Biology subjects

Low, K. E.

Publications and source records attributed to Low, K. E..

7 recordsLinked to original sources

bioRxiv2026

Layered phage therapy exploits capsule-loss escape and altered antibiotic susceptibility in CG23 hypervirulent Klebsiella pneumoniae

The rise of drug-resistant Klebsiella pneumoniae infections is prompting a re-evaluation of phage therapy as an alternative treatment. Phage therapy has achieved successful outcomes, yet important limitations persist, including the rapid emergence of phage resistance and the time required to source suitable phages. Combining multiple phages into a phage cocktail based on genetic diversity, morphology or distinct infection mechanisms is a common strategy to mitigate resistance. Phage pairing based on these criteria neither mitigates nor delays the emergence of resistance, using CG23 hypervirulent Klebsiella pneumoniae (hvKp) EC0675 as a model. In CG23 Kp strains, resistance arises through disruption of the capsular biosynthetic pathway, leading to capsule impairment and global cross-resistance to all capsule-active phages. Combining phages active against encapsulated wild-type bacteria with those active against capsule-deficient escape mutants can overcome this constraint, improving bacterial suppression in vitro and reducing bacterial burdens across multiple organs in a mouse systemic infection model. In parallel, phage-driven capsule loss increased susceptibility of hvKp EC0675 to selected antibiotics targeting the bacterial envelope or cell wall in vitro. These findings highlight the contribution of capsule-associated resistance to phage cross-resistance in the CG23 Kp strains examined, and support further evaluation of phage combinations targeting both wild-type bacteria and resistant derivatives, including their use alongside selected antibiotics, informing future clinical translation.

microbiology↗

bioRxiv2026

Improved 1H NMR and ATR-FTIR approaches for structural characterization of high-G-block and high-M-block alginic acids isolated from sugar kelp by a two-step gelation method

Two low-molecular-weight alginic acid fractions, G-block-rich SKP-G1 and M-block-rich SKP-G2, were sequentially isolated from a hot-water extract of sugar kelp (Saccharina latissima) alcohol-insoluble residue by acetic acid-induced and subsequent freeze-thaw-induced gelation. High-field (700 MHz) 2D 1H-1H COSY and TOCSY spectroscopy enabled comprehensive cross-peak assignments for selected alginate diad and triad sequences, supporting interpretation of 1D 1H NMR spectra. Sequence frequencies were combined with previously established inequalities [1] to calculate constrained frequency ranges for homoblocks beyond the triad level. For selected homoblock lengths up to a degree of polymerization of 18, comparison of the experimentally derived frequency ranges with frequencies predicted by chain-growth statistical models ruled out the Bernoulli model for both fractions and the first-order Markov model for SKP-G1. Applying the recently developed logarithmic cosine transformation (LCT) algorithm [2] to first- and second-derivative ATR-FTIR spectra enhanced the visualization of subtle spectral features and produced distinct fingerprints for the two fractions. As a proof of concept, LCT-transformed derivative ATR-FTIR spectra yielded distinct score distributions for the fractions in principal component analysis, suggesting their potential for chemometric differentiation of alginates with different block structures. In conclusion, extending 1H NMR-based sequence analysis to calculate constrained frequency ranges for homoblock polyads beyond the triad level, together with LCT-transformed derivative ATR-FTIR fingerprinting, expands the analytical toolkit for alginate block structure characterization.

biochemistry↗

bioRxiv2025

Bulk exocytosis of large intracellular apical precursor organelles establishes apical domain identity during de novo lumen formation

The formation of a microvilli-rich lumen is a key event in epithelial polarity development and tissue morphogenesis. During de novo lumenogenesis, epithelial cells establish luminal identity by directing apical cargo to an apical membrane initiation site (AMIS). Although this process has been widely studied, the mechanisms governing AMIS formation and its progression into a luminal precursor remain poorly understood. Here we combined quantitative light and electron microscopy with proximity proteomics to investigate the mechanistic basis of lumen initiation in MDCK-II cells. Contrary to prevailing models, we find that apical cargo is delivered to the AMIS in large intracellular apical precursor organelles, termed vacuolar apical compartments (VACs). VACs possess a preassembled microvilli-rich cortex and undergo exocytic fusion at the AMIS to generate a nascent lumen. Moreover, lumen initiation is tightly coordinated with the assembly and rearrangement of apical cell-cell junctions and requires the Crumbs complex protein PatJ, which controls the architecture of the apical-lateral border and connects the tight junction to the apical cortex. Together, our results identify PatJ as a critical organizer of the apical-lateral interface and indicate that VACs act as specialized transport organelles that deliver a preassembled apical cortex to the AMIS, enabling rapid and efficient lumen initiation.

cell biology↗

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↗

bioRxiv2023

The artemisinin-induced dormant stages of Plasmodium falciparum exhibit hallmarks of cellular senescence and drug resilience.

Recrudescent infections with human malaria parasite, Plasmodium falciparum, presented traditionally the major setback of artemisinin-based monotherapies. Although introduction of artemisinin combination therapies (ACT) largely solved the problem, the ability of artemisinin to induce dormant parasites still poses major obstacle for current as well as future malaria chemotherapeutics. Here, we developed a robust laboratory model for induction of dormant P. falciparum parasites and characterized their transcriptome, drug sensitivity profile and cellular ultrastructure. We show that P. falciparum dormancy requires a ~5-days maturation process during which the genome-wide gene expression pattern gradually transitions from the ring-like state to a highly unique form. The transcriptome of the mature dormant stage carries hallmarks of cellular senescence with downregulation of most cellular functions associated with growth and development, but upregulation of selected metabolic functions and DNA repair. Moreover, the P. falciparum dormant stage is considerably more resistant to essentially all antimalaria drugs compared to the fast-growing asexual stages. Finally, the unique cellular ultrastructure further suggests unique properties of this new developmental stage of the P. falciparum life cycle that should be taken into consideration by new malaria control strategies.

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↗