Biology subjects

Nguyen, L.

Publications and source records attributed to Nguyen, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Multi-omics Insight into Cardiac Myofibril Remodeling in Post-Prandial Burmese Pythons

Burmese pythons exhibit rapid cardiac remodeling in response to a dramatic increase in metabolic rate during digestion. Here, we performed single-myofibril mechanics measurements and myosin heavy chain metabolic assays to evaluate the impact of feeding on the cardiomyocyte sarcomere - the fundamental molecular unit of muscle contraction - using two experimental paradigms: normal feeding (one meal per month) and frequent feeding (eight meals per month). Myofibril tension and rate of relaxation increased during digestion in both paradigms, while frequent feeding was further associated with slower myofibril activation kinetics and faster myosin heavy chain ATP turnover. To identify molecular changes at the sarcomere and gain potential mechanistic insight, we performed multi-omics analyses. RNA sequencing identified increased expression of some sarcomere genes during digestion; however, proteomics analysis suggested a delay in sarcomere protein synthesis at the peak of remodeling, as expression of many sarcomere proteins decreased. Analysis of post-translational modifications (ubiquitinomics, phospho-proteomics, acetylomics) identified hundreds of significantly regulated sites on sarcomere proteins during digestion, including many on the tension-regulating titin and myosin heavy chain proteins. Our results detail the molecular underpinnings of cardiac remodeling in digesting Burmese pythons and suggest that natures solution for rapidly increasing cardiac contractility is a post-translational sarcomere tuning program.

molecular biology↗

bioRxiv2026

Investigating Quinclorac Binding to Human Serum Albumin using Spectroscopy and Molecular Docking

Human serum albumin (HSA) is the most abundant plasma protein and serves as a major transporter and reservoir for a wide range of endogenous ligands, including fatty acids, heme, bilirubin, prostaglandins, and metal ions, as well as numerous exogenous compounds, such as pharmaceuticals. HSA is a 66 kDa monomeric, multidomain protein containing two principal ligand-binding sites, Sudlow sites I and II. Sudlow site I contains Trp214, the sole tryptophan residue in HSA, whose intrinsic fluorescence provides a sensitive probe for studying ligand-protein interactions. In this study, the interaction between HSA and the persistent organochlorine herbicide quinclorac (QNC) was investigated using steady-state fluorescence spectroscopy and molecular docking. The binding of QNC to HSA is characterized by concentration-dependent quenching of HSAs intrinsic tryptophan fluorescence. Quantitative analysis revealed a high affinity of QNC for HSA, with [~] 1 M dissociation constant (Kd). Temperature-dependent fluorescence quenching experiments indicate a static quenching mechanism. Moreover, a competitive displacement assay using site-specific markers identified Sudlow site I as the primary binding site for QNC in HSA. Induced-fit docking further demonstrated that QNC is accommodated and stabilized by polar interactions, {pi}-stacking, and/or hydrophobic interactions within the Sudlow I binding pocket. Together, these results provide a biochemical and molecular understanding of how QNC, a persistent pesticide, binds to HSA.

biochemistry↗

bioRxiv2026

Autoinducer-2 and acyl homoserine lactones have contrasting effects on ammonia and nitrite-oxidizing sludge

Enhancing nitrification with quorum sensing manipulation has emerged as a promising strategy to overcome rate-limiting steps. This study examined how disrupting microbial cell-to-cell communication by supplementing or quenching signal molecules regulates ammonia- and nitrite-oxidizing activity within activated sludge. Prolonged enrichment of activated sludge over 180 days yielded stable and robust nitrifying consortia, increasing the ammonia oxidation rate (AOR) from 5.4 to 9.3 mg N g-{superscript 1} VSS h-{superscript 1} and the nitrite oxidation rate (NOR) from 0.6 to 4.8 mg N g-{superscript 1} VSS h-{superscript 1}, while reducing the hydraulic residence time by 50 % (from 72 h to 36 h). Exogenous addition of oxoacyl and long-chain acyl homoserine lactone (AHL) signals further boosted AOR up to 4.5-fold higher than the control activated sludge, predominantly through transcriptional activation of the amoA gene in Nitrosomonas eutropha. Acylase-mediated AHL quenching lowered AOR to 4.8 mg N g-{superscript 1} VSS h-{superscript 1} but improved functional resilience of nitrite oxidizing bacteria by enhancing mass transfer and oxygen diffusion via smaller flocs (123 {micro}m vs 357 {micro}m in AHL-treated sludge). Conversely, elevated autoinducer-2 (AI-2) levels suppressed ammonia-oxidizing activity (AOR = 2 mg N g-{superscript 1} VSS h-{superscript 1}) yet stimulated nitrite oxidation (NOR = 36 mg N g-{superscript 1} VSS h-{superscript 1}), particularly Nitrospira, underscoring the contrasting regulatory requirements of the two nitrifying guilds. Overall, the study demonstrates that AHLs and AI-2 serve as complementary yet opposing regulators of nitrification, primarily activating ammonia oxidizers and nitrite oxidizers, respectively. Maintaining these signaling molecules within an optimal physiological window thereby offers a biologically tunable approach for synchronized ammonia and nitrite oxidation, ultimately maximizing nitrogen removal in biological treatment systems.

microbiology↗

bioRxiv2026

Auxin coordinates cell states during Arabidopsis root development

Cell-to-cell variation in gene expression can be highly detrimental and, in some contexts, is actively buffered out; however, in other contexts, it is crucial and actively amplified. For example, variation must be minimized to build organs with consistent size and shape, yet the initiation of organogenesis requires a subset of cells to take on a new fate, a process that often relies on small differences between cells. In plants, much of development is controlled by the hormone auxin, which has been hypothesized to coordinate cell responses by inducing degradation of transcriptional repressors. To quantify the level of cell-to-cell variation and directly test its connection to auxin signaling, we assessed variation in expression of a lateral root founder cell marker GATA23 when auxin levels or responsiveness was modulated. We found that auxin acted as both an amplifier and a constrainer of transcriptional variation during the initiation of a new root. We then extended this work to analysis of root regeneration, where auxin was also found to play a critical role in coordinating cells during fate transitions. ARTICLE SUMMARYDuring organogenesis, cell-to-cell variation is induced, enabling some cells to adopt a new identity and differentiate. Despite this dependence on variation, organogenesis is robust in developmental stages and outcomes. In plants, organogenesis is usually controlled by the hormone auxin, and we hypothesized that auxin ensures coordination among differentiating cells to enable robust development. Using Arabidopsis lateral root development as a model, our results showed that cells receiving the highest auxin dosage both amplify their own auxin response and repress the auxin response in neighboring cells receiving lower auxin dosage, establishing separation between differentiating and non-differentiating cells and ensuring coordinated organogenesis.

developmental biology↗

bioRxiv2025

Associations between amygdala connectivity and experienced discrimination in children

Discrimination is a chronic stressor linked to adverse health outcomes, particularly in racial and ethnic minorities. Understanding associations between early discrimination and the brain in childhood may help identify mechanisms through which discrimination impacts future health. Data from 4512 children (ages 9-11) and a subsample of Black, Indigenous, and People of Color (BIPOC; N = 1567) from the Adolescent Brain and Cognitive Development (ABCD) Study(R) was used to create linear mixed-effects models that evaluated associations between Perceived Discrimination (PD) and amygdala resting-state fMRI connectivity (AC) to the salience network (SN), default mode network (DMN), and thalamus. PD was measured using the youth self-reported PD Scale. Results indicated that greater PD significantly predicted greater AC to the right thalamus in our full sample. In secondary analyses, environmental and behavioral factors were evaluated as potential moderators for associations significant at least at a trend level in both our full sample and BIPOC subsample. In our BIPOC subsample, traumatic events experienced moderated the relationship between PD and AC to the anterior cingulate cortex (ACC; SN), such that greater traumatic experiences predicted stronger positive associations between PD and this connection. Results suggest PD impacts neural connections in early life, highlighting the need to consider the impact of discrimination on risk for psychopathology.

neuroscience↗

bioRxiv2025

Genetic Analysis of F1 Cluster Phages that Infect Mycobacterium smegmatis Identifies Two Distinct Holin-Like Proteins that Regulate the Host Lysis Event

Phages Girr and NormanBulbieJr (NBJ) infect Gram-positive Mycobacterium smegmatis mc2 155. Both phages contain conserved lysis cassettes that harbor two endolysin genes (lysin A and lysin B) and two genes encoding transmembrane domain (TMD) holin-like proteins. The first holin-like protein, termed LysF1a is 88 amino acids, has two TMDs and a predicted N-in-C-in membrane topology. The second, termed LysF1b, has a single N-terminal TMD and a predicted N-out-C-in topology making it distinct from the type III holins or spanins in size and membrane topology. Deletion of lysF1b results in severe lysis defect phenotypes manifest by reduced plaque size and changes to lysis timing in liquid culture. Deletion of both lysF1a and lysF1b genes results in phages that show the same lysis phenotypes as the single lysF1b deletion. Phages with only lysF1b are lysis competent and trigger lysis prematurely when exposed to energy poisons while phages with lysF1a or lysF1a/lysF1b deletions do not trigger prematurely. Deletion of genes upstream of the lysis cassette did not impact lysis phenotypes. Lysis recovery mutants were isolated from phages lacking the lysF1b gene and these mutants generated wild type plaque size but triggered lysis prematurely and showed [~]65% reductions in burst size. Genome sequencing identified different point mutations that mapped to TMD1 or the C-terminal region of the lysF1a gene. Infection of an M. smegmatis strain that does not produce lipomannan and lipoarabinomannan by either wild type phages or phages carrying the lysF1b deletion showed modest plaque size increases but did not fully complement the lysis defect of phages lacking the lysF1b gene. Collectively, the findings show that both LysF1a and LysF1b proteins are required for efficient bacterial lysis by these F1 cluster phages. LysF1a does not function as a pure antiholin but requires the expression of the LysF1b protein for efficient lysis functioning.

microbiology↗

bioRxiv2025

Rapid assay optimization by plug-and-play MAPPIT

Studying protein-protein interactions, which are crucial for all cellular processes in both health and disease, offers valuable insights into underlying mechanisms and reveals promising therapeutic targets. While efforts have been made to vastly increase the scale of MAPPIT assays, covering the full protein interactome remains challenging, in particular when considering the availability of different assay configurations. In this study, we expanded our Golden Gate modular cloning platform to enable rapid, customizable construct assembly for MAPPIT assays. We demonstrate the strength of this expanded toolbox for multiple distinct protein-protein interactions, including a MAPPIT assay for six different intracellular VHH targeting the anti-viral effector protein MXA.

synthetic biology↗

bioRxiv2025

Species-specific Rates of Fatty Acid MetabolismSet the Scale of Temporal Patterning of Corticogenesisthrough Protein Acetylation Dynamics

Developmental processes display temporal differences across species, leading to divergence in organ size and composition. In the cerebral cortex, neurons of diverse identities are generated sequentially through a temporal patterning mechanism conserved throughout mammals. This corticogenesis process is considerably prolonged in the human species, leading to increased brain size and complexity, but the underlying molecular mechanisms remain largely unknown. Here we found that human cortical progenitors displayed lower levels of fatty acid oxidation than their mouse counterparts, in line with their protracted pattern. Treatments that enhance mitochondrial fatty acid oxidation (FAO) accelerated the development of human cortical organoids, including faster progression of neural progenitor cell fate and precocious generation of late-born neurons and glia. FAO accelerated temporal patterning through increased Acetyl-CoA-dependent protein acetylation, including on specific histone transcriptional marks. Thus, species-specific metabolic rates regulate the turnover of post-translation modifications to set the scale of temporal gene regulatory networks of corticogenesis.

neuroscience↗

bioRxiv2025

SAMBA: A Segment Anything Model-based tool for semi-automated Behavioural Analysis of Drosophila and other model organisms

Quantitative behavioural analysis is a powerful approach for linking genotype to phenotype, but many existing tools require specialised hardware, extensive preprocessing, or coding expertise. We present SAMBA (Segment Anything Model for Behavioural Analysis), an open-access, Google Colab-based pipeline that harnesses the Segment Anything Model 2 (SAM2) for accurate, semi-automated tracking without thresholding or background subtraction. With minimal user input, SAMBA extracts movement parameters, detects behavioural states, and supports batch processing. Validating SAMBA in a Drosophila melanogaster model of 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) deficiency revealed impaired locomotion, reduced speed, and altered decision-making, highlighting its ability to capture nuanced phenotypes in neurometabolic disease. We further demonstrate adaptability to adult Drosophila and larval zebrafish, underscoring its cross-species utility. By combining foundation-model segmentation with an accessible interface, SAMBA lowers technical barriers to high-throughput behavioural phenotyping and is readily extendable to diverse model organisms, life stages, and experimental paradigms. This flexibility positions SAMBA as a valuable platform for accelerating disease mechanism studies, genetic screens, and preclinical testing. SUMMARY STATEMENTWe present an easy-to-use, open-access tool designed for Drosophila larval movement analysis, and readily customised for other applications, enabling rapid, scalable assessment of organism behaviour without specialised equipment or coding expertise.

animal behavior and cognition↗

bioRxiv2025

H1.3 depletion in AML cells prompts H1.2 redistribution, chromatin remodeling and cell cycle defects

Linker histone H1 variants play critical, yet distinct, roles in chromatin organization and gene regulation. However, very little is known about their specificity in cancer cells. In this study, we investigated the specificity of the H1.3 variant in acute myeloid leukemia (AML) cells. Through chromatin mapping and transcriptomic analyses, we revealed that H1.3 was enriched explicitly in regions with a high GC content and co-localized with the repressive mark H3K27me3, supporting its role in chromatin compaction and transcriptional repression. Knockout of H1.3 induced specific changes in gene expression profiles and chromatin dynamics, characterized by the relocalization of H1.2, which was redistributed from its usual chromatin regions to the freed H1.3 regions. Consequently, locus-specific chromatin alterations associated with interferon-related signalling pathways and cell cycle deregulation were observed. Our findings emphasized an important and locus-specific function of H1.3 in AML cells. Overall, our study revealed a mechanistic connection between H1 variant imbalance, immune response activation, and cell cycle regulation, with implications for our understanding of epigenetic regulation in cancer cells.

genomics↗

bioRxiv2025

A Co-Evolutionary Multi-Objective Framework for Joint Topology and Parameter Discovery in Gene Regulatory Networks

Inferring gene regulatory networks (GRN) poses a complex discrete-continuous, multi-objective optimization problem that requires the simultaneous discovery of both network topology and kinetic parameters. Current methods are often limited because they address these two challenges separately. We propose a novel co-evolutionary multi-objective framework that evolves topology and parameter populations in tandem to optimize three competing objectives: dynamic fidelity, network simplicity, and robustness. This algorithm utilizes biologically-inspired operators and is grounded in theoretical results on Pareto optimality for mixed discrete-continuous spaces. In computational experiments on synthetic benchmarks, our approach showed superior performance, attaining the lowest mean squared error in three of four test cases against single-objective and topology-fixed methods. The framework successfully discovers multiple functionally equivalent network configurations, a finding that highlights the degeneracy inherent in biological systems and offers practical insights for synthetic biology, where function is often prioritized over precise structural accuracy.

systems biology↗

bioRxiv2025

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data

Telomeres protect chromosome ends and its length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many biological fields are interest in understanding its biological significance. Here we introduce Topsicle, a computational method that estimates telomere length from whole genome long read sequencing data using k-mer and change point detection analysis. Simulations showed Topsicle was robust to sequencing errors and coverage. Application of Topsicle on plant and human cancer cells showed high accuracy and comparable results to direct telomere length measurements. We predict Topsicle will be a useful tool for studying telomere biology.

genomics↗

bioRxiv2025

Discovery of orally bioavailable Zika and West Nile Virus antiviral compounds targeting the NS2B-NS3 protease

Flaviviruses are a class of pathogenic viruses with pandemic potential that are typically transmitted via infected arthropods. In addition, Zika virus is sexually transmissible and causes congenital malformations if infection occurs during pregnancy. Although over 1.5 million people were infected during the 2015-2016 Zika outbreak, to date, there are no clinical-stage vaccines or antivirals. Herein, we report the discovery of potent inhibitors of the Zika virus NS2B-NS3 protease that also show activity against the West Nile virus NS2B-NS3 protease. Starting from a crystallographic fragment screen, we employed a pharmacophore approach coupled with high-throughput library chemistry to elaborate fragments in the active site. Potent, metabolically stable, non-covalent, non-peptidomimetic inhibitors were identified with antiviral activity in vitro. The lead compound was progressed to a three-day Zika virus challenge study in AG129 mice, where it displayed significant viral RNA load reduction in both mouse plasma and spleen.

microbiology↗

bioRxiv2025

Clustered VEGF Nanoparticles in Microporous Annealed Particle (MAP) Hydrogel Accelerates Functional Recovery and Brain Tissue Repair after Stroke

Ischemic stroke, a blockage in the vasculature of the brain that results in insufficient blood flow, is one of the worlds leading causes of disability. The cascade of inflammation and cell death that occurs immediately following stroke drives vascular and functional loss that does not fully recover over time, and no FDA-approved therapies exist that stimulate regeneration post-stroke. We have previously developed a hydrogel scaffold that delivered heparin nanoparticles with and without VEGF bound to their surface to promote angiogenesis and reduce inflammation, respectively. However, the inclusion of the naked heparin nanoparticles warranted concern over the development of bleeding complications. Here, we explore how microporous annealed particle (MAP) scaffolds functionalized with VEGF coated heparin nanoparticles can both reduce inflammation and promote angiogenesis - without the inclusion of free heparin nanoparticles. We show that our updated design not only successfully promotes de novo tissue formation, including the development of mature vessels and neurite sprouting, but it also leads to functional improvement in a photothrombotic stroke model. In addition, we find increased astrocyte infiltration into the infarct site correlated with mature vessel formation. This work demonstrates how our biomaterial design can enhance endogenous regeneration post-stroke while eliminating the need for excess heparin.

bioengineering↗

bioRxiv2025

Loss of Elp3 impairs the maturation tempo of brain ependymal cells

Conditional deletion of Elp3 in the mouse forebrain leads to microcephaly at birth. In this study, we demonstrate that these mice also develop postnatal hydrocephalus, associated with an enlargement of the brain ventricles. In wild-type mice, ependymal motile cilia are properly aligned to facilitate the circulation of cerebrospinal fluid (CSF) within the ventricles. Our findings reveal that Elp3 loss induces endoplasmic reticulum (ER) stress and upregulation of ATF4 expression in ependymal cell progenitors, which compromises Notch signaling and accelerates their maturation. This is accompanied by a disruption in the establishment of rotational and translational polarities of the motile cilia of maturing ependymal cells, resulting in disorganized cilia bundles. Collectively, these molecular abnormalities lead to the premature and abnormal development of ependymal cells, culminating in cilia beating dysfunction, impaired CSF clearance, and the development of hydrocephalus.

neuroscience↗

bioRxiv2024

Structural Convergence and Water-Mediated Substrate Mimicry Enable Broad Neuraminidase Inhibition by Human Antibodies

Influenza has been responsible for multiple global pandemics and seasonal epidemics and claimed millions of lives. The imminent threat of a panzootic outbreak of avian influenza H5N1 virus underscores the urgent need for pandemic preparedness and effective countermeasures, including monoclonal antibodies (mAbs). Here, we characterize human mAbs that target the highly conserved catalytic site of viral neuraminidase (NA), termed NCS mAbs, and the molecular basis of their broad specificity. Cross-reactive NA-specific B cells were isolated by using stabilized NA probes of non-circulating subtypes. We found that NCS mAbs recognized multiple NAs of influenza A as well as influenza B NAs and conferred prophylactic protections in mice against H1N1, H5N1, and influenza B viruses. Cryo-electron microscopy structures of two NCS mAbs revealed that they rely on structural mimicry of sialic acid, the substrate of NA, by coordinating not only amino acid side chains but also water molecules, enabling inhibition of NA activity across multiple influenza A and B viruses, including avian influenza H5N1 clade 2.3.4.4b viruses. Our results provide a molecular basis for the broad reactivity and inhibitory activity of NCS mAbs targeting the catalytic site of NA through substrate mimicry.

immunology↗

bioRxiv2024

Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?

Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles.

microbiology↗

bioRxiv2024

Ccp1 depletion disrupts network integration of hippocampal parvalbumin interneurons

Post-translational modifications (PTMs) of microtubules (MTs) endow them with specific properties that are essential for key cellular functions, such as axonal transport. Polyglutamylation, a PTM that accumulates in long-lived MTs, has been linked to neurodegeneration in the cerebellum when in excess. While hyperglutamylation of MTs leads to neurodegeneration and disrupts the function of specific neuronal subtypes like Purkinje cells, cortical neurons, and hippocampal excitatory neurons, little is known about its impact on inhibitory interneurons and their functional integration into local networks. In this study, we generated a conditional knockout mouse model to deplete cytosolic carboxypeptidase 1 (Ccp1) in GABAergic neurons, a key MT deglutamylase expressed by hippocampal interneurons. Our findings reveal that the loss of Ccp1 has a profound effect on hippocampal parvalbumin (PV)-expressing interneurons, impairing their axonal transport and reducing their perisomatic inhibition of pyramidal cells (PCs) in the CA2 region of the hippocampus. Research TopicsMolecular Neuroscience, Cell Biology HighlightsO_LIDifferent subtypes of hippocampal interneurons express unique sets of (de)glutamylases and show varying levels of protein posttranslational glutamylation. C_LIO_LIParvalbumin interneurons become hyperglutamylated when Ccp1 activity is lost. C_LIO_LIThe loss of Ccp1 disrupts axonal transport in interneurons and is associated with decreased perisomatic inhibition of hippocampal pyramidal cells in the CA2 region. C_LI

neuroscience↗