Biology subjects

Low, A.

Publications and source records attributed to Low, A..

12 recordsLinked to original sources

bioRxiv2026

Asymmetric flagellar filaments shape Borreliella burgdorferi morphology and motility

The Lyme disease spirochete Borreliella burgdorferi possesses bipolar periplasmic flagella that are essential for its distinctive flat-wave morphology, motility, and infectivity. However, how the molecular architecture of these flagella contributes to spirochetal morphology and motility remains poorly understood. Here, using in situ single-particle cryo-electron microscopy, we determine near-atomic structures of native periplasmic flagellar filaments and reveal two distinct architectures: half-sheathed and unsheathed. We show that the spirochete-specific protein FlaA forms an asymmetric sheath along the convex surface of the conserved FlaB filament core, with sheath assembly restricted to the proximal filament region near the flagellar motor. Atomic models reveal that FlaA anchors to the FlaB core through specific interactions with two surface-exposed loops, while genetic and motility analyses demonstrate distinct roles for these loops in maintaining cell morphology and motility. Structural comparisons reveal that the FlaB core possesses intrinsic curvature and supercoiling, which are substantially amplified by asymmetric FlaA assembly. These findings support a model in which localized FlaA sheath assembly reinforces the proximal filament and potentially modulates its mechanical properties. Together, our results uncover a previously unrecognized mechanism by which asymmetric sheath assembly enhances flagellar supercoiling, providing a molecular basis for understanding the distinctive morphology and motility of spirochetes.

microbiology↗

bioRxiv2026

Quorum sensing and capsule expression enable subpopulation evasion of phage killing in Escherichia coli ST131: Implications for targeted therapy

Escherichia coli ST131 is a globally disseminated multidrug-resistant lineage frequently associated with recalcitrant urinary tract infections (UTIs) and bacteraemia. While bacteriophages offer a promising alternative treatment to antibiotics, their efficacy is often limited in physiologically relevant conditions in comparison to laboratory media. In this study, we have investigated the mechanisms by which the representative ST131 strain, EC958, evades elimination by a model phage, LUC4. We observed that in the urine environment, EC958 can transiently resist phage infection by a density dependent mechanism and by the production of protective polysaccharides. Based on this understanding, we developed a phage treatment strategy that can sterilise an EC958 culture in urine-based medium, even at high bacterial densities. The rational design of the successful phage therapy strategy utilises a tailored phage cocktail containing phage that encode depolymerase enzymes to degrade bacterial surface carbohydrates and the targeting of multiple receptors to prevent the emergence of fixed genetic resistant mutants. We found the addition of specific carbon sources renders the bacteria more susceptible to phage infection. By combining these findings with a simulated bladder wash to model voiding, we successfully achieved elimination of EC958 cultures in a urine environment. This study provides a framework for overcoming both fixed and reversible phage resistance, offering a translatable strategy for effectively treating urinary tract infections with phage. Author SummaryIn this study, we investigated how bacterial populations can overcome a phage infection. Phage are viruses that naturally kill bacteria and provide an alternative treatment to antibiotics. We focussed on a particularly aggressive and antibiotic resistant strain of E. coli, EC958, which belongs to a group of E. coli strains that are a leading cause of urinary tract infections and life-threatening bloodstream infections worldwide. We found that in a simulated bladder environment, these bacteria do not rely on genetic mutations to survive but they employ a range of hide and seek strategies. We showed that bacteria can coat themselves in a protective layer to block the phage and use social signalling to enter a dormant state when cell density is high. When they are in this sleep-like state the phage cannot successfully infect. To overcome these bacterial defences, we developed a treatment strategy combining effective phage with specific naturally occurring additives, that trick the bacteria into waking up and becoming vulnerable again to phage infection. By also simulating a clinical bladder wash to reduce bacterial numbers and therefore reduce social-signalling, we were able to eliminate the bacterial population. Our findings suggest that by understanding bacterial strategies we can design more effective and personalised phage therapies to treat bacterial infections.

microbiology↗

bioRxiv2026

Multi-Contrast MRI Inputs Enable Self-Consistent Tissue Segmentation & Robust Perivascular Space Identification

Different MRI image contrasts are designed to highlight various tissue properties and combining them allows extension of probabilistic segmentation beyond the commonly used "gray-white-CSF" models. This work describes a fully automated method that combines T1-weighted, T2-FLAIR, and conventional T2-weighted images to provide internal consistency across prediction of tissue segmentations including segmentation of superficial and deep gray matter, white matter hyperintensities, and MR-visible perivascular spaces. Results from 773 imaging datasets from 403 participants in the Mayo Clinic Study of Aging and Mayo Clinic Alzheimers Disease Research Center (ADRC) are presented.

neuroscience↗

bioRxiv2026

Tuning siRNA Specificity through Seed Region Incorporation of Deoxyribonucleotide Stereoisomers

Precise chemical design continues to drive advances in RNA-based therapeutics. Here, we report the synthesis and site-specific incorporation of four canonical phosphoramidites (U, C, A, and G), each bearing non-natural nucleoside configurations: {beta}-D-2'-deoxyxylonucleosides and -L-2'-deoxyribonucleosides. These stereochemically distinct nucleoside analogs were introduced at positions 6 and 7 within siRNA seed regions. When applied to siRNAs targeting Ttr, ACTN1, and Marc1, these modifications reduced off-target gene repression in functional assays and, in several cases, in transcriptome-wide differential expression analyses, while preserving robust on-target activity. In vivo, Marc1-targeting siRNAs containing these modified nucleosides showed decreased hepatotoxicity, as evidenced by reduced serum ALT and AST levels. Collectively, these findings establish {beta}-D-2'-deoxyxylonucleoside and -L-2'-deoxyribonucleoside analogs as promising chemical tools for enhancing the specificity and safety of siRNA therapeutics. This work underscores the power of integrating rational nucleoside design with comprehensive functional and in vivo evaluation to advance drug development based on RNA interference (RNAi). GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/699368v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@10e6e8aorg.highwire.dtl.DTLVardef@7b2797org.highwire.dtl.DTLVardef@1643f44org.highwire.dtl.DTLVardef@75a0a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Brain Network Analysis in Alzheimer's Disease and Mild Cognitive Impairment using High-Density Diffuse Optical Tomography

Dementia is associated with altered resting state connectivity, measures of which could aid in its early detection and monitoring. High-density diffuse optical tomography (HD-DOT) is well-suited to detect these alterations at scale due to its numerous practical advantages, but it has not yet been applied to dementia. In this study, we investigated resting state functional connectivity across the prefrontal cortex in individuals with Mild Cognitive Impairment (MCI, n = 22), Alzheimers Disease (AD, n = 21), and in healthy controls (n = 22). A graph theoretical approach was taken to characterise both global and local patterns of connectivity over a five-minute resting period. We found that individuals with AD and MCI exhibited denser and stronger networks, with shorter path lengths, as well as a loss of consistent key network hubs with worsening cognitive impairment. These results indicate that networks in dementia are more globally connected, albeit in a disorganised manner, perhaps reflecting the recruitment of additional connections for short-term stability which may be ultimately damaging in the long-term. Following the demonstration of HD-DOTs capacity to detect differences between healthy ageing and dementia, this work opens up new possibilities for the use of optical imaging in the study of this clinical population and HD-DOTs potential for scalable clinical use.

neuroscience↗

bioRxiv2024

Dissecting the heat stress altering immune responses and skin microbiota in fish in a recirculating aquaculture system in Singapore

Environmental factors, probiotics and feed additives affect microbiota diversity in fish. Water temperature disrupts the composition and diversity of microbiota, with temperature changes triggering stress and immune responses in fish. In Singapore, water heat treatment is used to control and prevent disease outbreaks in farmed fish. Although gut microbiota responses to heat stress have been reported, little is known about the effects of heat treatment on fish immune responses and fish skin microbiota dynamics. Over a 3-mo interval, we investigated microbiota dynamics and fish immune responses associated with a heat treatment practice in a commercial fish farm with a recirculating aquaculture system (RAS). Tank water temperature was raised to 37-39 {degrees}C for 1 hour, every 2 weeks. Tank water and fish microbial communities were analysed by 16S amplicon sequencing, and host molecular expressions were determined by qPCR. We inferred that heat treatment increased stress and immune responses that protected fish from opportunistic infections. However, overreaction to temperature stress can cause dysbiosis of the skin microbiota and death. We also suggested the value of the skin microbiota Pseudomonadota: Bacteroidota (P:B) ratio as a biomarker for aquaculture fish health. IMPORTANCEAquaculture is an emerging economic activity to supply high-quality animal protein and reduce reliance on wild-caught fish products. Recently, there has been emphasis on intensive aquaculture, using a Recirculating Aquaculture System (RAS). In RAS, management of pathogens/parasites prevalence is a major challenge. Developing practical solutions for producing healthy juveniles in nursery systems will make profound contributions to sustainable aquaculture. In this study, we used an unconventional strategy, exposing juveniles to the pathobiome in the environment, followed by non-lethal heat shock treatments to enhance immunity. Short-term stress induced heat shock proteins that protected fish from opportunistic infections. We concluded that manipulating environmental-microbial-host interactions, together with enhanced functional capacity of fish immune response, has potential for disease control in aquaculture.

systems biology↗

bioRxiv2023

LipidSIM: inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, systematic Markov Modeling framework

Lipid metabolism is a complex and dynamic system involving numerous enzymes at the junction of multiple metabolic pathways. Disruption of these pathways leads to systematic dyslipidemia, a hallmark of many pathological developments, such as nonalcoholic steatohepatitis and diabetes. Recent advances in computational tools can provide insights into the dysregulation of lipid biosynthesis, but limitations remain due to the complexity of lipidomic data, limited knowledge of interactions among involved enzymes, and technical challenges in standardizing across different lipid types. In this study, we present a low-parameter, biologically interpretable framework named Lipid Synthesis Investigative Markov model (LipidSIM), which models and predicts the source of perturbations in lipid biosynthesis from lipidomic data. LipidSIM achieves this by accounting for the interdependency between the lipid species via the lipid biosynthesis network and generates testable hypotheses regarding changes in lipid biosynthetic reactions. This feature allows the integration of lipidomics with other omics types, such as transcriptomics, to elucidate the direct driving mechanisms of altered lipidomes due to treatments or disease progression. To demonstrate the value of LipidSIM, we first applied it to hepatic lipidomics following Keap1 knockdown and found changes in mRNA expression of the lipid pathways were consistent with the LipidSIM-predicted fluxes. Second, we used it to study lipidomic changes following intraperitoneal injection of CCl4 to induce fast NAFLD/NASH development and the progression of fibrosis and hepatic cancer. Finally, to show the power of LipidSIM for classifying samples with dyslipidemia, we used a Dgat2-knockdown study dataset. Thus, we show that as it demands no a priori knowledge of enzyme kinetics, LipidSIM is a valuable and intuitive framework for extracting biological insights from complex lipidomic data.

bioinformatics↗

bioRxiv2022

Trans-interaction of risk loci 6p24.1 and 10q11.21 is associated with endothelial damage in coronary artery disease

Background and AimsSingle nucleotide polymorphism rs6903956 has been identified as one of the genetic risk factors for coronary artery disease (CAD). However, rs6903956 lies in a non-coding locus on chromosome 6p24.1. We aim to interrogate the molecular basis of 6p24.1 containing rs6903956 risk alleles in endothelial disease biology. Methods and ResultsWe generated induced pluripotent stem cells (iPSCs) from CAD patients (AA risk genotype at rs6903956) and normal controls (GG non-risk genotype at rs6903956). CRIPSR-Cas9-based deletions ({Delta}63-89bp) on 6p24.1, including both rs6903956 and a short tandem repeat variant rs140361069 in linkage disequilibrium, were performed to generate isogenic iPSC-derived endothelial cells. Edited CAD endothelial cells, with removal of A risk alleles, exhibited a global transcriptional downregulation of pathways relating to abnormal vascular physiology and activated endothelial processes. A CXC chemokine ligand on chromosome 10q11.21, CXCL12, was uncovered as a potential effector gene in CAD endothelial cells. Underlying this effect was the preferential inter-chromosomal interaction of 6p24.1 risk locus to a weak promoter of CXCL12, confirmed by chromatin conformation capture assays on our iPSC-derived endothelial cells. Functionally, risk genotypes AA/ AG at rs6903956 were associated significantly with elevated levels of circulating damaged endothelial cells in CAD patients. Circulating endothelial cells isolated from patients with risk genotypes AA/ AG were also found to have 10 folds higher CXCL12 transcript copies/ cell than those with non-risk genotype GG. ConclusionOur study reveals the trans-acting impact of 6p24.1 with another CAD locus on 10q11.21 and is associated with intensified endothelial injury.

molecular biology↗

bioRxiv2022

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Despite extensive efforts to address it, the vastness of uncharacterized dark matter microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were missing in short-read only analysis and with >28x N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3,413 strains that are unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of all strains were not represented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) not represented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal the significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.

genomics↗

bioRxiv2021

Longitudinal changes in diet cause repeatable and largely reversible shifts in gut microbial communities of laboratory mice and are observed across segments of the entire intestinal tract

Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet-switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance to expand sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.

microbiology↗

bioRxiv2020

Host-age prediction from fecal microbiome composition in laboratory mice

The life-long relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Changes in microbiome composition throughout the lifespan of a host remain, however, largely understudied. In this study, the fecal microbiome of conventionally raised C57BL/6J mice was analyzed throughout almost the entire expected lifespan, from maturing (9 weeks) until very old age (112 weeks). Analysis of alpha and beta diversity suggests that gradual microbiome changes occur throughout the entire murine life but appear to be more pronounced in maturing to middle-aged phases. Phylum-level analysis indicates a shift in the Firmicutes/Bacteroidetes ratio in favor of the Firmicutes in the second year of adulthood. Varying successional patterns throughout life were observed for many Firmicutes OTUs, while relative abundances of Bacteroidetes OTUs varied primarily in the early life phases. Microbiome configurations at given time points were used as training sets in a Bayesian model, which in turn effectively enabled the prediction of host age. The fecal microbiome composition may therefore serve as an accurate biomarker for aging. This study further suggests that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies. ImportanceThe life-long relationship between microorganisms and hosts has a profound impact on the overall physiology of the holobiont. Understanding the extent of gut microbiome compositional changes over the expected mouse lifespan may allow to better understand the interplay of microbiome and the host at the different life stages. In this study, we performed a two-year longitudinal study of murine fecal microbiome. Using fine-scale microbiome profiling we were able to predict the host age from the fecal microbiome composition. Moreover, we observed that the rate of compositional change appears to slow with age. The description of the compositional changes in commonly used C57BL/6J mice can be used to optimize selection of age-associated mouse models and highlights the use of microbiome-profiling as biomarker for aging.

microbiology↗

bioRxiv2017

Designing Anti-Zika Virus Peptides Derived from Predicted Human-Zika Virus Protein-Protein Interactions

The production of anti-Zika virus (ZIKV) therapeutics has become increasingly important as the propagation of the devastating virus continues largely unchecked. Notably, a causal relationship between ZIKV infection and neurodevelopmental abnormalities has been widely reported, yet a specific mechanism underlying impaired neurological development has not been identified. Here, we report on the design of several synthetic competitive inhibitory peptides against key pathogenic ZIKV proteins through the prediction of protein-protein interactions (PPIs). Often, PPIs between host and viral proteins are crucial for infection and pathogenesis, making them attractive targets for therapeutics. Using two complementary sequence-based PPI prediction tools, we first produced a comprehensive map of predicted human-ZIKV PPIs (involving 209 human protein candidates). We then designed several peptides intended to disrupt the corresponding host-pathogen interactions thereby acting as anti-ZIKV therapeutics. The data generated in this study constitute a foundational resource to aid in the multi-disciplinary effort to combat ZIKV infection, including the design of additional synthetic proteins.

synthetic biology↗