Biology subjects

Tran, T. D.

Publications and source records attributed to Tran, T. D..

7 recordsLinked to original sources

bioRxiv2026

First-Trimester Non-Invasive Prediction of Preterm Birth Using Cell-Free DNA Fragmentomics

ObjectiveTo develop and validate a cell-free DNA (cfDNA) fragmentomic classifier for the early prediction of spontaneous preterm birth (PTB) using routine first-trimester non-invasive prenatal testing (NIPT) data. MethodsA nested case-control study was conducted within a prospective multicenter Vietnamese cohort comprising 286 pregnancies, including 82 spontaneous PTB cases and 204 term controls. Maternal plasma cfDNA collected during routine first-trimester NIPT (median gestational age, 12 weeks) was sequenced to a depth of approximately 20 million reads per sample. Five fragmentomic feature categories including copy number alterations, end-motif composition, nucleosome distance, fragment length, and joint fragment-lengthxend-motif were evaluated for PTB prediction. Machine learning classifiers were developed in a training cohort (n = 228, 65 PTB vs 163TB) and tested in a validation cohort (n = 58, 17 PTB vs 41 TB). ResultsAmong the five fragmentomic feature classes evaluated, 4-mer end-motif (EM) profiles exhibited the most pronounced differences between PTB and term control samples. Consistent with these findings, the EM-based classifier demonstrated the highest discriminative performance in the validation cohort, achieving an AUC of 0.970 (95% CI, 0.912-1.000). At a specificity >90%, the model achieved a sensitivity of 94% (95% CI, 78-100%). ConclusionThese findings demonstrate that cfDNA EM signatures derived from routine first-trimester NIPT can accurately identify pregnancies at risk of spontaneous preterm birth, without additional blood collection or sequencing, thereby extending the clinical utility of existing prenatal screening infrastructure. KEY POINTSO_ST_ABSWhat is already known about this topic?C_ST_ABSO_LICurrent first-trimester prediction strategies based on maternal characteristics, cervical length, and biochemical markers have limited predictive accuracy, particularly in nulliparous women. C_LIO_LIExisting cfDNA-based approaches have shown only modest performance or require additional assays, limiting clinical applicability. C_LI What does this study add?O_LIExisting NIPT sequencing data can be repurposed (without additional blood sampling or sequencing) for accurate prediction of spontaneous preterm birth (AUC=0.970). C_LIO_LIA classifier employing 4-mer end-motif (EM) profiles achieved an AUC of 0.970. At a specificity >90%, the model achieved a sensitivity of 94%. C_LI

genomics↗

bioRxiv2026

High Intensity Interval Training in Aged Female Mice Preserves Physical, Cognitive, and Cardiovascular Function

BACKGROUNDAlong with advancing age comes declines in physical, cognitive, and cardiovascular function. This diminished capacity may lead to decreased ability to perform activities of daily living, disability onset, and loss of independence. Exercise is a regenerative medicine therapy that can mitigate this loss of function. High intensity interval training (HIIT) is an aerobic exercise paradigm consisting of intense activity periods interspersed with bouts of active recovery. Previously we demonstrated that HIIT preserved physical function in adult, middle-aged, and older male mice. However, whether HIIT preserves physical, cognitive, and cardiovascular function, mitigates frailty, and improves brain and heart health in older adult female mice remains unknown. HYPOTHESISCognitive, physical, and cardiovascular function in older adult female C57BL/6 will be preserved in exercised mice (HIIT) versus sedentary control (SED). METHODSMice (HIIT and SED, both n=9, 24m at end) were tested pre/post-intervention for physical (rotarod, treadmill, grip meter, inverted cling, voluntary wheel running, activity monitor), cognitive (open field, novel object recognition, puzzle box, y-maze), and cardiovascular (blood pressure, echocardiogram) function, body composition, and whole body calorimetry. The mice underwent 14-weeks of HIIT training with progressive volume and intensity. RESULTSHIIT significantly (p<0.05) increased or preserved function in many tests including: aerobic capacity (+71% HIIT versus, vs, no change, NC, in SED), four limb strength/endurance (-67% SED vs -28% HIIT), forelimb strength (-16% SED vs NC HIIT), overall motor function (NC SED vs +39% HIIT), executive function (NC SED vs +73% HIIT), and exploratory behavior, which improved across multiple tests with HIIT while remaining unchanged in SED. HIIT also reduced both systolic blood pressure by 12% (-17 mmHg) and mean arterial pressure by -16 mmHg. In addition, HIIT significantly reduced cardiac fibrosis, increased muscle fiber type 2a percentage, reduced IL-1{beta} expression in the hypothalamus, and mitigated frailty onset. CONCLUSIONHIIT significantly reduced age-related functional loss in all three domains assessed while preventing frailty onset in older adult females and improving markers of brain and heart health.

physiology↗

bioRxiv2025

A type III secretion system is required for Bordetella atropi host cell invasion in vivo

Bordetella atropi is an intracellular bacterial pathogen that infects the intestinal epithelia of the nematode host Oscheius tipulae. We previously showed that the bacteria use filamentation as a novel cell-to-cell spreading mechanism once inside the intestinal cell. However, how the bacteria invade the host cells and what factors contribute to B. atropi infection process remain unknown. In this study, we investigate the roles of type III (T3SS) and type VI secretion systems (T6SS) in B. atropi pathogenesis, which are employed by many bacterial pathogens, both extracellular and intracellular, to deliver effectors that manipulate host physiology to their advantage. We found that the two T6SSs encoded in B. atropi genome played no obvious roles in the invasion or intracellular spreading. In contrast, a T3SS was required for intestinal cell invasion. T3SS mutants showed loss of host cell protrusions from the apical surface that normally engulf invading wild type bacteria, as seen by both electron microscopy and confocal fluorescent microscopy. These protrusions bear morphological similarities to membrane ruffles triggered by the T3SS-mediated invasion seen in other pathogens such as Salmonella and Shigella spp. Additionally, we conducted dual transcriptomics and saw upregulation of T3SS in vivo, along with several putative effectors and the virulence regulator BvgS of the genus Bordetellae. We knocked out these effector candidates and found that deletion of one of these genes, deiA (decreased invasion protein A), leads to a reduction in the number of invasion events and overall percentage of infected animals in the population. In addition, deletion of the virulence regulator bvgS resulted in a complete loss of B. atropi invasion, suggesting it may regulate T3SS for host cell invasion.

microbiology↗

bioRxiv2022

Genomic and phenotypic evolution of nematode-infecting microsporidia

Microsporidia are a large phylum of intracellular parasites that can infect most types of animals. Species in the Nematocida genus can infect nematodes including Caenorhabditis elegans, which has become an important model to study mechanisms of microsporidia infection. To understand the genomic properties and evolution of nematode-infecting microsporidia, we sequenced the genomes of nine species of microsporidia, including two genera, Enteropsectra and Pancytospora, without any previously sequenced genomes. Core cellular processes, including metabolic pathways, are mostly conserved across genera of nematode-infecting microsporidia. Each species encodes unique proteins belonging to large gene families that are likely used to interact with host cells. Most strikingly, we observed one such family, NemLGF1, is present in both Nematocida and Pancytospora species, suggesting horizontal gene transfer between species from different genera. To understand how Nematocida phenotypic traits evolved, we measured the host range, tissue specificity, spore size, and polar tube length of several species in the genus. Our phylogenetic analysis shows that Nematocida is composed of two groups of species with distinct traits and that species with longer polar tubes infect multiple tissues. Together, our work details both genomic and trait evolution between related microsporidia species and provides a useful resource for further understanding microsporidia evolution and infection mechanisms. Author SummaryMicrosporidia are microbial parasites that can infect many animals. Nematodes have become a useful system to study microsporidia as these animals are commonly infected by microsporidia and these infections can be easily studied in a laboratory environment. To better understand how microsporidia evolve and change their properties as they infect different hosts, we sequenced the genomes of nine microsporidia species which infect nematodes. We found that metabolic pathways were mostly conserved between different clades of these species. Surprisingly, we found a family of proteins predicted to facilitate host interactions that is present in two distinct genera, suggesting that these genes were transferred between microsporidia species. We also determined the hosts and tissues that these microsporidia can infect as well as morphological properties of the microsporidia. We show that these properties are quite variable in related microsporidia species. Our results provide insight into the evolution of microsporidia and also provide a resource for studying microsporidia infections in nematodes.

microbiology↗

bioRxiv2021

Bacterial filamentation is an in vivo mechanism for cell-to-cell spreading

Intracellular pathogens are challenged with limited space and resources while replicating in a single host cell. Mechanisms for direct invasion of neighboring host cells have been discovered in cell culture, but we lack an understanding of how bacteria directly spread from cell-to-cell in vivo. Here, we describe the discovery of a bacterial species that uses filamentation as an in vivo mechanism for intracellular spreading between the intestinal epithelial cells of its host, the rhabditid nematode Oscheius tipulae. In vitro and in vivo filamentation by this bacterium, Bordetella atropi, requires a highly conserved nutrient-sensing pathway used by divergent bacteria to detect rich conditions and inhibit the divisome. Thus, B. atropi uses a distinct mechanism for cell-to-cell spreading by coopting a pathway that normally regulates bacterial cell size to trigger filamentation inside host cells.

microbiology↗

bioRxiv2019

Adaptive Bet-Hedging Revisited: Considerations of Risk and Time Horizon

Models of adaptive bet-hedging commonly adopt insights from Kellys famous work on optimal gambling strategies and the financial value of information. In particular, such models seek evolutionary solutions that maximize long term average growth rate of lineages, even in the face of highly stochastic growth trajectories. Here, we argue for extensive departures from the standard approach to better account for evolutionary contingencies. Crucially, we incorporate considerations of volatility minimization, motivated by interim extinction risk in finite populations, within a finite time horizon approach to growth maximization. We find that a game-theoretic competitive-optimality approach best captures these additional constraints and derive the equilibria solutions under various fitness payoff functions.

evolutionary biology↗

bioRxiv2018

New perspectives on multilocus ancestry informativeness

We present an axiomatic approach for multilocus informativeness measures for determining the amount of information that a set of polymorphic genetic markers provides about individual ancestry. We then reveal several surprising properties of a decision-theoretic based measure that is consistent with the set of proposed criteria for multilocus informativeness. In particular, these properties highlight the interplay between information originating from population priors and the information extractable from the population genetic variants. This analysis then reveals a certain deficiency of mutual information based multilocus informativeness measures when such population priors are incorporated. Finally, we analyse and quantify the inevitable inherent decrease in informativeness due to learning from finite population samples.

genetics↗