Biology subjects

Trinh, J.

Publications and source records attributed to Trinh, J..

15 recordsLinked to original sources

bioRxiv2026

Chemical stressors differentially induce prophage replication in Acinetobacter baumannii strains

Prophages are prevalent genomic elements that profoundly shape microbial communities by controlling host bacterial populations through lysis or enabling genetic recombination via transduction. Standard induction protocols rely heavily on DNA-damaging agents like mitomycin C, failing to capture the complex chemical landscapes bacteria encounter in natural and clinical settings where diverse environmental insults trigger excision. Furthermore, the regulatory variations governing polylysogenic hosts containing multiple co-habiting prophages under identical stressors remain largely uncharacterized. In this study, we surveyed a panel of five clinical Acinetobacter baumannii strains containing zero to four resident prophages against a library of 57 diverse chemical stressors. We demonstrate that chemical treatments, including distinct classes of antibiotics, drive differential prophage induction patterns across different host backgrounds. This could lead to a greater understanding of the importance of prophages in antibiotic treatment regimes.

microbiology↗

bioRxiv2026

Massive-scale single-nucleus multi-omics identifies novel rare noncoding drivers of Parkinson's disease

Most genetic variants contributing to complex diseases reside in the noncoding genome. While common variants uncovered by genome-wide association studies often fail to explain much of the observed heritability of these diseases, rare variants often have higher effect sizes and cumulatively explain a larger portion of heritability. However, rare variants, particularly rare noncoding variants, have remained under-characterized largely due to the difficulties of accurately predicting variant functionality at scale, given that each individual carries an average of [~]10,000 rare variants. Here, we generated multi-omic data from >3.3 million nuclei sampled from five brain regions across a cohort of 80 individuals with Parkinsons disease (PD) and 21 neurologically normal control individuals with matched 30x whole-genome sequencing. We use this data to identify cell type-specific features of PD, map cell type-specific chromatin accessibility and expression quantitative trait loci, and train machine learning models to predict the effect of variants on gene regulation. We identify rare noncoding variants statistically associated with sporadic PD and extend our approaches to predict drivers of familial PD of unknown genetic origin. Our results underscore the significance of rare noncoding variants in complex diseases and provide a roadmap for applying similar approaches in other disease systems.

genetics↗

bioRxiv2026

Discovery, induction, and screening of prophages in clinical Acinetobacter baumannii isolates

BackgroundAcinetobacter baumannii is a common bacterial pathogen in nosocomial infections. It has become one of the greatest threats to human health for its growing resistance to last resort antibiotics, which has led to a revival of phage therapy as a potential treatment. However, conventional methods for isolating A. baumannii-infecting phages are labor-intensive and often unsuccessful. MethodsOur approach involves a computational pipeline to identify temperate phages (prophages) integrated into A. baumannii genomes, followed by mitomycin C (MMC) induction of those strains to screen for active prophages. ResultsHere we show a prophage analysis for nearly 900 A. baumannii genomes. We observed MMC-triggered excision of nine prophages from eight A. baumannii strains by PCR and sequencing. Further we show four prophage form virions detectable by transmission electron microscopy, and two which can plaque on other A. baumannii isolates. ConclusionThis work demonstrates the utility and diversity of prophages for further development as therapeutics for antibiotic resistant A. baumannii.

microbiology↗

bioRxiv2024

The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model

The pathophysiology of Parkinsons disease (PD) involves gene-environment interactions that impair various cellular processes such as autophagy, lysosomal function, or mitochondrial dysfunction. Specifically, mitochondria-associated gene mutations increase PD risk, mitochondrial respiration is altered in the PD brain, and mitochondrial-damaging toxins cause PD-like motor and gastrointestinal symptoms in animal models. The gut microbiome is altered in PD patients and represents an environmental risk, however a relationship between mitochondrial function and the microbiome in PD has not been previously established. Herein, we report that striatal mitochondria are functionally overactive in -synuclein-overexpressing (ASO) mice, a model of PD, and that microbiome depletion restores respiration and mitochondria-associated gene expression patterns to wild-type levels. ASO mice harboring a complex microbiome produce increased reactive oxygen species in the striatum whereas germ-free counterparts express elevated levels of antioxidant proteins that may buffer against oxidative damage. Indeed, antioxidant treatment improves motor performance in ASO mice and, remarkably, blocking oxidant scavenging in germ-free mice induces -synuclein-dependent motor deficits. Thus, the gut microbiome increases mitochondrial respiration and oxidative stress in the brain, which enhances motor symptoms in a mouse model of PD.

physiology↗

bioRxiv2023

Odor imagery but not perception drives risk for food cue reactivity and increased adiposity

Mental imagery has been proposed to play a critical role in the amplification of cravings. Here we tested whether olfactory imagery drives food cue reactivity strength to promote adiposity in 45 healthy individuals. We measured odor perception, odor imagery ability, and food cue reactivity using self-report, perceptual testing, and neuroimaging. Adiposity was assessed at baseline and one year later. Brain responses to real and imagined odors were analyzed with univariate and multivariate decoding methods to identify pattern-based olfactory codes. We found that the accuracy of decoding imagined, but not real, odor quality correlated with a perceptual measure of odor imagery ability and with greater adiposity changes. This latter relationship was mediated by cue-potentiated craving and intake. Collectively, these findings establish odor imagery ability as a risk factor for weight gain and more specifically as a mechanism by which exposure to food cues promotes craving and overeating.

neuroscience↗

bioRxiv2022

Citrus relatives exhibit natural variation in perception and response magnitude to microbial features

Although much is known about the responses of model plants to microbial features, we still lack an understanding of the extent of variation in immune perception across members of a plant family. In this work, we analyzed immune responses in Citrus and wild relatives, surveying 86 Rutaceae genotypes with differing leaf morphologies and disease resistances. We found that responses to microbial features vary both within and between members. Species in two subtribes, the Balsamocitrinae and Clauseninae, can recognize all tested microbial features (flg22, csp22, chitin), including one from Candidatus Liberibacter species (csp22CLas), the bacterium associated with citrus greening disease aka Huanglongbing. We investigated differences at the receptor level for flagellin perception (FLS2 receptor) and chitin perception (LYK5 receptor) in citrus genotypes. We were able to characterize two genetically linked FLS2 homologs from Frost Lisbon lemon (responsive) and Washington navel orange (non-responsive). Surprisingly, FLS2 homologs from responding and non-responding genotypes were expressed in citrus and functional when transferred to a heterologous system. Washington navel orange weakly responds to chitin, but Tango mandarin exhibits a robust response. LYK5 alleles were identical or nearly-identical between the two genotypes and able to complement the Arabidopsis lyk4/lyk5-2 mutant with respect to chitin perception. Collectively, our data indicates that differences in chitin and flg22 perception in these citrus genotypes are not the result of sequence polymorphisms at the receptor level. These findings shed light onto the diversity of perception of microbial features and highlight genotypes capable of recognizing polymorphic pathogen features.

plant biology↗

bioRxiv2021

Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation under Ionic Liquid Stress

Corynebacterium glutamicum is an ideal microbial chassis for the production of valuable bioproducts including amino acids and next-generation biofuels. Here we resequence engineered isopentenol (IP) producing C. glutamicum BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence vs. absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of a C. glutamicum strain engineered to produce IP.

systems biology↗

bioRxiv2021

Engineering sorghum for higher 4-hydroxybenzoic acid content

Lignocellulosic biomass represents a renewable source of sugars for the manufacturing of bioproducts such as biofuels. The high cost associated with deconstruction of plant biomass to simple sugars remains one of the challenges preventing the deployment of economically sustainable advanced bioproducts. The accumulation in-planta of value-added coproducts such as platform chemicals can improve the economics of biofuels. Among other crops, sorghum is an ideal bioenergy feedstock due to its low input requirements, efficient nitrogen recycling, and high water use efficiency and biomass yields. In this work, we engineered sorghum to overproduce the valuable chemical 4-hydroxybenzoic acid (4-HBA) by co-expressing plastid-targeted versions of Escherichia coli chorismate pyruvate-lyase (UbiC) and feedback-resistant 3-deoxy-D-arabino-heptulonate-7-phosphate synthase (AroG*). Two independent lines containing the dual aroG*-ubiC construct were selected for characterization in the T2 generation. Using liquid chromatography-mass spectrometry, analysis of methanolic extracts obtained from biomass samples revealed an accumulation of 4-HBA in the two transgenic lines (corresponding to 1.56% and 1.72% dry weight, respectively), with 4-HBA glucose conjugates representing major forms. Measurements of biomass composition and several agronomic traits showed no significant difference between transgenic and wild-type control plants grown under controlled environment. This work demonstrates the transferability of the ubiC engineering approach to sorghum; generated lines will be useful to assess the agronomic performance of modified 4-HBA-rich sorghum under natural conditions.

plant biology↗

bioRxiv2021

Connectivity and Synaptic Physiology in the Mouse and Human Cortex

To elucidate cortical microcircuit structure and synaptic properties we present a unique, extensive, and public synaptic physiology dataset and analysis platform. Through its application, we reveal principles that relate cell type to synapse properties and intralaminar circuit organization in the mouse and human cortex. The dynamics of excitatory synapses align with the postsynaptic cell subclass, whereas inhibitory synapse dynamics partly align with presynaptic cell subclass but with considerable overlap. Despite these associations, synaptic properties are heterogeneous in most subclass to subclass connections. The two main axes of heterogeneity are strength and variability. Cell subclasses divide along the variability axis, while the strength axis accounts for significant heterogeneity within the subclass. In human cortex, excitatory to excitatory synapse dynamics are distinct from those in mouse and short-term plasticity varies with depth across layers 2 and 3. With a novel connectivity analysis that enables fair comparisons between circuit elements, we find that intralaminar connection probability among cell subclasses exhibits a strong layer dependence.These and other findings combined with the analysis platform create new opportunities for the neuroscience community to advance our understanding of cortical microcircuits.

neuroscience↗

bioRxiv2021

A bacteriophage cocktail significantly reduces Listeria monocytogenes without deleterious impact on the commensal gut microbiota under simulated gastro-intestinal conditions

In this study, we examined the effect of a bacteriophage cocktail (tentatively designated FOP, for Foodborne Outbreak Pill) on the levels of Listeria monocytogenes in simulated small intestine, large intestine, and Caco-2 model systems. We found that FOP survival during simulated passage of the upper gastrointestinal was dependent on stomach pH, and that FOP robustly inhibited L. monocytogenes levels with effectiveness comparable to antibiotic treatment (ampicillin) under simulated ilium and colon conditions. FOP did not inhibit the commensal bacteria, whereas ampicillin treatment led to dysbiosis-like conditions. FOP was also more effective than antibiotic in protecting Caco-2 cells from adhesion and invasion by L. monocytogenes, while not triggering an inflammatory response. Our data suggest that FOP may provide a robust protection against L. monocytogenes should the bacterium enter the human gastrointestinal tract (e.g., by consumption of contaminated food), without deleterious impact on the commensal bacteria.

microbiology↗

bioRxiv2021

Analysis of mitochondrial genome methylation using Nanopore single-molecule sequencing

The level and the biological significance of mitochondrial DNA (mtDNA) methylation in human cells is a controversial topic. Using long-read third-generation sequencing technology, mtDNA methylation can be detected directly from the sequencing data, which overcomes previously suggested biases, introduced by bisulfite treatment-dependent methods. We investigated mtDNA from whole blood-derived DNA and established a workflow to detect CpG methylation with Nanopolish. In order to obtain native mtDNA, we adjusted a whole-genome sequencing protocol and performed ligation library preparation and Nanopore sequencing. To validate the workflow, 897bp of methylated and unmethylated synthetic DNA samples at different dilution ratios were sequenced and CpG methylation was detected. Interestingly, we observed that reads with higher methylation in the synthetic DNA did not pass Guppy calling, possibly affecting conclusions about DNA methylation in Nanopore sequencing. We detected in all blood-derived samples overall low-level methylation across the mitochondrial genome, with exceptions at certain CpG sites. Our results suggest that Nanopore sequencing is capable of detecting low-level mtDNA methylation. However, further refinement of the bioinformatical pipelines including Guppy failed reads are recommended.

genetics↗

bioRxiv2021

High Throughput Fitness Profiling Reveals Loss Of GacS-GacA Regulation Improves Indigoidine Production In Pseudomonas putida

Pseudomonas putida KT2440 is an emerging industrial microbe amenable for use with renewable carbon streams including aromatics such as para-coumarate (pCA). We examined this microbe under common stirred-tank bioreactor parameters with quantitative fitness assays using a pooled transposon library containing nearly all (4,778) non-essential genes. Assessing differential fitness values by monitoring changes in mutant strain abundance over time identified 31 genes with improved fitness in multiple bioreactor-relevant parameters. Twenty-one genes from this subset were reconstructed, including GacA, a signaling protein, TtgB, an ABC transporter, and PP_0063, a lipid A acyltransferase. Twelve deletion strains with roles in varying cellular functions were evaluated for conversion of pCA, to a heterologous bioproduct, indigoidine. Several mutants, such as the {Delta}gacA strain improved both fitness in a bioreactor and showed an 8-fold improvement in indigoidine production (4.5 g/L, 0.29 g/g pCA, 23% MTY) from pCA as the carbon source.

systems biology↗

bioRxiv2021

Fat and carbohydrate interact to potentiate food reward in healthy weight but not in overweight or obesity

Prior work suggests that actual, but not estimated, energy density drives the reinforcing value of food [1,2] and that energy from fat and carbohydrate can interact to potentiate reward [2]. Here we sought to replicate these findings in an American sample and to determine if the effects are influenced by body mass index (BMI). Thirty participants with healthy weight (HW; BMI 21.92 {+/-} 1.77; M {+/-} SD) and 30 participants with overweight/obesity (OW/OB; BMI 29.42 {+/-} 4.44) rated pictures of common American snacks in 120-kcal portions for liking, familiarity, frequency of consumption, expected satiety, healthiness, energy content, energy density, and price. Participants then completed an auction task where they bid for the opportunity to consume each food. Snacks contained either primarily carbohydrate, primarily fat, or roughly equal portions of fat and carbohydrate (combo). Replicating prior work, we found that participants with HW bid the most for combo foods in linear mixed model analyses. This effect was not observed among individuals with OW/OB. Additionally, in contrast with previous reports [1,2], our linear regression analyses revealed a negative relationship between the actual energy density of the snacks and bid amount that was mediated by food price. Our findings support altered macronutrient reinforcement in obesity and highlight potential influences of the food environment on the regulation of food reward.

neuroscience↗

bioRxiv2020

High fidelity electrophysiological, morphological, and transcriptomic cell characterization using a refined Patch-seq protocol

The Patch-seq approach is a powerful variation of the standard patch clamp technique that allows for the combined electrophysiological, morphological, and transcriptomic characterization of individual neurons. To generate Patch-seq datasets at a scale and quality that can be integrated with high-throughput dissociated cell transcriptomic data, we have optimized the technique by identifying and refining key factors that contribute to the efficient collection of high-quality data. To rapidly generate high-quality electrophysiology data, we developed patch clamp electrophysiology software with analysis functions specifically designed to automate acquisition with online quality control. We recognized a substantial improvement in transcriptomic data quality when the nucleus was extracted following the recording. For morphology success, the importance of maximizing the neurons membrane integrity during the extraction of the nucleus was much more critical to success than varying the duration of the electrophysiology recording. We compiled the lab protocol with the analysis and acquisition software at https://github.com/AllenInstitute/patchseqtools. This resource can be used by individual labs to generate Patch-seq data across diverse mammalian species and that is compatible with recent large-scale publicly available Allen Institute Patch-seq datasets.

neuroscience↗

bioRxiv2019

Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinsons disease

ObjectiveTo assess genetic modifiers of Parkinsons disease (PD) age at onset (AAO) penetrance in individuals carrying common and rare LRRK2 risk alleles\n\nMethodsWe analysed reported genetic modifier DNM3 rs2421947 in 724 LRRK2 p.G2019S heterozygotes using linear regression of AAO. We meta-analysed our data with previously published data (n=754). VAMP4 is in close proximity to DNM3 and is associated with PD. We analysed the effect of the rs11578699 VAMP4 variant on pG2019S penetrance in 786 LRRK2 p.G2019S heterozygotes. We also evaluated the impact of VAMP4 variants using AAO regression in 4882 patients with PD carrying a common LRRK2 risk variant (rs10878226).\n\nResultsThere was no evidence for linkage disequilibrium between DNM3 rs2421947 and VAMP4 rs11578699. Our linear regression AAO of 724 p.G2019S carriers showed no relationship between DNM3 rs2421947 and AAO (beta = -1.19, p = 0.55, n =708). Meta-analysis with previously published data did not indicate a significant effect on AAO (beta = -2.21, p = 0.083, n = 1304), but there was significant heterogeneity in the analyses of new and previously published data. VAMP4 rs11578699 was nominally associated with AAO in patients dichotomized by the common LRRK2 risk variant rs10878226 (beta=1.68, se=0.81 p=0.037).\n\nInterpretationAnalysis of DNM3 in previously unpublished data does not show an interaction between DNM3 and LRRK2 G2019S for AAO, however the inter-study heterogeneity may indicate ethnic-specific effects of DNM3 rs2421947. Analysis of sporadic PD patients stratified by the PD risk variant rs10878226 indicates a possible interaction between LRRK2 and VAMP4.

genetics↗