Biology subjects

Nguyen, T. H.

Publications and source records attributed to Nguyen, T. H..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

pH-dependent structural dynamics of the neuropeptide Y in aqueous solution

ABSTRACT. The neuropeptide Y regulates key molecular processes in the brain. Its interaction with the cell membrane, where it binds to specialized receptors with key physiological roles, likely depends on the pH. The structural ensembles of the porcine and human peptides, solved by Nuclear Magnetic Resonance (NMR) acid pH in aqueous solution, indicate an -helical core with unstructured termini. However, the protonation states of the carboxylic and histidine residues of the peptide, and the interplay between protonation states and peptide conformational dynamics, have not been explored. Here we perform constant pH simulations and graph-based analyses to investigate dynamics and H-bond patterns of the neuropeptide Y in the pH range from 3.0 to 7.0. We find that an -helical core, as observed in the NMR experiments, is presented at all pH values, though its length can vary by 2-3 residues depending on the pH. The pKa of Asp16, part of the -helix, and of Asp11 may shift by more than on pH unit. Based on these findings, we suggest that performing constant pH simulations may be required to describe accurately the interactions of the peptide with its cellular partners at the pH values of interest.

biophysics↗

bioRxiv2024

The evolution of root hydraulic traits in wheat over 100 years of breeding

Wheat (Triticum aestivum L.) plays a vital role in global food security, and understanding its root traits is essential for improving water uptake under varying environmental conditions. This study investigates how breeding over a century has influenced root morphological and hydraulic properties in six German winter wheat cultivars released between 1895 and 2002. Field and hydroponic experiments were used to measure root diameter, root number, branching density, and whole root system hydraulic conductance (Krs). Results showed a significant decline in root axes number and Krs over time, while root diameter remained stable across cultivars. Additionally, dynamic functional-structural modeling using the whole-plant model CPlantBox was employed to simulate the development of Krs with root system growth, revealing that older cultivars consistently had higher hydraulic conductance than modern ones. The combined approach of field phenotyping and modeling provided a comprehensive view of the changes in root traits with breeding. These findings suggest that breeding may have unintentionally favored cultivars with smaller root systems and more conservative water uptake strategies, under the high-input, high-density conditions of modern agriculture. The lessons from this study may inform future breeding efforts aimed at optimizing wheat root systems, helping to develop cultivars with water uptake better tailored to locally changing environmental conditions.

plant biology↗

bioRxiv2024

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells ([~]1:100), but a much larger ratio of phage genomes to bacterial genomes ([~]4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage, phage-plasmids, etc.). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occurs at a low average rate ([~]0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone, while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.

microbiology↗

bioRxiv2024

Nutrient competition predicts gut microbiome restructuring under drug perturbations

Human gut commensal bacteria are routinely exposed to various stresses, including therapeutic drugs, and collateral effects are difficult to predict. To systematically interrogate community-level effects of drug perturbations, we screened stool-derived in vitro communities with 707 clinically relevant small molecules. Across [~]5,000 community-drug interaction conditions, compositional and metabolomic responses were predictably impacted by nutrient competition, with certain species exhibiting improved growth due to adverse impacts on competitors. Changes to community composition were generally reversed by reseeding with the original community, although occasionally species promotion was long-lasting, due to higher-order interactions, even when the competitor was reseeded. Despite strong selection pressures, emergence of resistance within communities was infrequent. Finally, while qualitative species responses to drug perturbations were conserved across community contexts, nutrient competition quantitatively affected their abundances, consistent with predictions of consumer-resource models. Our study reveals that quantitative understanding of the interaction landscape, particularly nutrient competition, can be used to anticipate and potentially mitigate side effects of drug treatment on the gut microbiota.

microbiology↗

bioRxiv2024

Enhanced detection for antibiotic resistance genes in wastewater samples using CRISPR-enriched metagenomic method

The spread of antibiotic resistance genes (ARGs) in the environment is a global public health concern. To date, over 5,000 genes have been identified to express resistance to antibiotics. ARGs are usually low in abundance for wastewater samples, making them difficult to detect. Metagenomic sequencing and quantitative polymerase chain reaction (qPCR), two conventional ARG detection methods, have low sensitivity and low throughput limitations, respectively. We developed a CRISPR-Cas9-modified next-generation sequencing (NGS) method to enrich the targeted ARGs during library preparation. The false negative and false positive of this method were determined based on a mixture of bacterial isolates with known whole-genome sequences. Low values of both false negative (2/1,208) and false positive (1/1,208) proved the methods reliability. We compared the results obtained by this CRISPR-NGS and the conventional NGS method for six untreated wastewater samples. As compared to the ARGs detected in the same samples using the regular NGS method, the CRISPR-NGS method found up to 1,189 more ARGs and up to 61 more ARG families in low abundances, including the clinically important KPC beta-lactamase genes in the six wastewater samples collected from different sources. Compared to the regular NGS method, the CRISPR-NGS method lowered the detection limit of ARGs from the magnitude of 10-4 to 10-5 as quantified by qPCR relative abundance. The CRISPR-NGS method is promising for ARG detection in wastewater. A similar workflow can also be applied to detect other targets that are in low abundance but of high diversity.

microbiology↗

bioRxiv2024

Ancestral sequence reconstruction of Mic60 reveals a residue signature supporting respiration in yeast

In eukaryotes, cellular respiration takes place in the cristae of mitochondria. The mitochondrial inner membrane protein Mic60, a core component of the mitochondrial contact site and cristae organizing system (MICOS), is crucial for the organization and stabilization of crista junctions and its associated functions. While the C-terminal Mitofilin domain of Mic60 is necessary for cellular respiration, the sequence determinants for this function have remained unclear. Here, we used ancestral sequence reconstruction to generate Mitofilin ancestors up to and including the last opisthokont common ancestor (LOCA). We found that yeast-lineage derived Mitofilin ancestors as far back as the LOCA rescue respiration. By comparing Mitofilin ancestors, we identified four residues sufficient to explain the respiratory difference between yeast- and animal-derived Mitofilin ancestors. Our results provide a foundation for investigating the conservation of Mic60-mediated cristae junction interactions.

evolutionary biology↗

bioRxiv2024

A patient-derived amyotrophic lateral sclerosis blood-brain barrier cell model reveals focused ultrasound-mediated anti-TDP-43 antibody delivery.

BackgroundAmyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disorder with minimally effective treatment options. An important hurdle in ALS drug development is the non-invasive therapeutic access to the motor cortex currently limited by the presence of the blood-brain barrier (BBB). Focused ultrasound and microbubble (FUS+MB) treatment is an emerging technology that was successfully used in ALS patients to temporarily open the cortical BBB. However, FUS+MB-mediated drug delivery across ALS patients BBB has not yet been reported. Similarly, the effects of FUS+MB on human ALS BBB cells remain unexplored. MethodsHere we established the first FUS+MB-compatible, fully-human ALS patient-cell-derived BBB model based on induced brain endothelial-like cells (iBECs) to study anti-TDP-43 antibody delivery and FUS+MB bioeffects in vitro. ResultsGenerated ALS iBECs recapitulated disease-specific hallmarks of BBB pathology, including changes to BBB integrity, permeability and TDP-43 proteinopathy. Our results also identified differences between sporadic ALS and familial (C9orf72 expansion carrying) ALS iBECs reflecting patient heterogeneity associated with disease subgroups. Studies in these models revealed successful ALS iBEC monolayer opening in vitro with a lack of adverse cellular effects of FUS+MB. This was accompanied by the molecular bioeffects of FUS+MB in ALS iBECs including changes in expression of tight and adherens junction markers, and drug transporter and inflammatory mediators, with sporadic and C9orf72 ALS iBECs generating transient specific responses. Additionally, we demonstrated an effective increase in the delivery of anti-TDP-43 antibody with FUS+MB in C9orf72 (2.7-fold) and sporadic (1.9-fold) ALS iBECs providing the first proof-of-concept evidence that FUS+MB can be used to enhance the permeability of large molecule therapeutics across the BBB in a human ALS in vitro model. ConclusionsTogether, our study describes the first characterisation of cellular and molecular responses of ALS iBECs to FUS+MB and provides a fully-human platform for FUS+MB-mediated drug delivery screening on an ALS BBB in vitro model.

neuroscience↗

bioRxiv2024

Breakthrough in Dicot Prime Editing: Enabling Heritable Desired Edits in Tomato and Arabidopsis

Prime editing (PE) enables almost all types of precise genome editing in animals and plants. It has been successfully adapted to edit several plants at variable efficiency and versatility. However, this technique is inefficient for dicots for unknown reasons. Here, by employing novel combinations of PE components, including an RNA chaperone and modified epegRNAs driven by a PolII-PolIII composite promoter and a viral replicon system, we obtained up to 9.7% of the desired PE efficiency at the callus stage assessed by targeted deep sequencing. Subsequently, we identified that up to 38.2% of transformants contained desired PE alleles in tomatoes and Arabidopsis, marking the first successful heritable PE transmission in dicots. Our PE tools also showed high accuracy, specificity, and multiplexing capability, which unlocked the potential for practical PE applications in dicots, paving the way for transformative advancements in plant sciences.

synthetic biology↗

bioRxiv2024

The transcription factor IRF-5 is essential for the metabolic rewiring of CD8 T cells during chronic infection

Numerous transcription factors are involved in promoting an intricate gene expression program that leads to CD8 T cell exhaustion. Here, we found that the transcription factor IRF-5 is involved in limiting functional exhaustion of CD8 T cells by regulating the cell cycle and contributing to sustaining the mitochondrial functions and oxidative phosphorylation during the chronic stage of LCMV Cl13 infection. CD8 T cells lacking IRF-5 display reduced survival capacity and show increased signs of functional exhaustion during the chronic stage of infection. IRF-5-deficiency also resulted in a severely defective lipid metabolism, in a faulty mitochondrial envelope, and in the reduced capacity to produce ATP. Additionally, we observed increased lipid peroxidation in CD8 T cells lacking IRF-5, when compared with WT cells. These findings identify IRF-5 as a pivotal regulator of the metabolic rewiring that occurs in CD8 T cells during the chronic stages of infection and highlight its role in protecting cells from cell death, possibly by lipid peroxidation. SummaryIRF-5 is critical for regulating mitochondrial functions and oxidative phosphorylation in CD8 T cells during chronic stages of LCMV Cl13 infection.

immunology↗

bioRxiv2023

Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks

BackgroundCell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation atlas to TOO detection in low depth cfDNA samples. MethodsWe constructed a tumor-specific methylation atlas (TSMA) using whole-genome bisulfite sequencing (WGBS) data from five types of tumor tissues (breast, colorectal, gastric, liver and lung cancer) and paired white blood cells (WBC). TSMA was used with a non-negative least square matrix factorization (NNLS) deconvolution algorithm to identify the abundance of tumor tissue types in a WGBS sample. We showed that TSMA worked well with tumor tissue but struggled with cfDNA samples due to the overwhelming amount of WBC-derived DNA. To construct a model for TOO, we adopted the multi-modal strategy and used as inputs the combination of deconvolution scores from TSMA with other features of cfDNA. ResultsOur final model comprised of a graph convolutional neural network using deconvolution scores and genome-wide methylation density features, which achieved an accuracy of 69% in a held-out validation dataset of 239 low-depth cfDNA samples. ConclusionsIn conclusion, we have demonstrated that our TSMA in combination with other cfDNA features can improve TOO detection in low-depth cfDNA samples.

cancer biology↗

bioRxiv2023

Root hydraulic properties: an exploration of their variability across scales

Root hydraulic properties are key physiological traits that determine the capacity of root systems to take up water, at a specific evaporative demand. They can strongly vary among species, cultivars or even within the same genotype, but a systematic analysis of their variation across plant functional types (PFTs) is still missing. Here, we reviewed published empirical studies on root hydraulic properties at the segment-, individual root-, or root system scale and determined its variability and the main factors contributing to it. We observed an extremely large range of variation (of orders of magnitude) in root hydraulic properties, but this was not caused by systematic differences among PFTs. Rather, the (combined) effect of factors such as root system age, driving force used for measurement, or stress treatments shaped the results. We found a significant decrease in root hydraulic properties under stress conditions (drought and aquaporin inhibition) and a significant effect of the driving force used for measurement (hydrostatic or osmotic gradients). Furthermore, whole root system conductance increased significantly with root system age across several crop species, causing very large variation in the data (> 2 orders of magnitude). Interestingly, this relationship showed an asymptotic shape, with a steep increase during the first days of growth and a flattening out at later stages of development. This behaviour was also observed in simulations with computational plant models, suggesting common patterns across studies and species. These findings provide better understanding of the main causes of root hydraulic properties variations observed across empirical studies. They also open the door to better representation of hydraulic processes across multiple plant functional types and at large scales. All data collected in our analysis has been aggregated into an open access database (https://roothydraulic-properties.shinyapps.io/database/), fostering scientific exchange.

plant biology↗

bioRxiv2023

Cholesterol regulates plasma membrane bending by prominin-family proteins

Prominin-1 (Prom1) is a five-transmembrane-pass integral membrane protein that associates with curved regions of the plasma membrane. Prom1 interacts with membrane cholesterol and actively remodels the plasma membrane. Membrane bending activity is particularly evident in photoreceptors, where Prom1 loss-of-function mutations cause failure of outer segment homeostasis, leading to cone-rod retinal dystrophy (CRRD). The Tweety Homology (Ttyh) protein family has been proposed to be homologous to Prominin, but it is not known whether Ttyh proteins have an analogous membrane-bending function. Here, we characterize the membrane-bending activity of human Prom1 and Ttyh1 in native bilayer membranes. We find that Prom1 and Ttyh1 both induce formation of extracellular vesicles (EVs) in cultured mammalian cells and that the EVs produced are physically similar. Ttyh1 is more abundant in EV membranes than Prom1 and produces EVs with membranes that are more tubulated than Prom1 EVs. We further show that Prom1 interacts more stably with membrane cholesterol than Ttyh1 and that this may contribute to membrane bending inhibition in Prom1 EVs. Intriguingly, a loss-of-function mutation in Prom1 associated with CRRD induces particularly stable cholesterol binding. These experiments provide mechanistic insight into Prominin function in CRRD and suggest that Prom and Ttyh belong to a single family of functionally related membrane-bending, EV-generating proteins.

biochemistry↗

bioRxiv2023

Non-antibiotic drugs break colonization resistance against pathogenic Gammaproteobacteria

Non-antibiotic drugs can alter the composition of the gut microbiome, with largely undefined implications for human health. Here we compared the susceptibility of commensal and pathogenic bacteria to non-antibiotic drugs and found that pathogens show higher drug resistance, which could favor their expansion after treatment. We then developed a model system to screen for drug-microbiome interactions that increase the risk of enteropathogenic infections. Approximately 35% of the >50 drugs we tested increased the abundance of Salmonella Typhimurium in synthetic and human stool-derived microbial communities. This was due to direct effects of non-antibiotics on individual commensals, altered microbial interactions within communities and the potential of Salmonella to exploit different metabolic niches. Non-antibiotic drugs that favored Salmonella expansion in vitro also promoted other enteric pathogens and increased Salmonella loads in gnotobiotic and conventional mice. These findings may inform future strategies to control pathogen proliferation and to assess individual microbiota-drug-pathogen risks for infection.

microbiology↗

bioRxiv2023

Temporal profiling of Salmonella transcriptional dynamics during macrophage infection using a comprehensive reporter library

The transcriptome of Salmonella enterica serovar Typhimurium (S. Tm) dynamically responds to the rapid environmental shifts intrinsic to S. Tm lifestyle, exemplified by entry into the Salmonella-containing vacuole (SCV) within macrophages. Intracellular S. Tm must respond to the acidity of the SCV, accumulation of reactive oxygen/nitrogen species, and fluctuations in nutrient availability. Despite thorough RNA-seq-based investigations, the precise transcriptional timing of the expression of many secretion systems, metabolic pathways, and virulence effectors involved in infection has yet to be elucidated. Here, we construct a comprehensive library of GFP-reporter strains representing [~]3,000 computationally identified S. Tm promoter regions to study the dynamics of transcriptional regulation. We quantified promoter activity during in vitro growth in defined and complex media and throughout the timeline of intracellular infection of RAW 246.7 macrophages. Using bulk measurements and single-cell imaging, we uncovered condition-specific transcriptional regulation and population-level heterogeneity in the activity of virulence-related promoters, including SPI2 genes such as ssaR and ssaG. We discovered previously unidentified transcriptional activity from 234 genes, including ones with novel activity during infection that are associated with pathogenecity islands and are involved in metabolism and metal homeostasis. Our library and data sets should provide powerful resources for systems-level interrogation of Salmonella transcriptional dynamics.

microbiology↗

bioRxiv2023

Improving the discovery of rare variants associated with alcohol problems by leveraging machine learning phenotype prediction and functional information.

Alcohol use disorder (AUD) is moderately heritable with significant social and economic impact. Genome-wide association studies (GWAS) have identified common variants associated with AUD, however, rare variant investigations have yet to achieve well-powered sample sizes. In this study, we conducted an interval-based exome-wide analysis of the Alcohol Use Disorder Identification Test Problems subscale (AUDIT-P) using both machine learning (ML) predicted risk and empirical functional weights. This research has been conducted using the UK Biobank Resource (application number 30782.) Filtering the 200k exome release to unrelated individuals of European ancestry resulted in a sample of 147,386 individuals with 51,357 observed and 96,029 unmeasured but predicted AUDIT-P for exome analysis. Sequence Kernel Association Test (SKAT/SKAT-O) was used for rare variant (Minor Allele Frequency (MAF) < 0.01) interval analyses using default and empirical weights. Empirical weights were constructed using annotations found significant by stratified LD Score Regression analysis of predicted AUDIT-P GWAS, providing prior functional weights specific to AUDIT-P. Using only samples with observed AUDIT-P yielded no significantly associated intervals. In contrast, ADH1C and THRA gene intervals were significant (False discovery rate (FDR) <0.05) using default and empirical weights in the predicted AUDIT-P sample, with the most significant association found using predicted AUDIT-P and empirical weights in the ADH1C gene (SKAT-O P Default= 1.06 x 10-9 and P Empirical weight = 6.25 x 10-11). These findings provide evidence for rare variant association of the ADH1C gene with the AUDIT-P and highlight the successful leveraging of ML to increase effective sample size and prior empirical functional weights based on common variant GWAS data to refine and increase the statistical significance in underpowered phenotypes.

genetics↗

bioRxiv2023

A study of genetic variants associated with skin traits in the Vietnamese population

BackgroundMost skin-related traits have been studied from Caucasian genetic background. A comprehensive study on skin-associated genetic effects on under-represented populations like Vietnam is needed to fill the gaps in the field. ObjectivesTo develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole genome sequencing (WGS) data of 1000 genomes project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). By using this information we may have a better understanding of the susceptibility of Vietnamese people. MethodsVietnamese cohorts of whole genome sequencing (WGS) of 1008 healthy individuals for the reference and 96 genotyping samples (which do not have any skin cutaneous issues) by Infinium Asian Screening Array-24 v1.0 BeadChip were employed to predict skin-associated genetic variants of 25 skin-related and micronutrients requirement traits in population analysis and correlation analysis. Simultaneously, we compared the landscape of cutaneous issues of Vietnamese people with other populations by assessing their genetic profiles. ResultsThe skin-related genetic profile of Vietnamese cohorts is similar at most with East Asian (JPT: Fst=0.036, CHB: Fst=0.031, CHS: Fst=0.027, CDX: Fst=0.025) in the population study. In addition, we identified pairs of skin traits being at high risk of frequent co-occurrence (such as skin aging and wrinkles (r = 0.45, p =1.50e-5) or collagen degradation and moisturizing (r = 0.35, p = 1.1e-3). ConclusionThis is the first investigation in Vietnam to explore genetic variants of facial skin. These findings could improve inadequate skin-related genetic diversity in the currently published database.

bioinformatics↗

bioRxiv2023

Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly

Baculoviruses are insect-infecting pathogens with wide applications as biological pesticides, in vitro protein production vehicles and gene therapy tools. Its cylindrical nucleocapsid, which encapsulates and protects the circular double-stranded viral DNA encoding proteins for viral replication and entry, is formed by the highly conserved major capsid protein VP39. The mechanism for VP39 assembly remains unknown. We determined a 3.2 [A] electron cryomicroscopy helical reconstruction of an infectious nucleocapsid of Autographa californica multiple nucleopolyhedrovirus, revealing how dimers of VP39 assemble into a 14-stranded helical tube. We show that VP39 comprises a unique protein fold conserved across baculoviruses, which includes a Zinc finger domain and a stabilizing intra-dimer sling. Analysis of sample polymorphism revealed that VP39 assembles in several closely-related helical geometries. This VP39 reconstruction reveals general principles for baculoviral nucleocapsid assembly.

biophysics↗

bioRxiv2023

Assembly of gut-derived bacterial communities follows "early-bird" resource utilization dynamics

Diet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities cultured in vitro from human feces to uncover simple assembly rules and develop a predictive model of community composition upon addition of single nutrients from central carbon metabolism to a complex medium. Community membership was largely determined by the donor feces, whereas relative abundances were determined by the supplemental carbon source. The absolute abundance of most taxa was independent of the supplementing nutrient, due to the ability of fast-growing organisms to quickly exhaust their niche in the complex medium and then exploit and monopolize the supplemental carbon source. Relative abundances of dominant taxa could be predicted from the nutritional preferences and growth dynamics of species in isolation, and exceptions were consistent with strain-level variation in growth capabilities. Our study reveals that community assembly follows simple rules of nutrient utilization dynamics and provides a predictive framework for manipulating gut commensal communities through nutritional perturbations.

microbiology↗