Navigating the maze of mass spectra: a machine-learning guide to identifying diagnostic ions in O-glycan analysis.

Structural details of oligosaccharides, or glycans, often carry biological relevance, which is why they are typically elucidated using tandem mass spectrometry. Common approaches to distinguish isomers rely on diagnostic glycan fragments for annotating topologies or linkages. Diagnostic fragments are often only known informally among practitioners or stem from individual studies, with unclear validity or generalizability, causing annotation heterogeneity and hampering new analysts.

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.

Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes.

Predicting glycan structure from tandem mass spectrometry via deep learning.

Glycans constitute the most complicated post-translational modification, modulating protein activity in health and disease. However, structural annotation from tandem mass spectrometry (MS/MS) data is a bottleneck in glycomics, preventing high-throughput endeavors and relegating glycomics to a few experts. Trained on a newly curated set of 500,000 annotated MS/MS spectra, here we present CandyCrunch, a dilated residual neural network predicting glycan structure from raw liquid chromatography-MS/MS data in seconds (top-1 accuracy: 90.

Decoding glycomics with a suite of methods for differential expression analysis.

Glycomics, the comprehensive profiling of all glycan structures in samples, is rapidly expanding to enable insights into physiology and disease mechanisms. However, glycan structure complexity and glycomics data interpretation present challenges, especially for differential expression analysis. Here, we present a framework for differential glycomics expression analysis.

GlycoDraw: a python implementation for generating high-quality glycan figures.

Glycans are essential to all scales of biology, with their intricate structures being crucial for their biological functions. The structural complexity of glycans is communicated through simplified and unified visual representations according to the Symbol Nomenclature for Glycans (SNFGs) guidelines adopted by the community. Here, we introduce GlycoDraw, a Python-native implementation for high-throughput generation of high-quality, SNFG-compliant glycan figures with flexible display options.

Interband cascade laser absorption of hydrogen chloride for high-temperature thermochemical analysis of fire-resistant polymer reactivity.

A mid-infrared absorption spectroscopy technique has been developed to quantitatively and spatially resolve gas temperature and molecular abundance of $ ^1{{\rm H}^{35}}{\rm Cl} $HCl in the high-temperature pyrolysis and oxidation layers of chlorinated polymers. Two transitions in the R-branch of the fundamental vibrational band of HCl near 3.34 µm are selected due to their relative strength and spectral isolation from other combustion products at elevated temperatures, and they are probed using a distributed feedback interband cascade laser.

Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources.

The aerobic degradation of phenol, chlorobenzene and dichlorobenzene as a sole carbon source has been observed in bacterial Gram-positive strain G2PT isolated from a wastewater bioprocessor. Cells display branching mycelia fragmenting into rod and coccoid elements when grown on TSA. Aerial hyphae formation occurs when grown on phenol and chlorinated aromatics as the sole carbon source.

Alcaligenes faecalis subsp. phenolicus subsp. nov. a phenol-degrading, denitrifying bacterium isolated from a graywater bioprocessor.

A Gram (-) coccobacillary bacterium, J(T), was isolated from a graywater bioprocessor. 16S rRNA and biochemical analysis has revealed strain J(T) closely resembles Alcaligenes faecalis ATCC 8750T and A. faecalis subsp.

A mammalian cell regulatory agent, CeReS-18, inhibits yeast cell proliferation but not bacterial replication.

A cell regulatory sialoglycopeptide, CeReS-18, purified from intact bovine cerebral cortex cells, has exhibited the capability of reversibly inhibiting cellular DNA synthesis and the proliferation of a wide array of mammalian cells. In the present study, the effect of CeReS-18 on the proliferation of bacterial ( Bacillus cereus and Escherichia coli) and yeast ( Saccharomyces cerevisiae and Schizosaccharomyces pombe) cells was investigated. The results showed that replication and viability of the bacterial cells were not affected by CeReS-18 at any concentration tested, including 15-fold higher than that used for inhibiting mouse 3T3 cell proliferation.

Assessment of bioaerosols in swine barns by filtration and impaction.

Bioaerosol concentrations inside one naturally ventilated and one mechanically ventilated swine finishing barn were assessed by sampling air using membrane filtration and impaction (six-stage Andersen sampler), and assayed by culture method. The barns, located on the same commercial farm in northeast Kansas, did not show any significant difference (p > 0.05) in concentrations of total and respirable airborne microorganisms.