Biology subjects

Abbott, D. W.

Publications and source records attributed to Abbott, D. W..

9 recordsLinked to original sources

bioRxiv2026

HIGH DOSE GAMMAHERPESVIRUS INFECTION IN MACROPHAGES RESULTS IN INFLAMMATORY MULTIMODAL CELL DEATH

Human gammaherpesviruses (gHVs) including Epstein-Barr Virus and Kaposis sarcoma associated herpesvirus are linked to cancer and inflammatory disease development. The outcome of gHV infection is highly regulated by cell type, with macrophages identified as an important early infection target that can also serve as a latency reservoir. Here, we used the mouse gHV model, murine gammaherpesvirus (MHV68), to identify a dose-dependent outcome of MHV68 infection of macrophages, with high dose infection resulting in extensive morphological changes, viral gene expression, and a pronounced inflammatory cell death not observed under conditions of lytic replication occurring at lower infectious dose. Virion envelope and tegument components were not sufficient for this dose-dependent cell death, which required intact viral DNA and virus transcription, yet occurred independently of viral DNA replication and late gene transcription. Necrostatin-1 (Nec-1) treatment, an anti-inflammatory therapeutic, limited cell death and reduced cell morphology alterations, with no impact on virus replication, uncoupling cell death from lytic replication. Activation of autophagy profoundly limited high dose infection outcomes, with increased cell survival and reduced viral gene expression. Despite the improved cell survival observed in cells treated with Nec-1, biochemical analysis of infected cultures identified robust apoptosis induction with subsequent activation of gasdermin E, suggesting a multi-modal cell death mechanism culminating in pyroptosis. Our findings suggest that high dose macrophage infection byMHV68 is a major driver of inflammatory cell death to potentially shape downstream inflammation and immune responses.

microbiology↗

bioRxiv2025

2D HSQC-derived "dark forest" image with enhanced local resolution via first derivative processing-logarithmic cosine transformation (FDP-LCT): Demonstration on per-O-ethylated kappa- and iota-carrageenans

Solution-state two-dimensional (2D) 1H-13C HSQC NMR is a powerful tool for polysaccharide structure elucidation but often suffers from limited sensitivity and broad peaks due to the low natural abundance of 13C and poor digital resolution of the indirect dimension, respectively, as well as the typically low concentration and high viscosity of polysaccharide solutions. It is therefore pivotal to improve the resolution of 2D 1H-13C HSQC spectra for accurate peak picking and assignment, particularly in the indirect 13C dimension. In this study, we developed an algorithm that combines first derivative processing with a novel logarithmic cosine transformation (FDP-LCT) to convert 2D 1H-13C HSQC spectra into local-resolution-enhanced images resembling a dark forest of straight, densely standing trees. These images revealed sharpened spectral features and enabled extraction of precise 1H and 13C chemical shifts, as demonstrated using per-O-ethylated kappa-and iota-carrageenans, two sulfated galactans differing only by a single substitution at the O-2 position of anhydrogalactose. In conclusion, this approach provides an effective post-acquisition strategy for enhancing digital resolution in 2D HSQC spectra and improving the structural analysis of closely related complex polysaccharides. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/689839v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@c85f3dorg.highwire.dtl.DTLVardef@e4ded2org.highwire.dtl.DTLVardef@1e0b7b5org.highwire.dtl.DTLVardef@3cebcf_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- An algorithm combining first derivative processing and logarithmic cosine transformation was developed for 2D HSQC. - The algorithm was used to boost the local resolution of 2D HSQC spectra of the per-O-ethylated carrageenans. - Structures were distinguished by complete interpretation of 2D NMR spectra. - A post-processing workflow was developed to facilitate chemical shift extraction from sharpened HSQC.

biochemistry↗

bioRxiv2025

Global distribution of microbial carrageenan foraging pathways reveals widespread latent traits within the genetic dark matter of ruminant intestinal microbiomes

Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we applied functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the distal gut over the rumen, and bacterial isolates had capacity to use carrageenans as a sole carbon source. Carrageenan-active polysaccharide utilization loci (CarPULs) were identified and recombinant enzymes were characterized to provide insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining revealed that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a globally distributed latent trait within the order Ruminantia and carried within microbiome as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.

microbiology↗

bioRxiv2024

Microbial alginate foraging is conserved in geographically and taxonomically distinct ruminant microbiomes

Seaweed plays a crucial role in carbon cycling and is expected to be a valuable resource for sustainable biomass, with applications in biofuel production, human nutrition, and animal feed. Although seaweed has historically been used as a feed source for livestock grazing near coastlines, the process by which it is digested in the rumen remains unknown. Here, we show how the brown algae Saccharina latissima is catabolized in the rumen ecosystem of two different species using in vivo and in vitro experimental systems. We determined that the ruminal decomposition of alginate, a prominent component of the brown algae cell wall, requires microbial catabolic pathways complete with alginate lyases and transport proteins. Evidence of digestion was obtained through a combination of animal models, bacterial imaging, multilayered meta-omics, and enzyme biochemistry. The evolution of and implications for acquisition of alginate utilization loci within geographically and taxonomically distinct ruminants are considered. Graphical abstractSaccharina latissima is a brown alga commonly found in the North Atlantic, Arctic and Pacific oceans. S. latissima was collected from the west coast and Canada and Norway for microbiome studies. Alginate constitutes a substantial portion of the cell wall of S. latissima (SL), and its digestion requires a specific set of enzymes, alginate lyases. We investigated if and how S. latissima is metabolized in geographically distinct rumen ecosystems through in vivo lamb feeding experiments (2.5 and 5% inclusion, DM basis) and in vitro cattle-based rumen simulation technique, RUSITEC, experiments (up to 50% inclusion). Evidence supporting ruminal degradation of alginate was explored using a combination of multilayered meta-omics, physiology (fluorescently labelled S. latissima hot water extracts (FLA-SLAT)) and biochemical characterization of PL6 alginate lyases. O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/628917v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@eebe40org.highwire.dtl.DTLVardef@c6fb8org.highwire.dtl.DTLVardef@7a9b1borg.highwire.dtl.DTLVardef@15d30d7_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Glycogen degrading activities of catalytic domains of α-amylase and α-amylase-pullulanase enzymes conserved in Gardnerella spp. from the vaginal microbiome

Gardnerella spp. are associated with bacterial vaginosis, in which normally dominant lactobacilli are replaced with facultative and anaerobic bacteria including Gardnerella spp. Co-occurrence of multiple species of Gardnerella is common in the vagina and competition for nutrients such as glycogen likely contributes to the differential abundances of Gardnerella spp. Glycogen must be digested into smaller components for uptake; a process that depends on the combined action of glycogen degrading enzymes. In this study, the ability of culture supernatants of 15 isolates of Gardnerella spp. to produce glucose, maltose, maltotriose and maltotetraose from glycogen was demonstrated. Carbohydrate active enzymes were identified bioinformatically in Gardnerella proteomes using dbCAN2. Identified proteins included a single domain -amylase (EC 3.2.1.1) (encoded by all 15 isolates) and an -amylase-pullulanase (EC 3.2.1.41) containing amylase, carbohydrate binding modules and pullulanase domains (14/15 isolates). To verify the sequence-based functional predictions, the amylase and pullulanase domains of the -amylase-pullulanase, and the single domain -amylase were each produced in E. coli. The -amylase domain from the -amylase-pullulanase released maltose, maltotriose and maltotetraose from glycogen, and the pullulanase domain released maltotriose from pullulan and maltose from glycogen, demonstrating that the Gardnerella -amylase-pullulanase is capable of hydrolyzing -1,4 and -1,6 glycosidic bonds. Similarly, the single domain -amylase protein also produced maltose, maltotriose and maltotetraose from glycogen. Our findings show that Gardnerella spp. produce extracellular amylase enzymes as public goods that can digest glycogen into maltose, maltotriose and maltotetraose that can be used by the vaginal microbiota. ImportanceIncreased abundance of Gardnerella spp. is a diagnostic characteristic of bacterial vaginosis, an imbalance in the human vaginal microbiome associated with troubling symptoms, and negative reproductive health outcomes, including increased transmission of sexually transmitted infections and preterm birth. Competition for nutrients is likely an important factor in causing dramatic shifts in the vaginal microbial community but little is known about the contribution of bacterial enzymes to the metabolism of glycogen, a major food source available to vaginal bacteria. The significance of our research is characterizing the activity of enzymes conserved in Gardnerella species that contribute to the ability of these bacteria to utilize glycogen.

microbiology↗

bioRxiv2022

Dissecting the Pyrenophora tritici-repentis (tan spot of wheat) pangenome

We sequenced the genome of a global collection (40 isolates) of the fungus Pyrenophora tritici-repentis (Ptr), a major foliar pathogen of wheat and model for the evolution of necrotrophic pathogens. Ptr exhibited an open-pangenome, with 43% of genes in the core set and 57% defined as accessory (present in only a subset of isolates), of which 56% were singleton genes (present in only one isolate). A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around the effector coding genes, were explored further using the annotated genomes of two isolates sequenced by PacBio RS II and Illumina HiSeq. The Ptr genome exhibited major chromosomal rearrangements, including chromosomal fusion, translocation, and segment duplications. An intraspecies translocation of ToxA, the necrosis-inducing effector-coding gene, was facilitated within Ptr via a 143 kb Starship transposon (dubbed Horizon). Additionally, ToxB, the gene encoding the chlorosis-inducing effector, was clustered as three copies on a 294 kb transposable element in a ToxB-producing isolate. ToxB and its carrying transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and the transposon were both present in another non-coding isolate. The Ptr genome also appears to exhibit a one-compartment organization, but may still possess a two-speed genome that is facilitated by copy-number variation as reported in other fungal pathosystems. IMPORTANCEPtr is one of the most destructive wheat pathogens worldwide. Its genome is a mosaic of present and absent effectors, and serves as a model for examining the evolutionary processes behind the acquisition of virulence in necrotrophs and disease emergence. In this work, we took advantage of a diverse collection of pathogenic Ptr isolates with different global origins and applied short- and long-read sequencing technologies to dissect the Ptr genome. This study provides comprehensive insights into the Ptr genome and highlights its structural organization as an open pangenome with one-compartment. In addition, we identified the potential involvement of transposable elements in genome expansion and the movement of virulence factors. The ability of effector-coding genes to shuffle across chromosomes on large transposons was illustrated by the intraspecies translocation of ToxA and the multi-copy ToxB. In terms of gene contents, the Ptr genome exhibits a large percentage of orphan genes, particularly in non-pathogenic or weakly-virulent isolates.

genomics↗

bioRxiv2020

Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria

Gut microbiomes have vast catabolic potential and are essential to host health and nutrition. An in-depth understanding of the metabolic pathways in these ecosystems will enable us to design treatments (i.e. prebiotics) that influence microbiome structure and enhance host physiology. Currently, the investigation of metabolic pathways relies on inferences derived from metagenomics or in vitro cultivations, however, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to accurately assess metabolic abilities. Here, we present a multi-faceted study using complimentary next-generation physiology and omics approaches to characterize the microbial adaptation to a prebiotic in the rumen ecosystem. Using fluorescently labeled polysaccharides, we identified bacteria that actively metabolize a glycan prebiotic in the rumen microbiome ex vivo. Subsequently, we characterized strain-level variability in carbohydrate utilization systems and predict metabolic strategies of isolated bovine-adapted strains of Bacteroides thetaiotaomicron using comparative whole genome sequencing, RNA-Seq, and carbohydrate-active enzyme fingerprinting.

microbiology↗

bioRxiv2020

Characterization of an α-glucosidase enzyme conserved in Gardnerella spp. isolated from the human vaginal microbiome

Gardnerella spp. in the vaginal microbiome are associated with bacterial vaginosis, a dysbiosis in which a lactobacilli dominant microbial community is replaced with mixed aerobic and anaerobic bacteria including Gardnerella species. The co-occurrence of multiple Gardnerella species in the vaginal environment is common, but different species are dominant in different women. Competition for nutrients, particularly glycogen present in the vaginal environment, could play an important role in determining the microbial community structure. Digestion of glycogen into products that can be taken up and further processed by bacteria requires the combined activities of several enzymes collectively known as amylases, which belong to glycoside hydrolase family 13 (GH13) within the CAZy classification system. GH13 is a large and diverse family of proteins, making prediction of their activities challenging. SACCHARIS annotation of the GH13 family in Gardnerella resulted in identification of protein domains belonging to eight subfamilies. Phylogenetic analysis of predicted amylase sequences from 26 Gardnerella genomes demonstrated that a putative -glucosidase-encoding sequence, CG400_06090, was conserved in all species in the genus. The predicted -glucosidase enzyme was expressed, purified and functionally characterized. The enzyme was active on a variety of maltooligosaccharides over a broad pH range (4.0 - 8) with maximum activity at pH 7. The Km, kcat and kcat/Km values for the substrate 4-nitrophenyl -D-glucopyranoside were 8.3 M, 0.96 min-1 and 0.11 M-1min-1 respectively. Glucose was released from maltose, maltotriose, maltotetraose and maltopentaose, but no products were detected on thin layer chromatography when the enzyme was incubated with glycogen. Our findings show that Gardnerella spp. produce an -glucosidase enzyme that may contribute to the complex and multistep process of glycogen metabolism by releasing glucose from maltooligosaccharides.

microbiology↗

bioRxiv2019

Phospho-tuning immunity through Denisovan, modern human, and mouse TNFAIP3 gene variants

Resisting or tolerating microbes are alternative strategies to survive infection, but little is known about the evolutionary mechanisms controlling this balance. Here, genomic analyses of anatomically modern humans, extinct Denisovan hominins, and mice revealed a series of missense variants in the immune response inhibitor A20 (encoded by TNFAIP3), substituting non-catalytic residues of the ubiquitin protease domain to diminish I{kappa}B-dependent phosphorylation and activation of A20. Two A20 variants with partial phosphorylation deficits appeared beneficial: one originating in Denisovans and introgressed in modern humans throughout Oceania, and another in a mouse strain resistant to Coxsackievirus. By contrast, a variant with 95% loss of phosphorylation caused spontaneous inflammatory disease in humans and mice. Analysis of the partial phosphorylation variant in mice revealed diminished tolerance of bacterial lipopolysaccharide or to poxvirus inoculation as trade-offs for enhanced immunity.\n\nOne Sentence SummaryModern and ancient variants reveal a genetically tunable element for balancing immunity and microbial tolerance.

immunology↗