Biology subjects

Nguyen, D. H.

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

10 recordsLinked to original sources

bioRxiv2026

Structural Analysis of Prostate Cancer N-Glycans Using Graph-Based Structural Metrics

The N-linked glycans are structurally complex carbohydrate modifications that regulate protein folding, immune recognition, and cellular signaling, and their expression is extensively remodeled during cancer progression, making them promising biomarkers. In this study, prostate cancer-associated N-glycans from a range of relevant peer-reviewed studies were curated and digitized to develop a versatile computational framework that quantitatively encodes their spatial complexity across diverse biological systems. We invented two indices--the Distance & Connectivity Index (DCI) and the Position & Composition Index (PCI)--to capture the spatial information in N-glycans as layered architectures, enabling calculation of residue-level path lengths, branching structure, and compositional diversity. DCI summarizes glycan structure as both a scalar and matrix representation, while PCI does the same but also captures monosaccharide diversity, linkage heterogeneity, and cross-layer branching features. These metrics were computed with GlycoAssessor, an open-source platform that extracts information for the DCI and PCI from glycans drawn via Symbol Nomenclature for Glycans (SNFG) notation. Principal Component Analysis (PCA) was applied to evaluate whether glycans from prostate cancer tissues cluster distinctly in a disease-relevant manner. Results show that the spatial information in N-glycans: (1) increased in a multi-dimensional, non-linear manner, (2) objectively segregated structural themes, (3) could function as a potential prostate cancer biomarker that is distinct from mass-to-charge ratio and relative abundance, and (4) could objectively quantify novel subtype classifications of glycans associated with disease states and progression.

bioinformatics↗

bioRxiv2026

A Shape Analysis Algorithm Quantifies Spatial Morphology and Context of 2D to 3D Cell Culture for Correlating Novel Phenotypes with Treatment Resistance

SUMMARYThis article explains how novel morphological features in cells and organoids can be quantified using the linearized compressed polar coordinates (LCPC) transform, a spatial algorithm that captures properties that traditional metrics, such as area, volume, and surface area, cannot. Best practices for shape orientation and alignment are discussed. Numerous studies have shown that the morphological phenotype of a cell or organoid correlates with its susceptibility to anti-cancer agents. However, traditional methods of measuring phenotype rely on spatial metrics such as area, volume, perimeter, and signal intensity, which work but are limited. These approaches cannot measure many crucial features of spatial context, such as chirality, a property of left- and right-handedness. Volume cannot register chirality because the left and right shoes hold the same volume. Though spatial context in the form of chirality, gravity direction, and polarity axis is intuitive to humans, the traditional metrics used by cell biologists, pathologists, radiologists, and machine learning practitioners to date cannot capture these fundamental notions. The Linearized Compressed Polar Coordinates (LCPC) transform is a novel algorithm that can capture spatial context unlike any other metric. The LCPC transform translates a two-dimensional (2D) contour into a discrete sinusoidal wave by overlaying a grid system that tracks the points of intersection between the contour and the grid lines. It turns the contour into a series of sequential pairs of discrete coordinates, with the independent coordinate (x-coordinate) being consecutive positions in 2D space. Each dependent coordinate (y-coordinate) consists of the distance between an intersection of the contour and gridline to the origin or baseline of the grid system. In the form of a discrete sinusoid wave, the Fast Fourier Transform is then applied to the data. In this way, the shapes of cells in 2D and 3D cell culture are systematically and multidimensionally represented, enabling robust quantitative stratification that will reveal insights into treatment resistance.

bioinformatics↗

bioRxiv2025

A tissue-scale strategy for sensing threats in barrier organs

Barrier organs rely on a limited set of pattern recognition receptors (PRRs) to detect diverse immunogenic challenges. How organs assess threats and adjust immune responses to balance host protection with collateral tissue damage remains unclear. Here, by analyzing influenza infection in the lung using single-molecule imaging and spatial transcriptomics, we discovered a tiered threat-sensing strategy at the tissue scale, where the probability of detecting and responding to infection is lowest in the outermost epithelia and highest in the inner stroma. This strategy emerges from spatially graded PRR expression that results in cell-type-specific probabilities of threat-sensing across the tissue, a design broadly adopted by barrier organs. Selectively increasing PRR expression in lung epithelia in vivo exacerbated tissue damage upon inflammatory challenge. These results reveal a spatially tiered strategy to tolerate threats restricted within the epithelia, and yet enable progressively potent immune responses as threats invade deeper into the tissue.

immunology↗

bioRxiv2024

Post-translational modifications on protein VII are important during the early stages of adenovirus infection.

Due to the importance of post-translational modification (PTM) in cellular function, viruses have evolved to both take advantage of and be susceptible to such modification. Adenovirus encodes a multifunctional protein called protein VII, which is packaged with the viral genome in the core of virions and disrupts host chromatin during infection. Protein VII has several PTMs whose addition contributes to the subnuclear localization of protein VII. Here, we used mutant viruses that abrogate or mimic these PTMs on protein VII to interrogate their impact on protein VII function during adenovirus infection. We discovered that acetylation of the lysine in positions 2 or 3 (K2 or K3) is deleterious during early infection as mutation to alanine led to greater intake of protein VII to the nucleus and enhanced early gene expression. Furthermore, we determined that protein VII is acetylated at alternative residues late during infection which may compensate for the mutated sites. Lastly, due to the role of the early viral protein E1A in viral gene activation, we investigated the interaction between protein VII and E1A and demonstrated that protein VII interacts with E1A through a chromatin-mediated interaction. Together, these results emphasize that the complexity of virus-host interactions is intimately tied to post-translational modification. ImportanceAdenoviruses are a ubiquitous human pathogen that cause a variety of diseases, such as respiratory infections, gastroenteritis, and conjunctivitis. While often viewed as a self-limiting infection in healthy individuals, adenoviruses are particularly harmful for immunocompromised patients. Here, we investigate the functional role of post-translational modifications (PTMs) on an essential adenovirus core protein, protein VII, describing how they regulate its function during early and late stages of infection. Our study focuses on how specific PTMs on protein VII influence transcription, localization, and interactions with other proteins, highlighting how PTMs are employed by viruses to alter protein function.

microbiology↗

bioRxiv2024

Human cytomegalovirus induces neuronal gene expression for viral maturation

Viral invasion of the host cell causes some of the most dramatic changes in biology. Human cytomegalovirus (HCMV) extensively remodels host cells, altering nuclear shape and generating a cytoplasmic viral-induced assembly compartment (vIAC). How these striking morphology changes take place in the context of host gene regulation is still emerging. Here, we discovered that histone variant macroH2A1 is essential for producing infectious progeny. Because virion maturation and cellular remodeling are closely linked processes, we investigated structural changes in the host cell upon HCMV infection. We discovered that macroH2A1 is necessary for HCMV-induced reorganization of the host nucleus, cytoskeleton, and endoplasmic reticulum. Furthermore, using RNA-seq we found that while all viral genes were highly expressed in the absence of macroH2A1, many HCMV-induced host genes were not. Remarkably, hundreds of these HCMV-induced macroH2A1-dependent host genes are associated with neuronal synapse formation and vesicle trafficking. Knock-down of these HCMV-induced neuronal genes during infection resulted in malformed vIACs and smaller plaques, establishing their importance to HCMV infection. Together, our findings demonstrate that HCMV manipulates host gene expression by hijacking a dormant neuronal secretory pathway for efficient virion maturation.

microbiology↗

bioRxiv2022

Coevolution of Patch Selection in Stochastic Environments

AO_SCPLOWBSTRACTC_SCPLOWSpecies interact in landscapes where environmental conditions vary in time and space. This variability impacts how species select habitat patches. Under equilibrium conditions, coevolution of this patch selection can result in ideal-free distributions where per-capita growth rates are zero in occupied patches and negative in unoccupied patches. These ideal-free distributions, however, dont explain why species occupy sink patches, competitors have overlapping spatial ranges, or why predators avoid highly productive patches. To understand these patterns, we analyze multi-species Lotka-Volterra models accounting for spatial heterogeneity and environmental stochasticity. In occupied patches at the coESS, we show that the differences between the local contributions to the mean and the variance of the long-term population growth rate are equalized. Applying this characterization to models of antagonistic interactions reveals that environmental stochasticity can partially exorcize the ghost of competition past, select for new forms of enemy-free and victimless space, and generate Hydra effects over evolutionary time scales. Viewing our results through the economic lens of Modern Portfolio Theory highlights why the coESS for patch selection is often a bet-hedging strategy coupling stochastic sink populations. Our results highlight how environmental stochasticity can reverse or amplify evolutionary outcomes due to species interactions or spatial heterogeneity.

evolutionary biology↗

bioRxiv2021

Co-infection of a novel Chlamydia-like organism and Henneguya sp. (Myxosporea, Myxobolidae) in snakeskin gourami Trichopodus pectoralis (Regan 1910), in Thailand

The present study describes a simultaneous infection of a novel Chlamydia-like organism (CLO) with a Myxozoa parasite, Henneguya sp. in snakeskin gourami Trichopodus pectoralis in Thailand. A new CLO is proposed "Candidatus Piscichlamydia trichopodus" (CPT) based on 16S rRNA phylogenetic analysis. Systemic intracellular CPT infection was confirmed by histological examination, in situ hybridization, PCR assay, and sequencing of 16S rRNA. This novel pathogen belongs to the order Chlamydiales but differs in certain aspects from other species. The histopathological changes associated with CPT infection were different from the typical pathological lesions of epitheliocystis caused by previously known CLO. Unlike other CLO, CPT localized in the connective tissue rather than in the epithelial cells and formed smaller clumps of intracellular bacteria that stained dark blue with hematoxylin. On the other hand, typical myxospores of the genus Henneguya with tails were observed in the gill sections. Infection with Henneguya sp. resulted in extensive destruction of the gill filaments, most likely leading to respiratory distress. Due to the frequency of co-infections and the unavailability of culture methods for CLO and Henneguya sp, it was difficult to determine which pathogens were directly responsible for the associated mortality. However, co-infections may increase the negative impact on the host and the severity of the disease. Given the commercial importance of the snakeskin gourami and its significant aquaculture potential, the findings of this study are important for further studies on disease prevention.

pathology↗

bioRxiv2020

Local Field Potentials in a Pre-motor Region Predict Learned Vocal Sequences

Neuronal activity within the premotor region HVC is tightly synchronized to, and crucial for, the articulate production of learned song in birds. Characterizations of this neural activity typically focuses on patterns of sequential bursting in small carefully identified subsets of single neurons in the HVC population. Much less is known about population dynamics beyond the scale of individual neurons. There is a rich history of using local field potentials (LFP), to extract information about behavior that extends beyond the contribution of individual cells. These signals have the advantage of being stable over longer periods of time and have been used to study and decode complex motor behaviors, such as human speech. Here we characterize LFP signals in the putative HVC of freely behaving male zebra finches during song production, to determine if population activity may yield similar insights into the mechanisms underlying complex motor-vocal behavior. Following an initial observation that structured changes in the LFP were distinct to all vocalizations during song, we show that it is possible to extract time varying features from multiple frequency bands to decode the identity of specific vocalization elements (syllables) and to predict their temporal onsets within the motif. This demonstrates that LFP is a useful signal for studying motor control in songbirds. Surprisingly, the time frequency structure of putative HVC LFP is qualitatively similar to well established oscillations found in both human and non-human mammalian motor areas. This physiological similarity, despite distinct anatomical structures, may give insight to common computational principles for learning and/or generating complex motor-vocal behaviors. Author SummaryVocalizations, such as speech and song, are a motor process that requires the coordination of several muscle groups receiving instructions from specific brain regions. In songbirds, HVC is a premotor brain region required for singing and it is populated by a set of neurons that fire sparsely during song. How HVC enables song generation is not well understood. Here we describe network activity in putative HVC that precedes the initiation of each vocal element during singing. This network activity can be used to predict both the identity of each vocal element (syllable) and when it will occur during song. In addition, this network activity is similar to activity that has been documented in human, non-human primate, and mammalian premotor regions tied to muscle movements. These similarities add to a growing body of literature that finds parallels between songbirds and humans in respect to the motor control of vocal organs. Given the similarities of the songbird and human motor-vocal systems these results suggest that the songbird model could be leveraged to accelerate the development of clinically translatable speech prosthesis.

neuroscience↗

bioRxiv2020

A comparative study of isothermal nucleic acid amplification methods for SARS-CoV-2 detection at point of care

COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread worldwide and put most of the world under lockdown. Despite that there have been emergently approved vaccines for SARS-CoV-2, COVID-19 cases, hospitalizations, and deaths have remained rising. Thus, rapid diagnosis and necessary public health measures are still key parts to contain the pandemic. In this study, the colorimetric isothermal nucleic acid amplification tests (iNAATs) for SARS-CoV-2 detection based on loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and polymerase spiral reaction (PSR) were designed and evaluated. The three methods showed the same limit of detection (LOD) value of 1 copy of the targeted gene per reaction. However, for the direct detection of SARS-CoV-2 genomic-RNA, LAMP outperformed both CPA and PSR, exhibiting the LOD value of roughly 43.14 genome copies/reaction. The results can be read with the naked eye within 45 minutes, without cross-reactivity to closely related coronaviruses. Moreover, the direct detection of SARS-CoV-2 RNA in simulated patient specimens by iNAATs was also successful. Finally, the ready-to-use lyophilized reagents for LAMP reactions were shown to maintain the sensitivity and LOD value of the liquid assays. The results indicate that the colorimetric lyophilized LAMP kit developed herein is highly suitable for detecting SARS-CoV-2 nucleic acids at point-of-care.

molecular biology↗

bioRxiv2019

Apoptosis in the fetal testis eliminates developmentally defective germ cell clones

Many germ cells (GCs) are eliminated during development, long before differentiating to egg or sperm, but it is not clear why. Here, we examined how GC composition in the mouse fetal testis is altered by scheduled apoptosis during sex differentiation. Multicolored-lineage tracing revealed that apoptosis affects clonally-related GCs, suggesting that this fate decision occurs autonomously based on shared intrinsic properties. We identified extensive transcriptional heterogeneity among fetal GCs including an apoptosis-susceptible subpopulation delineated by high Trp53 and deviant differentiation. Alternatively, the GC subpopulation most likely to survive was advanced in differentiation. These results indicate that GC developmental fate is based upon discrete and cell-heritable fitnesses and imply that a dichotomy between sex-differentiation and apoptosis coordinates the removal of developmentally incompetent cells to improve gamete quality. Evidence that GC subpopulations are in different epigenetic states suggests that errors in epigenetic reprogramming form the basis of aberrant differentiation and apoptotic selection.\n\nOne sentence summaryGerm cells undergo autonomous selection in the fetal testis to promote male differentiation

developmental biology↗