Biology subjects

Liu, C.-W.

Publications and source records attributed to Liu, C.-W..

8 recordsLinked to original sources

bioRxiv2026

Molecular Dosimetry of DNA Adducts in Mice Exposed to Ethylene Oxide

Ethylene oxide (EtO) is a highly reactive industrial chemical and classified as a known human carcinogen with a putative mutagenic mode of action (MOA). Its genotoxic potential is primarily mediated through alkylation of DNA, resulting in the formation of the mutagenic adduct O6-(2-hydroxyethyl)-2-deoxyguanosine (O6-HE-dG). The N7-(2-hydroxyethyl)guanine (N7-HE-G) adduct is formed in greater abundance and is generally considered to be non-mutagenic. However, dose-response relationships of these DNA adducts, particularly at low inhalation exposure levels (i. e., below 3 ppm), remain unknown. These data are necessary to inform the biological plausibility of different statistical dose-response models that have been applied to human or animal data used for cancer risk assessment. In the present study, male and female B6C3F1 mice were exposed to EtO (0, 0.05, 0.1, 0.5, 1, 50, 100, and 200 ppm) 6 hours/day for 28 consecutive days. Immediately following the last exposure, DNA was extracted from lung, liver, bone marrow, and mammary gland, and further utilized to measure DNA adduct levels using highly sensitive mass spectrometry platforms. N7-HE-G was detected in all tissues and exposure groups, showing linear dose-response relationships in the low-dose range ([≤]1 ppm) and increased sharply and exposure-disproportionately in the high-dose range ([≥]50 ppm). Despite a very low limit of detection, O6-HE-dG, in contrast, was not detected at exposures <50 ppm in any tissue consistent with at most a shallow linear exposure response. At higher exposures ([≥]50 ppm), O6-HE-dG exhibited a dose-response pattern of N7-HE-G. Notably the mammary gland, despite being anatomically distant from the site of inhalation, exhibited the second-highest levels of both adducts at higher doses. This study provides the first reliable quantitative dose-response evidence of DNA adducts in tumor target and non-target (liver) tissues across a wide range of EtO exposures. The two DNA adducts differ markedly in their abundance, repairability and mutagenic potential and together provide a molecular MOA dose-response framework to inform both quantitative cancer risk assessment and genotoxic hazard characterization.

pharmacology and toxicology↗

bioRxiv2025

Formaldehyde Exposure Induces Systemic Epigenetic Alterations in Histone Methylation and Acetylation

Formaldehyde (FA) is a pervasive environmental organic pollutant and a Group 1 human carcinogen. While FA has been implicated in various cancers, its genotoxic effects, including DNA damage and DNA-protein crosslinking, have proven insufficient to fully explain its role in carcinogenesis, suggesting the involvement of epigenetic mechanisms. Histone post-translational modifications (PTMs) on H3 and H4, critical for regulating gene expression, may contribute to FA-induced pathogenesis as lysine and arginine residues serve as targets for FA-protein adduct formation. This study aimed to elucidate the effects of FA on histone methylation and acetylation patterns. Human bronchial epithelial cells (BEAS-2B) were exposed to low-dose (100 M) and high-dose (500 M) FA for 1 hour, and their histone extracts were analyzed using high-resolution liquid chromatography-tandem mass spectrometry-based proteomics, followed by PTM-combined peptide analysis and single PTM site/type comparisons. We identified 40 peptides on histone H3 and 16 on histone H4 bearing epigenetic marks. Our findings revealed that FA exposure induced systemic alterations in H3 and H4 methylation and acetylation, including hypomethylation of H3K4 and H3K79 and changes in H3K9, H3K14, H3K18, H3K23, H3K27, H3K36, H3K37, and H3R40, as well as modifications in H4K5, H4K8, H4K12, and H4K16. These FA-induced histone modifications exhibited strong parallels with epigenetic alterations observed in cancers, leukemia, and Alzheimers disease. This study provides novel evidence of FA epigenetic toxicity, offering new insights into the potential mechanisms underlying FA-driven pathogenesis.

pharmacology and toxicology↗

bioRxiv2024

Rapid colorimetric detection of citrus tristeza virus combining portable sample preparation and reverse transcription-loop mediated isothermal amplification

AbstractsA sensing platform combining semi-automated sample preparation protocol and one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) is reported for rapid colorimetric detection of citrus tristeza virus (CTV) in a greenhouse. An OmniLyse micro-homogenizer and cellulose paper disks were integrated for quick sample preparation of total nucleic acids (<15 min). RT-LAMP assays were optimized in terms of primers concentrations and minimization of false positives for both CTV and cytochrome oxidase (COX) detections. Specifically, the optimal reaction time for lab-based RT-LAMP assays was determined as 40 minutes with the detection limits of CTV and COX as 43 copies/L (equivalent to 86 copies/mg of tissue) and 5 copies/L (equivalent to 10 copies/mg of tissue), respectively. Additionally, an in-greenhouse colorimetric RT-LAMP assay with lyophilized reaction mix for endpoint CTV detection was successfully conducted in 35 minutes without a false response in either colorimetric or fluorometric assays. Overall, this quick sample preparation protocol integrated with the lyophilized RT-LAMP assays showed high efficiency and reliability in plant pathogen detection in a greenhouse. This strategy holds great potential to be integrated into a portable, autonomous system and be universally adopted for in-field diagnosis of different pathogens.

bioengineering↗

bioRxiv2024

A 3D-printed handheld device for quick citrus tissue lysis and nucleic acid extraction

AbstractsA 3D-printed handheld device has been developed for rapid and efficient sample preparation from citrus leaves, aimed at streamlining protocols traditionally reliant on mortar and pestle. With its high-speed motor, knurled lysis chamber for rapid sample lysis, and quick nucleic acid extraction using paper disks, this device can yield ready-to-use extracts in just 12 minutes, significantly reducing the time required for sample preparation. The device was optimized for maximum sample lysis by evaluating operation voltages and chamber features. The results showed that the lysis chamber with internal knurling and the motor operated at 7.5 V was sufficient for effective sample lysis in 1 minute, achieving total RNA concentrations up to 87.6% of those obtained with a mortar and pestle. Furthermore, concerns regarding heat generation and resin release during the lysis process were found to not impact sample quality. To further facilitate in-field diagnosis, the capability of in-device sample preparation was verified with citrus sources infected with citrus tristeza virus and Spiroplasma citri in qPCR-based assays, where low assay variations were demonstrated (< 3.8%). Overall, the in-device sample preparation integrated with the paper disks showed good reliability and compatibility across different pathogens for downstream analysis. An eco-friendly sterilization protocol using household bleach and vitamin C solution was also developed to safely reuse the device for in-field deployment.

bioengineering↗

bioRxiv2023

Trans-Lesion Synthesis and Mismatch Repair Pathway Crosstalk Defines Chemoresistance and Hypermutation Mechanisms in Glioblastoma

Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides a new aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define novel molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.

cancer biology↗

bioRxiv2022

Identification of combinatorial colistin resistance mutations in Shewanella algae

BackgroundColistin is one of the last-line antimicrobial agents against drug-resistant gram-negative bacteria. Currently, little is known about the genetic mechanisms underlying colistin resistance in Shewanella algae, partly due to complex epistatic interactions among multiple genes. Methodology/Principal FindingsThis study sequenced, assembled, and compared the genomes of 23 mcr-negative colistin-resistant Shewanella algae from marine, clam, oyster, and human. Comparative genomics and computational approach were applied to find combinatorial mutations. A combination of three mutations (PmrB451, PmrE168, PmrH292) was found to be strongly associated with colistin resistance in Shewanella algae. Conclusions/SignificanceThis study demonstrates a computational approach for identifying epistatic-interacted mutations. Author summaryShewanella algae is an emerging pathogen related to Neglected Tropical Diseases (NTDs), including cobra-bite wound infections, marine injuries or ingestion of contaminated seafood. Shewanella algae is intrinsic resistant to various classes of {beta}-lactams. Additionally, growing resistance to colistin in mcr-negative Shewanella algae further limits therapeutic options, especially in resource-limited regions. Currently, little is known about the genetic mechanisms underlying colistin resistance in Shewanella algae, partly due to complex epistatic interactions among multiple genes. We conduct comparative genomics to identify combinatorial colistin resistance mutations in mcr-negative colistin-resistant Shewanella algae and a combination of three mutations (PmrB451, PmrE168, PmrH292) is strongly associated with colistin-resistance.

genomics↗

bioRxiv2022

RPG acts as a central determinant for infectosome formation and cellular polarization during intracellular rhizobial infections

Host-controlled intracellular accommodation of nitrogen-fixing bacteria is essential for the establishment of a functional Root Nodule Symbiosis (RNS). In many host plants, this occurs via transcellular tubular-structures (infection threads - ITs) that extend across cell layers via polar tip- growth. Comparative phylogenomic studies have identified RPG (RHIZOBIUM-DIRECTED POLAR GROWTH) among the critical genetic determinants for bacterial infection. In Medicago truncatula, RPG is required for effective IT progression within root hairs but the cellular and molecular function of the encoded protein remain elusive. Here, we show that RPG resides in the protein complex formed by the core endosymbiotic components VAPYRIN (VPY) and LUMPY INFECTION (LIN) required for IT polar growth, co- localizes with both VPY and LIN in IT tip- and perinuclear-associated puncta of M. truncatula root hairs undergoing infection and is necessary for VPY recruitment to puncta. Fluorescence Lifetime Imaging Microscopy (FLIM) of phosphoinositide species during bacterial infection revealed that functional RPG is required to sustain strong membrane polarization at the advancing tip of the IT. In addition, loss of RPG functionality alters the cytoskeleton-mediated connectivity between the IT tip and the nucleus and affects polar secretion of the cell wall modifying enzyme NODULE PECTATE LYASE (NPL). Our results integrate RPG into a core host machinery required to support symbiont accommodation, suggesting that its occurrence in plant host genomes is essential to co-opt a multimeric protein module committed to endosymbiosis to sustain IT-mediated bacterial infection.

plant biology↗

bioRxiv2020

Two-photon microscopy at >500 volumes/second

We demonstrate a multi-focal multi-photon volumetric microscopy via combination of 32-beam parallel lateral-scanning, a 70-kHz axial-scanning acoustic lens, and a 32-channel photodetector, enabling unprecedented data rate (2-10 GHz) and >500-volumes/second imaging speed over ~200x200x200-m3.

biophysics↗