostic accuracy of breath analysis is unknown. Objective: To evaluate the diagnostic accuracies of breath analysis on detecting patients with COVID-19 when the SARS-CoV-2 Delta and Omicron variants were most prevalent. Design, Setting, and Participants: This diagnostic study included a cohort of patients who had positive and negative test results for COVID-19 using reverse transcriptase polymerase chain reaction between April 2021 and May 2022, which covers the period when the Delta variant was overtaken by Omicron as the major variant. Patients were enrolled through intensive care units and the emergency department at the University of Michigan Health System. Patient breath was analyzed with portable gas chromatography. Main Outcomes and Measures: Different sets of VOC biomarkers were identified that distinguished between COVID-19 (SARS-CoV-2 Delta and Omicron variants) and non-COVID-19 illness. Results: Overall, 205 breath samples from 167 adult patients were analyzed. A total of 77 patients (mean [SD] age, 58.5 [16.1] years; 41 [53.2%] male patients; 13 [16.9%] Black and 59 [76.6%] White patients) had COVID-19, and 91 patients (mean [SD] age, 54.3 [17.1] years; 43 [47.3%] male patients; 11 [12.1%] Black and 76 [83.5%] White patients) had non-COVID-19 illness. Several patients were analyzed over multiple days. Among 94 positive samples, 41 samples were from patients in 2021 infected with the Delta or other variants, and 53 samples were from patients in 2022 infected with the Omicron variant, based on the State of Michigan and US Centers for Disease Control and Prevention surveillance data. Four VOC biomarkers were found to distinguish between COVID-19 (Delta and other 2021 variants) and non-COVID-19 illness with an accuracy of 94.7%. However, accuracy dropped substantially to 82.1% when these biomarkers were applied to the Omicron variant. Four new VOC biomarkers were found to distinguish the Omicron variant and non-COVID-19 illness (accuracy, 90.9%). Breath analysis distinguished Omicron from the earlier variants with an accuracy of 91.5% and COVID-19 (all SARS-CoV-2 variants) vs non-COVID-19 illness with 90.2% accuracy. Conclusions and Relevance: The findings of this diagnostic study suggest that breath analysis has promise for COVID-19 detection. However, similar to rapid antigen testing, the emergence of new variants poses diagnostic challenges. The results of this study warrant additional evaluation on how to overcome these challenges to use breath analysis to improve the diagnosis and care of patients.

Integrated Transcriptome and Metabolome Dissecting Interaction between Vitis vinifera L. and Grapevine Fabavirus.

Grapevine fabavirus (GFabV) is a novel member of the Fabavirus genus associated with chlorotic mottling and deformation symptoms in grapevines. To gain insights into the interaction between GFabV and grapevines, V. vinifera cv. 'Summer Black' infected with GFabV was investigated under field conditions through physiological, agronomic, and multi-omics approaches. GFabV induced significant symptoms on 'Summer Black', and caused a moderate decrease in physiological efficiency. In GFabV-infected plants, alterations in carbohydrate- and photosynthesis-related genes might trigger some defense responses. In addition, secondary metabolism involved in plant defense was progressively induced by GFabV. Jasmonic acid and ethylene signaling were down-regulated in GFabV-infected leaves and berries along with the expression of proteins related to LRR and protein kinases, suggesting that GFabV can block the defense in healthy leaves and berries. Furthermore, this study provided biomarkers for early monitoring of GFabV infection in grapevines, and contributed to a better understanding of the complex grapevine-virus interaction.