Fungicide Metabolite MS2 Spectral Libraries for Comprehensive Human Biomonitoring.

Fungicides undergo rapid metabolism and are excreted in the urine. There are few methods for screening these ubiquitous compounds, which have a high potential for human exposure. High-resolution mass spectrometry (HRMS) is a suitable technique to assess fungicide exposures; however, there is a lack of spectral libraries for fungicide annotation and in particular for downstream metabolites. We created spectral libraries for 32 fungicides for suspect screening. Fungicide standards were administered to mice, and 24-h urine was analyzed using hydrophilic interaction and reversed-phase chromatography coupled to hybrid quadrupole-orbitrap mass spectrometry. Suspect metabolite MS2 spectra for library creation were selected based on the ratio of exposed-to-control mouse urine. MS2 libraries were applied to urine collected from female university students (n = 73). Several tetraconazole and tebuconazole metabolites were detected in 3% (2/73) of the samples. The creation of comprehensive suspect screening MS2 libraries is a useful tool to detect fungicide exposure for human biomonitoring.

Feasibility of magnetomyography with optically pumped magnetometers in a mobile magnetic shield.

While magnetomyography (MMG) using optically pumped magnetometers (OPMs) is a promising method for non-invasive investigation of the neuromuscular system, it has almost exclusively been performed in magnetically shielded rooms (MSRs) to date. MSRs provide extraordinary conditions for biomagnetic measurements but limit the widespread adoption of measurement methods due to high costs and extensive infrastructure. In this work, we address this issue by exploring the feasibility of mobile OPM-MMG in a setup of commercially available components. From field mapping and simulations, we find that the employed zero-field OPM can operate within a large region of the mobile shield, beyond which residual magnetic fields and perturbations become increasingly intolerable. Moreover, with digital filtering and moderate averaging a signal quality comparable to that in a heavily shielded MSR is attained. These findings facilitate practical and cost-effective implementations of OPM-MMG systems in clinical practice and research.

Multi-labeling Live Imaging to Quantify Gene Expression Dynamics During Drosophila Embryonic Development.

Transcription in developing metazoans is inherently stochastic, involving transient and dynamic interactions among transcriptional machinery. A fundamental challenge with traditional techniques, including fixed-tissue protein and RNA staining, is the lack of temporal resolution. Quantifying kinetic changes in transcription can elucidate underlying mechanisms of interaction among regulatory modules. In this protocol, we describe the successful implementation of a combination of MS2/MCP and PP7/PCP systems in living Drosophila embryos to further our understanding of transcriptional dynamics during development. Our technique can be extended to visualize transcriptional activities of multiple genes or alleles simultaneously, characterize allele-specific expression of a target gene, and quantitatively analyze RNA polymerase II activity in a single-cell resolution.

Deciphering the Thermal Stability of Bacteriophage MS2-Derived Virus-like Particle and Its Engineered Variant.

RNA bacteriophage MS2-derived virus-like particles (VLPs) have been widely used in biomedical research as model systems to study virus assembly, structure-function relationships, vaccine development, and drug delivery. Considering the diverse utility of these VLPs, a systemic engineering approach has been utilized to generate smaller particles with optimal serum stability and tissue penetrance. Additionally, it is crucial to demonstrate the overall stability of these mini MS2 VLPs, ensuring cargo protection until they reach their target cell/organ. However, no detailed analysis of the thermal stability and heat-induced disassembly of MS2 VLPs has yet been attempted. In this work, we investigated the thermal stability of both wild-type (WT) MS2 VLP and its "mini" variant containing S37P mutation (mini MS2 VLP). The mini MS2 VLP exhibits a higher capsid melting temperature (Tm) when compared to its WT MS2 VLP counterpart, possibly attributed to its smaller interdimer angle. Our study presents that the thermal unfolding of MS2 VLPs follows a sequential process involving particle destabilization, nucleic acid exposure/melting, and disassembly of VLP. This observation underscores the disruption of cooperative intersubunit interactions and protein-nucleic acid interactions, shedding light on the mechanism of heat-induced VLP disassembly.

Determining KRAS4B-Targeting Compound Specificity by Top-Down Mass Spectrometry.

We present a novel method to determine engagement and specificity of KRAS4B-targeting compounds in vitro. By employing top-down mass spectrometry (MS), which analyzes intact and modified protein molecules (proteoforms), we can directly visualize and confidently characterize each KRAS4B species within compound-treated samples. Moreover, by employing targeted MS2 fragmentation, we can precisely localize each compound molecule to a specific residue on a given KRAS4B proteoform. This method allows us to comprehensively evaluate compound specificity, clearly detect nonspecific binding events, and determine the order and frequency with which they occur. We provide two proof-of-concept examples of our method employing publicly available compounds, along with detailed protocols for sample preparation, top-down MS data acquisition, targeted proteoform MS2 fragmentation, and analysis of the resulting data. Our results demonstrate the concentration dependence of KRAS4B-compound engagement and highlight the ability of top-down MS to directly map compound binding location(s) without disrupting the KRAS4B primary structure. Our hope is that this novel method may help accelerate the identification of new successful targeted inhibitors for KRAS4B and other RAS isoforms.

Detection and Quantitation of Endogenous Membrane-Bound RAS Proteins and KRAS Mutants in Cancer Cell Lines Using 1D-SDS-PAGE LC-MS2.

In healthy cells, membrane-anchored wild-type RAS proteins (i.e., HRAS, KRAS4A, KRAS4B, and NRAS) regulate critical cellular processes (e.g., proliferation, differentiation, survival). When mutated, RAS proteins are principal oncogenic drivers in approximately 30% of all human cancers. Among them, KRAS mutants are found in nearly 80% of all patients diagnosed with RAS-driven malignancies and are regarded as high-priority anti-cancer drug targets. Due to the lack of highly qualified/specific RAS isoform and mutant RAS monoclonal antibodies, there is a vital need for an effective antibody-free approach capable of identifying and quantifying membrane-bound RAS proteins in isoform- and mutation-specific manner. Here, we describe the development of a simple antibody-free protocol that relies on ultracentrifugation to isolate the membrane fraction coupled with single-dimensional (1D) sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to fractionate and enrich membrane-bound endogenous RAS isoforms. Next, bottom-up proteomics that utilizes in-gel digestion followed by reversed-phase high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS2) is used for detection and relative quantitation of all wild-type RAS proteins (i.e., HRAS, KRAS4A, KRAS4B, and NRAS) and corresponding RAS mutants (e.g., G12D, G13D, G12S, G12V). Notably, this simple 1D-SDS-PAGE-HPLC-MS2-based protocol can be automated and widely applied to multiple cancer cell lines to investigate concentration changes in membrane-bound endogenous RAS proteins and corresponding mutants in the context of drug discovery.

Bioinformatics Pipeline for Processing Single-Cell Data.

Single-cell proteomics can offer valuable insights into dynamic cellular interactions, but identifying proteins at this level is challenging due to their low abundance. In this chapter, we present a state-of-the-art bioinformatics pipeline for single-cell proteomics that combines the search engine Sage (via SearchGUI), identification rescoring with MS2Rescore, quantification through FlashLFQ, and differential expression analysis using MSqRob2. MS2Rescore leverages LC-MS/MS behavior predictors, such as MS2PIP and DeepLC, to recalibrate scores with Percolator or mokapot. Combining these tools into a unified pipeline, this approach improves the detection of low-abundance peptides, resulting in increased identifications while maintaining stringent FDR thresholds.

Microinjection of the CRISPR/Cas9 editing system through the germ pore of a wheat microspore induces mutations in the target Ms2 gene.

BACKGROUND: Microinjection is a direct procedure for delivering various compounds via micropipette into individual cells. Combined with the CRISPR/Cas9 editing technology, it has been used to produce genetically engineered animal cells. However, genetic micromanipulation of intact plant cells has been a relatively unexplored area of research, partly due to the cytological characteristics of these cells. This study aimed to gain insight into the genetic micromanipulation of wheat microspores using microinjection procedures combined with the CRISPR/Cas9 editing system targeting the Ms2 gene. METHODS AND RESULTS: Microspores were first reprogrammed by starvation and heat shock treatment to make them structurally suitable for microinjection. The large central vacuole was fragmented and the nucleus with cytoplasm was positioned in the center of the cell. This step and an additional maltose gradient provided an adequate source of intact single cells in the three wheat genotypes. The microcapillary was inserted into the cell through the germ pore to deliver a working solution with a fluorescent marker. This procedure was much more efficient and less harmful to the microspore than inserting the microcapillary through the cell wall. The CRISPR/Cas9 binary vectors injected into reprogrammed microspores induced mutations in the target Ms2 gene with deletions ranging from 1 to 16 bp. CONCLUSIONS: This is the first report of successful genome editing in an intact microspore/wheat cell using the microinjection technique and the CRISPR/Cas9 editing system. The study presented offers a range of molecular and cellular biology tools that can aid in genetic micromanipulation and single-cell analysis.

Phage detection by a bacterial NLR-related protein is mediated by DnaJ.

Bacteria encode a wide range of antiphage systems and a subset of these proteins are homologous to components of the human innate immune system. Mammalian nucleotide-binding and leucine-rich repeat containing proteins (NLRs) and bacterial NLR-related proteins use a central NACHT domain to link infection detection with initiation of an antimicrobial response. Bacterial NACHT proteins provide defense against both DNA and RNA phages. Here we determine the mechanism of RNA phage detection by the bacterial NLR-related protein bNACHT25 in E. coli. bNACHT25 was specifically activated by Emesvirus ssRNA phages and analysis of MS2 phage suppressor mutants that evaded detection revealed Coat Protein (CP) was sufficient for activation. bNACHT25 and CP did not physically interact. Instead, we found bNACHT25 requires the host chaperone DnaJ to detect CP. Our data suggest that bNACHT25 detects a wide range of phages by guarding a host cell process rather than binding a specific phage-derived molecule.

Predicting Odor Sensory Attributes of Unidentified Chemicals in Water Using Fragmentation Mass Spectra with Machine Learning Models.

Knowing odor sensory attributes of odorants lies at the core of odor tracking when addressing waterborne odor issues. However, experimental determination covering tens of thousands of odorants in authentic water is not pragmatic due to the complexity of odorant identification and odor evaluation. In this study, we propose the first machine learning (ML) model to predict odor perception/threshold aiming at odorants in water, which can use either molecular structure or MS2 spectra as input features. We demonstrate that model performance using MS2 spectra is nearly as good as that using unequivocal structures, both with outstanding accuracy. We particularly show the model's robustness in predicting odor sensory attributes of unidentified chemicals by using the experimentally obtained MS2 spectra from nontarget analysis on authentic water samples. Interpreting the developed models, we identify the intricate interaction of functional groups as the predominant influence factor on odor sensory attributes. We also highlight the important roles of carbon chain length, molecular weight, etc., in the inherent olfactory mechanisms. These findings streamline the odor sensory attribute prediction and are crucial advancements toward credible tracking and efficient control of off-odors in water.

Studying Plant Specialized Metabolites Using Computational Metabolomics Strategies.

Plant specialized metabolites have diversified vastly over the course of plant evolution, and they are considered key players in complex interactions between plants and their environment. The chemical diversity of these metabolites has been widely explored and utilized in agriculture and crop enhancement, the food industry, and drug development, among other areas. However, the immensity of the plant metabolome can make its exploration challenging. Here we describe a protocol for exploring plant specialized metabolites that combines high-resolution mass spectrometry and computational metabolomics strategies, including molecular networking, identification of structural motifs, as well as prediction of chemical structures and metabolite classes.

Purification of Single-Stranded RNA Bacteriophages and Host Receptors for Structural Determination Using Cryo-Electron Microscopy.

Single-stranded RNA bacteriophages (ssRNA phages) are small viruses with a compact genome (~3-4 kb) that infect gram-negative bacteria via retractile pili. These phages have been applied in various fields since their discovery approximately 60 years ago. To understand their biology, it is crucial to analyze the structure of mature virions. Cryo-electron microscopy (cryo-EM) has been employed to determine the structures of two ssRNA phages, MS2 and Qß. This chapter presents a method for purifying these two phages and their receptor, the F-pilus, to allow examination using cryo-EM.

Polyphenol-rich fermented hempseed ethanol extracts improve obesity, oxidative stress, and neural health in high-glucose diet-induced Caenorhabditis elegans.

Whole hempseed (WHS), fermented whole hempseed (FWHS), dehulled hempseed (DHS), and fermented dehulled hempseed (FDHS) ethanol extracts were tested for their toxicity and physiological benefits in relation to their phenolic profiles. The safety of all samples was confirmed by the absence of toxic effects on HepG2 cells. FWHS exhibited the highest capacity to inhibit lipase activity (70.80%) and acetylcholinesterase (AChE) (78.94%) in vitro. Similarly, in HepG2 cells, FWHS revealed the greatest ability to reduce the accumulation of reactive oxygen species (ROS). Fermented hempseed demonstrated superior antioxidant, neuroprotective and anti-fat potential, counteracting ageing in high glucose diet-induced C. elegans than unfermented. HPLC and UHPLC-Q-TOF-MS/MS2 phenolic identification revealed the presence of diverse flavonoids, phenolic acids, lignanamides, and phenylamides in hempseed extracts. Among these polyphenols, quercetin, gallic acid, and kaempferol exhibited excellent antioxidant potential, whereas N-trans-feruloyl tyramine displayed the highest anti-lipase potential. This study suggests that polyphenol-rich hempseed exhibits potent antioxidant, and anti-obesity effects, and could improve neural health.

BT100, a three-in-one, multipurpose disinfecting, deodorizing, and air-cleaning solution with an effective, gradual, and continuous gaseous chlorine dioxide-releasing substance.

Aerosols carrying viruses that are released from the oral cavity of infected individuals are the primary, if not the only, means of transmission during viral respiratory disease epidemics. This makes crowded rooms and tiny, enclosed public areas like bathrooms prime environments for the transmission of diseases. Volatile organic compounds (VOCs) and formaldehyde are two contaminants that pose serious threats to human health and well-being in indoor environments. The varied disinfectant properties of chlorine dioxide (ClO2) make it a key player in treating a range of air quality issues. To balance effectiveness and safety, however, the careful application of chlorine dioxide is essential to achieving the best results in air quality while preserving human health and well-being. This study explores the many functions of chlorine dioxide, including the prevention of the spread of viruses, the elimination of harmful gases like ammonia and hydrogen sulfide, and its effects on formaldehyde and total volatile organic compounds (TVOCs) in indoor environments using BT100. The results indicate a reduction of 98.5%, 81.01%, 62.22%, 46.5%, and 63.84% in minimizing aerosolized viruses, ammonia, and hydrogen sulfide gas in addition to formaldehyde and total volatile organic compounds.

Metabolic and elemental profiling as potential discriminating features among the black mahlab seeds (Monechma ciliatum) grown in three different regions.

INTRODUCTION: Black mahlab (Monechma ciliatum) seed is a rich source of metabolites and minerals and is usually believed to have a similar composition between different areas of cultivation. Until now, no studies have assessed changes in black mahlab seeds (BMSs) to determine those constituents that help to discriminate them according to geographical origin. OBJECTIVES: The present study attempted to compare the metabolomics and elemental profiles of BMSs of different geographical origins and identified the potential markers using ultrahigh-performance liquid chromatography quadrupole Orbitrap tandem mass spectrometry (UHPLC-Q-Orbitrap-MS2), and inductively coupled plasma mass spectrometry (ICP-MS) techniques and established the chemometric model to identify the potential markers and discriminate them according to cultivation sites. MATERIAL AND METHODS: In this work, data from metabolites analysis by UHPLC-Q-Orbitrap-MS2 and multi-elemental data obtained from ICP-MS were combined with chemometrics for tracing the geographical origin of BMSs. Principal component analysis (PCA) was used to evaluate the overall grouping of samples. In contrast, partial least squares-discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were employed for authentication. RESULTS: PLS-DA and OPLS-DA models were fully validated (R2Y and Q2 values > 0.5). Variable importance of various projections was applied to obtain valuable data about differential elements (seven markers were identified) and metabolites (23 markers were identified) with high discrimination potential. The outcomes presented in this study serve as an appropriate framework for developing novel discrimination approaches in food origin screening.

Strategy strengthens structural identification through hyphenating full collision energy ramp-MS2 and full exciting energy ramp-MS3 spectra: An application for metabolites identification of rosmarinic acid.

"MS/MS spectrum to structure" analysis is the most challenging task for MS/MS-relied qualitative characterization. The conventional database- and computation-assisted strategies cannot reach confirmative identification, notably for isomers. Hence, an advanced strategy was proposed here through tackling the two determinant obstacles such as the transformation from elemental compositions to fragment ion structures and the linkage style amongst substructures. As typical conjugated structures, esters were measured for strategy illustration, and metabolite identification of a famous natural antioxidant namely rosmarinic acid (RosA) in rat was undertaken for applicability justification. Through programming online energy-resolved (ER)-MS for the first collision cell of Qtrap-MS device, full collision energy ramp (FCER)-MS2 spectrum was configured for [M-H]- ion of each ester to provide optimal collision energies (OCEs) for all concerned diagnostic fragment ions (DFIs), i.e. a-, b-, c-, y-, and z-type ions. The linear correlations between masses and OCEs were built for each ion type to facilitate DFIs recognition from chaotic MS2 spectrum. To identify 1st-generation fragment ions, full exciting energy ramp (FEER)-MS3 spectra were configured for key DFIs via programming the second ER-MS in the latter collision chamber. FEER-MS3 spectrum of 1st-generation fragment ion for ester was demonstrated to be identical with FEER-MS2 spectrum of certain hydrolysis product when sharing the same structure. After applying the advanced strategy to recognize DFIs and identify 1st-generation fragment ions, a total of forty metabolites (M1-M40), resulted from hydrolysis, methylation, sulfation, and glucuronidation, were unambiguously identified for RosA after oral administration. Together, the advanced bottom-up strategy hyphenating FCER-MS2 and FEER-MS3 spectra, is meaningful to strengthen "MS/MS spectrum to structure" analysis through recognizing and identifying fragment ions.

Dissecting quantitative trait nucleotides by saturation genome editing.

Genome editing technologies have the potential to transform our understanding of how genetic variation gives rise to complex traits through the systematic engineering and phenotypic characterization of genetic variants. However, there has yet to be a system with sufficient efficiency, fidelity, and throughput to comprehensively identify causal variants at the genome scale. Here we explored the ability of templated CRISPR editing systems to install natural variants genome-wide in budding yeast. We optimized several approaches to enhance homology-directed repair (HDR) with donor DNA templates, including donor recruitment to target sites, single-stranded donor production by bacterial retrons, and in vivo plasmid assembly. We uncovered unique advantages of each system that we integrated into a single superior system named MAGESTIC 3.0. We used MAGESTIC 3.0 to dissect causal variants residing in 112 quantitative trait loci across 32 environmental conditions, revealing an enrichment for missense variants and loci with multiple causal variants. MAGESTIC 3.0 will facilitate the functional analysis of the genome at single-nucleotide resolution and provides a roadmap for improving template-based genome editing systems in other organisms.

Comparing the Fate and Transport of MS2 Bacteriophage and Sodium Fluorescein in a Karstic Chalk Aquifer.

Groundwater flow and contaminant migration tracing is a vital method of identifying and characterising pollutant source-pathway-receptor linkages in karst aquifers. Bacteriophages are an attractive alternative tracer to non-reactive fluorescent dye tracers, as high titres (>1012 pfu mL-1) can be safely released into the aquifer, offering improved tracer detectability. However, the interpretation of bacteriophage tracer breakthrough curves is complicated as their fate and transport are impacted by aquifer physicochemical conditions. A comparative tracer migration experiment was conducted in a peri-urban catchment in southeast England to characterise the behaviour of MS2 bacteriophage relative to sodium fluorescein dye in a karstic chalk aquifer. Tracers were released into a stream sink and detected at two abstraction boreholes located 3 km and 10 km away. At both sites, the loss of MS2 phage greatly exceeded that of the solute tracer. In contrast, the qualitative shape of the dye and phage breakthrough curves were visually very similar, suggesting that the bacteriophage arriving at each site was governed by comparable transport parameters to the non-reactive dye tracer. The colloid filtration theory was applied to explain the apparent contradiction of comparable tracer breakthrough patterns despite massive phage losses in the subsurface. One-dimensional transport models were also fitted to each breakthrough curve to facilitate a quantitative comparison of the transport parameter values. The model results suggest that the bacteriophage migrates through the conduit system slightly faster than the fluorescent dye, but that the former is significantly less dispersed. These results suggest that whilst the bacteriophage tracer cannot be used to predict receptor concentrations from transport via karstic flow paths, it can provide estimates for groundwater flow and solute contaminant transit times. This study also provides insight into the attenuation and transport of pathogenic viruses in karstic chalk aquifers.

A high-throughput analytical method for complex contaminant mixtures in biosolids.

Biosolids are rich in organic matter and other nutrients that contribute to environmental and agricultural sustainability by improving soil textural and biological properties and enhancing plant growth when applied to agricultural crops. Land application of biosolids encourages resource recovery and circumvents drawbacks associated with landfilling or incineration. However, biosolids contain numerous chemicals at trace levels, and quantitative analysis of such mixtures in this complex matrix is crucial for understanding and managing application risks. There are currently few analytical methods available that are capable of extracting and quantifying a large range of the emerging contaminants found in biosolids. In this study, a simplified, rapid, and robust method of analysis was developed and validated for a high-priority organic contaminant mixture of 44 endocrine disrupting compounds known to occur in biosolids. Analytes consisted of chemicals from many classes with a wide range of physiochemical properties (e.g., log Kow values from -1.4 to 8.9). The biosolids extraction and cleanup protocol was validated for 42 of the targeted compounds. The UPLC-MS2 parameters were validated for all 44 organic contaminants targeted for study. From the two batches of biosolids tested using this analytical method, most of the targeted contaminants (86%) were detected with 100% frequency at concentrations ranging from 0.036 to 10,226 µg/kg dw. Performance results highlighted that internal standards alone could not negate biosolids matrix effects; thus, internal standards and the standard addition method were used for residue quantification. This was the first study to detect and quantify 6PPD-q in biosolids, and the first to quantify lidocaine and 11 other chemicals in biosolids using a single analytical method. This method may be expanded for analysis of additional chemicals in biosolids and comparable matrices.

Multifaceted effects on even-skipped transcriptional dynamics upon Krüppel dosage changes.

Although fluctuations in transcription factor (TF) dosage are often well tolerated, TF dosage modulation can change the target gene expression dynamics and result in significant non-lethal developmental phenotypes. Using MS2/MCP-mediated quantitative live imaging in early Drosophila embryos, we analyzed how changing levels of the gap gene Krüppel (Kr) affects transcriptional dynamics of the pair-rule gene even-skipped (eve). Halving the Kr dosage leads to a transient posterior expansion of the eve stripe 2 and an anterior shift of stripe 5. Surprisingly, the most significant changes are observed in eve stripes 3 and 4, the enhancers of which do not contain Kr-binding sites. In Kr heterozygous embryos, both stripes 3 and 4 display narrower widths, anteriorly shifted boundaries and reduced mRNA production levels. We show that Kr dosage indirectly affects stripe 3 and 4 dynamics by modulating other gap gene dynamics. We quantitatively correlate moderate body segment phenotypes of Kr heterozygotes with spatiotemporal changes in eve expression. Our results indicate that nonlinear relationships between TF dosage and phenotypes underlie direct TF-DNA and indirect TF-TF interactions.