Pangenome graph construction with nf-core/pangenome, pangenome graphs, single cell multi-omics, RNA foundation models, Nextflow for B-cell receptor sequencing from nontargeted bulk RNA-seq, ...

Context It has been hypothesized that multiple-antigen vaccines, such as measles-mumps-rubella vaccine, or aggregated vaccine exposure could lead to immune dysfunction, resulting in nontargeted infect...

Detecting PFAS is challenging due to their diverse chemical structures, lack of standards, complex sample matrices, and the need for sensitive equipment to measure trace levels. Background contaminati...

A combination of transcriptomic, proteomic, and nontargeted metabolomic analyses of a global regulatory gacS mutant in comparison with the wild-type strain Pseudomonas donghuensis SVBP6 allowed ident...

Brominated disinfection byproducts (Br-DBPs) generated during water treatment pose significant health risks due to their high toxicity. This study conducted a comparative nontargeted analysis of Br-DBPs generated during chlorination and chloramination using ultra-performance liquid chromatography (UPLC) coupled with high-resolution (HR) mass spectrometry (MS), including MS and tandem MS experiments. An advanced halogen extraction code identified halogenated compounds via isotopic patterns of chlorine (Cl) and bromine (Br), with MFAssignR assigning molecular formulas. Chlorination resulted in a total of 154 Br-DBPs, most containing carbon, hydrogen, oxygen, and bromine (CHOBr), whereas chloramination generated 79 Br-DBPs, predominantly nitrogenous Br-DBPs (CHONBr), including 57 CHOBr and 22 CHONBr, effectively preserving aromatic structures within natural organic matter (NOM). Several Br-DBPs with strong instrument responses, including brominated aliphatic carboxylic acids and aromatic phenolic acids formed primarily during chlorination, were identified, whereas nitrogenous Br-DBPs were exclusive to chloramination. In silico toxicity assessments indicate that many Br-DBPs identified in this study, particularly those with multiple bromine substitutions and functional groups such as nitro and carboxylic acids in aromatic structures, exhibit substantially higher acute toxicity and mutagenic potential compared to regulated DBPs like bromoform and dibromacetic acid. These findings highlight the need to prioritize polybrominated, aromatic, and nitrogenous Br-DBPs in water treatment research and regulation.

Despite advancements in high-resolution screening techniques, the identification of novel perfluoroalkyl and polyfluoroalkyl substances (PFAS) remains challenging without prior structural information. In view of this, we proposed and implemented a new data-driven algorithm to calculate spectral similarity among PFAS, facilitating the generation of molecular networks to screen for unknown compounds. Using this approach, 81 PFAS across 12 distinct classes were identified in soil samples collected near an industrial park in Shandong Province, China, including the first reported occurrence of 12 iodine-substituted PFAS. Among them, the standards of four iodine-substituted polyfluorinated ether sulfonates (I-PFESA) were successfully synthesized, enabling structural confirmation and subsequent quantitative analysis. Although the median concentration of ∑I-PFESA (0.74 ng/g dw) in soil samples was lower than that of ∑H-PFESA (hydrogen-substituted, 61.96 ng/g dw) and ∑Cl-PFESA (chlorine-substituted, 2.98 ng/g dw), embryotoxicity assays in zebrafish revealed that 6:2 I-PFESA exhibited greater toxicity compared to 6:2 Cl-PFESA of the same chain length. This highlights the need for a closer examination of the toxic effects of I-PFESA. Notably, the proposed algorithm, based on novel PFAS spectral similarity, provides new perspectives on the environmental behavior and transformation of I-PFESA, although further investigation is required to elucidate the underlying mechanisms of their toxicity.

Biosolids are a byproduct of wastewater treatment that can be beneficially applied to agricultural land as a fertilizer. While U.S. regulations limit metals and pathogens in biosolids intended for lan...

Measles is a contagious, vaccine-preventable viral disease that can be shed into wastewater by infected individuals. In September 2025, as part of an ongoing, nontargeted, ultra-deep metagenomic se...

Measles is a contagious, vaccine-preventable viral disease that can be shed into wastewater by infected individuals. In September 2025, as part of an ongoing, nontargeted, ultra-deep metagenomic se...

Metagenomics holds promise as a comprehensive, nontargeted tool for environmental monitoring. However, one key limitation is that the quantitative capacity of metagenomics is not well-defined. Here, w...

Liquid chromatography electrospray ionization high-resolution mass spectrometry (LC/ESI/HRMS) is frequently employed in nontargeted screening (NTS) due to its high selectivity and sensitivity. However...