Biology subjects

Men, Y.

Publications and source records attributed to Men, Y..

17 recordsLinked to original sources

bioRxiv2026

Bacterial Membrane Vesicles in Wastewater Disseminate Antibiotic Resistance Genes

Bacterial membrane vesicles (BMVs) have emerged as important contributors to the dissemination of antibiotic resistance genes (ARGs) in the environment. Here, we developed a high-performance immunomagnetic isolation method that improves the purity and selectivity of BMV recovery from wastewater, minimizes contamination from eDNA and viruses, and enables differentiation of BMVs originating from Gram-positive versus Gram-negative bacteria with minimal cross-reactivity. Using this approach, we found that ARGs such as the kanamycin resistance gene (kanR) was highly abundant in BMVs from both raw and treated wastewater, exhibited persistence following treatment, and retained the ability to generate antibiotic-resistant bacteria via transformation. Metagenomic sequencing further revealed that tetracycline resistance genes were the most abundant ARG class across all wastewater samples, while the composition of BMV-associated ARGs differed from the bulk ARG profile. These findings highlight the critical yet underrecognized role of BMVs in the spread of antimicrobial resistance and underscore the need to address BMV-mediated pathways within a One Health framework linking environmental and human health.

microbiology↗

bioRxiv2026

Lung-Targeting Interleukin-10 mRNA Lipid Nanoparticles Ameliorate Acute Lung Injury

Acute respiratory distress syndrome (ARDS) is the most severe manifestation of acute lung injury (ALI), characterized by diffuse pulmonary inflammation, impaired gas exchange, and high morbidity and mortality. Despite its clinical significance, no specific or effective pharmacological therapies are currently available for its treatment. In this study, we developed a lung -targeted mRNA-sulfonium lipid nanoparticle (mRNA/sLNP) delivery system for the treatment of ALI in a mouse model. We first optimized sulfonium lipid structures, and the optimized sLNP was comprehensively characterized and subsequently loaded with interleukin-10 (IL-10) mRNA. In a lipopolysaccharide (LPS)-induced ALI mousemodel, IL-10/sLNPdemonstrated both prophylactic and therapeutic efficacy, significantly attenuating pulmonary and systemic inflammation, restoring barrier integrity, and reducing tissue injury.

bioengineering↗

bioRxiv2026

Biotransformation and biodefluorination of chlorinated polyfluorocarboxylic acids by Acetobacterium species

Chlorinated per- and polyfluoroalkyl substances (Cl-PFAS) represent an important subgroup in replacement chemicals for legacy PFAS, and they have been detected in various environments including water bodies, soil, as well as air particles. However, the biodegradability of these chemicals is largely unknown. A recent study reported dechlorination triggered anaerobic biodefluorination of Cl-PFCAs by activated sludge communities. In this study, we further investigated the biodefluorination of Cl-PFCAs by pure cultures. Six of ten selected Cl-PFCAs displayed significant defluorination by Acetobacterium bakii, and corresponding pathways were proposed according to transformation product analysis. Several additional Acetobacterium species were all capable of defluorinating 3,5,7,8-tetrachloro-2,2,3,4,4,5,6,6,7,8,8- undecafluorooctanoic acid (CTFE4) with >50% removal of organic fluorine. On the contrary, Clostridium homopropionicum cannot defluorinate CTFE4. Crude protein extraction experiment showed that the enzymes responsible for CTFE4 dechlorination and defluorination required anaerobic atmosphere to function. Differential gene expression was analyzed according to RNA sequencing analysis, and the results indicated vitamin B12 related enzymes may involve in CTFE4 dechlorination.

microbiology↗

bioRxiv2025

Ribosomal Epistatic Interactions Drive the Emergence of High-Level Streptomycin Resistance in Escherichia coli

The widespread use of antibiotics has raised serious concerns about the emergence and dissemination of antibiotic resistance in the environment. Studies reveal that environmental exposures to antibiotics and other non-antibiotic pollutants can promote the development of high-level antibiotic resistance via de novo mutations. However, specific genotypes conferring strong resistance in resistant mutants, particularly the roles of co-occurring mutations, remained poorly understood. This study fills this knowledge gap by constructing site-specific Escherichia coli mutants and demonstrating that it was the epistatic interactions that conferred the observed strong streptomycin resistance in native E. coli isolates. Three ribosomal mutations (rpsED142N, rpsLR86S and rsmGW150fs), which co-evolved under environmentally relevant selection pressures, acted synergistically to confer resistance far exceeding that of each individual mutation. The interactions between the rsmG frameshift mutation and other reported rpsL point mutations were also investigated. The findings unravel the essential but previously overlooked role played by specific co-evolving mutations in the acquisition of both high-level streptomycin resistance and fitness compensation. The findings also underscore a strong and increasing need to investigate whole genomes of antibiotic-resistant bacteria and identify potential epistatic mutations conferring resistance phenotypes. The integration of those genetic mutations as antibiotic resistance biomarkers will complement with the resistome profiling and enable more accurate antibiotic resistance monitoring and environmental risk assessment. SynopsisMultiple ribosomal mutations co-evolved under environmentally relevant exposure conferred high-level streptomycin resistance via epistatic interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/694165v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@e47b2borg.highwire.dtl.DTLVardef@525e27org.highwire.dtl.DTLVardef@1a36e4dorg.highwire.dtl.DTLVardef@9eaf34_HPS_FORMAT_FIGEXP M_FIG Table of Contents Graphic C_FIG

microbiology↗

bioRxiv2025

Environmental Heterogeneity Altered the Growth Fitness of Antibiotic-Resistant Mutants and the Resistance Prevalence in Escherichia coli populations

Antibiotic resistance is one of the most critical issues in public health. As antibiotic-resistant bacteria emerge under certain selection pressure, their further proliferation can facilitate the prevalence and maintenance of the antibiotic resistance. Here, we investigated which environmental factors could affect the growth fitness of antibiotic-resistant Escherichia coli strains using growth competition assays. We found that when antibiotic resistance selection pressure was removed, lower temperature and nutrient limitations, especially iron (Fe) deficiency, fostered a better fitness to resistant mutants when co-cultivated with the wild type, whereas changes in pH or salinity (Na or K) did not. Moreover, the growth advantage of resistant mutants under the selection pressure was reversed by suboptimal conditions like acidic/basic pH, high K salinity, and Fe limitation. These identified key environmental factors influencing the growth fitness of antibiotic-resistant mutants provide important insights into the prediction and mitigation of antibiotic resistance in heterogeneous environments.

microbiology↗

bioRxiv2025

CRISPR-On-Beads: A Simple and Sensitive Approach for Bacterial DNA Detection

CRISPR/Cas12a, recognized for its high efficiency and specificity in nucleic acid recognition, has found extensive applications in infectious disease sensing. Nonetheless, a significant challenge persists in devising a simple method for the rapid, convenient, and accurate visualization of detection results. In this study, we demonstrate an innovative and simple CRISPR-on-beads assay for visual detection of methicillin-resistant Staphylococcus aureus (MRSA). This approach combines isothermal target amplification, CRISPR/LbCas12a-mediated cleavage, and magnetic bead-based probe binding for signal amplification, enabling rapid and convenient identification of bacterial DNA. Our results show that this detection method exhibits both high sensitivity and specificity, with a detection limit as low as 30 CFU/L. This newly developed biosensing approach can easily be integrated with a portable fluorescence microscope for medical diagnostics in resource-limited settings.

bioengineering↗

bioRxiv2023

Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. drive defluorination of perfluorinated unsaturated carboxylic acids

Enzymatic cleavage of C-F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of , {beta}-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. Two critical molecular features in Acetobacterium species enabling reductive defluorination are (i) a functional fluoride efflux transporter (CrcB) and (ii) an electron-bifurcating caffeate reduction pathway (CarABCDE). The fluoride transporter was required for detoxification of released fluoride. Car enzymes were implicated in defluorination by the following evidence: (i) only Acetobacterium spp. with car genes catalyzed defluorination; (ii) caffeate and PFAS competed in vivo; (iii) models from the X-ray structure of the electron-bifurcating reductase (CarC) positioned the PFAS substrate optimally for reductive defluorination; (iv) products identified by 19F-NMR and high-resolution mass spectrometry were consistent with the model. Defluorination biomarkers identified here were found in wastewater treatment plant metagenomes on six continents.

microbiology↗

bioRxiv2023

Pneumatic Nano-Sieve for CRISPR-based Detection of Drug-resistant Bacteria

The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieve an on-chip concentration factor of 15 for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU/mL. This developed approach provides a rapid, precise, and centrifuge-free solution suitable for point-of-care diagnostics, with the potential to significantly improve patient outcomes in resource-limited medical conditions.

bioengineering↗

bioRxiv2022

Koisio Technology-Modulated Cell Culture Media can Significantly Increase the Antioxidant Capacity of Mouse Fibroblasts

Oxidative stress is not only a critical common pathological factor of numerous diseases, but also an important factor in the aging process. It is highly valuable to discover novel and economic substances for enhancing the antioxidant capacity of human body. In this study we used a cell culture model to determine the antioxidant capacity of Koisio technology-modulated solutions without additions of any external substances. Our study has obtained the following findings: First, the cells cultured in Koisio technology-modulated cell culture media (KM) showed significantly greater capacity to decrease H2O2-induced oxidative stress, compared with the cells cultured in regular cell culture media; second, the cells cultured in KM showed significantly greater capacity to resist H2O2-induced decreases in cell number, compared with the cells cultured in regular cell culture media; and third, the H2O2 prepared in Koisio technology-modulated MEM produced significantly lower levels of decreases in cell number, compared with the H2O2 prepared in MEM. Collectively, our study has indicated that Koisio technology can increase the antioxidant capacity of both solutions and cells without additions of any external substances. Based on our previous findings, we proposed that Koisio technology-modulated solutions increase cellular antioxidant capacity at least partially by increasing intracellular ATP levels.

cell biology↗

bioRxiv2022

Differential Effects of Koisio Technology-Modulated Solutions on the Growth of Lung Fibroblast Cell Cultures and Lung Cancer Cell Cultures

Cell growth is a crucial biological property of cells, which plays key roles in several major biological processes including organ development, tissue repair and cancer development. It is of both scientific and medical significance to discover new strategies to modulate cell growth. Koisio technology is a novel technology that modulates the properties of water solely by physical approaches without additions of any external substances. In our current study we obtained the following findings regarding the effects of Koisio technology-modulated solutions on cell growth: First, compared with the lung fibroblast (L929) cell cultures cultured in normal media, the L929 cells cultured in Koisio technology-modulated media grew at approximately 20% higher speed; second, compared with the lung cancer cell cultures (LLC cells) cultured in normal media, the LLC cells cultured in Koisio technology-modulated media grew at approximately 9% lower speed; and third, compared with the telomere lengths of the L929 cells cultured in normal media, the L929 cells cultured in Koisio technology-modulated media had approximately 14% longer telomere length. Collectively, our study has provided the first evidence indicating that Koisio technology-modulated solutions affect differentially the growth of lung fibroblast cell cultures and that of lung cancer cell cultures. The capacity of the Koisio technology-modulated solutions to promote the growth of lung fibroblast cell cultures may result at least partially from its capacity to protect the telomere length.

cell biology↗

bioRxiv2022

Koisio Technology-Modulated Cell Culture Media can Lead to Markedly Increased Intracellular ATP Levels of Fibroblast Cell Cultures

It has been reported that Koisio technology-modulated water without external additions of any substances can enter several types of aquaporins with significantly higher rate. In this study we determined the effects of Koisio technology-modulated cell culture media (Koisio media) on the energy state of cells. We found that for the lung fibroblast (L929) cell cultures, Koisio media without any additions of external substances led to approximately an 57% increase in the intracellular ATP levels of the cell cultures at the Cell Passage 6 - 18, compared with regular cell culture media. Seemingly surprisingly, we did not find that Koisio media could significantly affect the mitochondrial membrane potential of the cells, compared with regular cell culture media. Collectively, our study has provided first evidence indicating that Koisio media can lead to remarkable increases in the intracellular ATP levels of the L929 cell cultures, suggesting significant potential of Koisio technology in generating energy-enhancing water. Our finding that Koisio media did not affect the mitochondrial membrane potential has suggested that novel mechanisms may underlie the effects of Koisio media on cellular energy.

cell biology↗

bioRxiv2021

MetaLogo: a generator and aligner for multiple sequence logos

Sequence logos are used to visually display conservations and variations in short sequences. They can indicate the fixed patterns or conserved motifs in a batch of DNA or protein sequences. However, most of the popular sequence logo generators are based on the assumption that all the input sequences are from the same homologous group, which will lead to an overlook of the heterogeneity among the sequences during the sequence logo making process. Heterogeneous groups of sequences may represent clades of different evolutionary origins, or genes families with different functions. Therefore, it is essential to divide the sequences into different phylogenetic or functional groups to reveal their specific sequence motifs and conservation patterns. To solve these problems, we developed MetaLogo, which can automatically cluster the input sequences after multiple sequence alignment and phylogenetic tree construction, and then output sequence logos for multiple groups and aligned them in one figure. User-defined grouping is also supported by MetaLogo to allow users to investigate functional motifs in a more delicate and dynamic perspective. MetaLogo can highlight both the homologous and nonhomologous sites among sequences. MetaLogo can also be used to annotate the evolutionary positions and gene functions of unknown sequences, together with their local sequence characteristics. We provide users a public MetaLogo web server (http://metalogo.omicsnet.org), a standalone Python package (https://github.com/labomics/MetaLogo), and also a built-in web server available for local deployment. Using MetaLogo, users can draw informative, customized and publishable sequence logos without any programming experience to present and investigate new knowledge on specific sequence sets.

bioinformatics↗

bioRxiv2021

Specific phenotypic, genomic, and fitness evolutionary trajectories toward antibiotic resistance induced by pesticide co-stressors in Escherichia coli

To explore how co-occurring non-antibiotic environmental stressors affect evolutionary trajectories toward antibiotic resistance, we exposed susceptible Escherichia coli K-12 populations to environmentally relevant levels of pesticides and streptomycin for 500 generations. The coexposure substantially changed the phenotypic, genotypic, and fitness evolution trajectories, resulting in much stronger streptomycin resistance (>15-fold increase) of the populations. Antibiotic target modification mutations in rpsL and rsmG, which emerged and dominated at late stages of evolution, conferred the strong resistance even with less than 1% abundance, while the off-target mutations in nuoG, nuoL, glnE, and yaiW dominated at early stages only led to mild resistance (2.5 - 6-fold increase). Moreover, the strongly resistant mutants exhibited lower fitness costs even without the selective pressure and had lower minimal selection concentrations than the mildly resistant ones. Removal of the selective pressure did not reverse the strong resistance of coexposed populations at a later evolutionary stage. The findings suggest higher risks of the selection and propagation of strong antibiotic resistance in environments potentially impacted by antibiotics and pesticides.

microbiology↗

bioRxiv2020

Siderophores provoke extracellular superoxide production by carbon-starving Arthrobacter strains when carbon sources recover

Superoxide and other reactive oxygen species (ROS) in the environment shape microbial communities1 and drive transformation of metals2,3 and inorganic/organic matter4,5. Taxonomically diverse bacteria and phytoplankton can produce extracellular superoxide during laboratory cultivation6-11. Understanding the physiological reasons for extracellular superoxide production by aerobes in the environment is a crucial question yet not fully solved. Here, we showed that iron-starving Arthrobacter sp. QXT-31 (referred to as A. QXT-31 hereafter) secreted a type of siderophore (deferoxamine, DFO), which provoked extracellular superoxide production by carbon-starving A. QXT-31 when carbon sources were recovered. Several other siderophores also demonstrated similar effects. RNA-Seq data hinted that DFO stripped iron from iron-bearing proteins in the electron transfer chain (ETC) of metabolically active A. QXT-31, resulting in electron leakage from the electron-rich (resulting from carbons source metabolism) ETC and superoxide production. Considering that most aerobes secrete siderophore(s)12 and often suffer from carbon starvation in the environment, certain aerobes are expected to produce extracellular superoxide when carbon source(s) recover/fluctuate, thus influencing the microbial community and cycling of many elements. In addition, an artificial iron-chelator (diethylenetriamine pentaacetic acid, DTPA) was widely used in microbial superoxide quantification. Our results showed that DTPA provoked superoxide production by A. QXT-31 and highlighted its potential interference in microbial superoxide quantification.

microbiology↗

bioRxiv2020

Astroglial FMRP modulates synaptic signaling and behavior phenotypes in FXS mouse model

Fragile X syndrome (FXS) is one of the most common inherited intellectual disability (ID) disorders, in which the loss of FMRP protein induces a range of cellular signaling changes primarily through excess protein synthesis. Although neuron-centered molecular and cellular events underlying FXS have been characterized, how different CNS cell types are involved in typical FXS synaptic signaling changes and behavioral phenotypes is largely unknown. Recent evidence suggests that selective loss of astroglial FMRP is able to dysregulate glutamate uptake, increase spine density, and impair motor-skill learning. Here we investigated the effect of astroglial FMRP on synaptic signaling and FXS-related behavioral and learning phenotypes in astroglial Fmr1 cKO and cON mice in which FMRP expression is selectively diminished or restored in astroglia. We found that selective loss of astroglial FMRP contributes to cortical hyperexcitability by enhancing NMDAR-mediated evoked but not spontaneous miniEPSCs and elongating cortical UP state duration. Selective loss of astroglial FMRP is also sufficient to increase locomotor hyperactivity, significantly diminish social novelty preference, and induce memory acquisition and extinction deficits in astroglial Fmr1 cKO mice. Importantly, re-expression of astroglial FMRP is able to significantly rescue the hyperactivity (evoked NMDAR response, UP state duration, and open field test) and social novelty preference in astroglial Fmr1 cON mice. These results demonstrate a profound role of astroglial FMRP in the evoked synaptic signaling, spontaneously occurring cortical UP states, and FXS-related behavioral and learning phenotypes and provide important new insights in the cell type consideration for the FMRP reactivation strategy.

neuroscience↗

bioRxiv2019

Digital polymerase chain reaction in an array of microfluidic printed droplets

Digital polymerase chain reaction (PCR) is a fast-developed technology, which makes it possible to provide absolute quantitative results. However, this technology has not been widely used in research field or clinical diagnostics. Although digital PCR has been born for two decades, the products on this subject still suffer from either high cost or cumbersome user experience, hence very few labs have the willingness or budget to routinely use such product; On the other hand, the unique sensitivity of dPCR over traditional qPCR shows great potential applications. Here, a cost-effective digital PCR method based on a microfluidic printing system was introduced, trying to overcome those shortcomings. The microfluidic droplet printing technology was utilized in this study to directly generate droplet array containing PCR reaction solution onto the simple glass substrate for the subsequent PCR and imaging, which could be done with any regular flat-panel PCR machine and microscope. The method introduces a new perspective in droplet-based digital PCR in that the droplets generated with this method aligns well in an array without touch with each other, therefore the regular glass and oil could be used without any special surfactant. With simple analysis, the data generated with this method showed reliable quality, which followed the Poisson distribution trend. Compared with other expensive digital PCR methods, this system is more affordable and simpler to integrate, especially for those biological or medical labs which are in need for the digital PCR options but short in budget. Therefore, this method is believed to have the great potential in the future market application.

molecular biology↗

bioRxiv2019

Exposure to environmental level pesticides stimulates and diversifies evolution in Escherichia coli towards greater antibiotic resistance

Antibiotic resistance is one of the most challenging issues in public health. Antibiotic resistance can be selected by antibiotics at sub-inhibitory concentrations, the concentrations typically occurring in natural and engineered environments. Meanwhile, many other emerging organic contaminants such as pesticides are frequently co-occurring with antibiotics in agriculture-related environments and municipal wastewater treatment plants. To investigate the effects of the co-existing, non-antibiotic pesticides on the development of antibiotic resistance, we conducted long-term exposure experiments using a model Escherichia coli strain. The results revealed that 1) the exposure to a high level (in mg/L) of pesticides alone led to the emergence of mutants with significantly higher resistance to streptomycin; 2) the exposure to an environmental level (in {micro}g/L) of pesticides together with a sub-inhibitory level (in sub mg/L) of ampicillin synergistically stimulated the selection of ampicillin resistance and the cross-selection of resistance to three other antibiotics (i.e., ciprofloxacin, chloramphenicol, and tetracycline). Resistance levels of mutants selected from co-exposure were significantly higher than those of mutants selected from ampicillin exposure only. The comparative genomic and transcriptomic analyses indicate that distinct and diversified genetic mutations in ampicillin- and ciprofloxacin-resistant mutants were selected from co-exposure, which likely caused holistic transcriptional regulation and the increased antibiotic resistance. Together, the findings provide valuable fundamental insights into the development of antibiotic resistance under environmentally relevant conditions, as well as the underlying molecular mechanisms of the elevated antibiotic resistance induced by the exposure to pesticides.\n\nSignificance statementAntibiotic resistance is a major threat to public health globally. Besides clinically relevant environments, the emergence and spread of resistant bacteria in non-clinical environments can also potentially pose risks of therapy failures. This study showed that the long-term, environment-level exposure to pesticides with and without antibiotics significantly stimulated the development of greater antibiotic resistance. The resistant strains selected from the exposure to pesticides are genetically and metabolically distinct from the ones selected by the antibiotic only. Although it is still being debated regarding whether or not a large use of antibiotics in plant agriculture is harmful, our findings provide the first fundamental evidence that greater concerns of antibiotic resistance may result if antibiotics are applied together with non-antibiotic pesticides.

microbiology↗