Biology subjects

Xian, Y.

Publications and source records attributed to Xian, Y..

4 recordsLinked to original sources

bioRxiv2025

Observing Grazing Behavior Transitions in Cafeteria roenbergensis with Video-Rate Two-Photon Microscopy

Grazing behavior of free-living aquatic heterotrophic nanoflagellates (HNFs) on bacteria plays a central role in shaping microbial community structure and nutrient cycling. However, direct observation of these interactions has been limited by the rapid motility of flagellates and the transient nature of predator-prey encounters. To address this gap, this study presents a novel application of video-rate two-photon fluorescence microscopy for high resolution, real-time imaging of fast-moving microorganisms. HNF Cafeteria roenbergensis is used as a model system to investigate dynamic grazing interactions between fluorescently stained bacteria and the flagellates, where the flagellates are detected via their intrinsic cellular autofluorescence. This two-photon microscope combined with real-time imaging capability enables continuous capture of contact, capture, ingestion, and digestion steps during grazing. Quantitative analysis across varying prey concentration reveals phase-specific durations and saturation behavior in grazing activities. Furthermore, transitions in grazing dynamics across two continuous periods of flagellates in starved and fed conditions are observed in live time series videos. This technique provides a powerful new tool to study rapid microbial interactions in situ and can be broadly applicable to diverse microbe-microbe systems. With the integration of targeted fluorescent molecular probes, this technique holds significant potential for uncovering mechanical and biochemical interactions underlying microbial feeding and communication. SignificanceThis study significantly advances microbial ecology by applying video-rate two-photon fluorescence microscopy to directly visualize and quantify the rapid grazing behavior of flagellates on bacteria. By enabling real-time observation of contact, ingestion, and digestion during the grazing events, the technique overcomes limitations of traditional imaging. It captures behavioral transitions tied to physiological states, offering quantitative insight into microbial predator-prey dynamics. This method establishes a broadly applicable platform for studying fast, transient microbial interactions. Although current limitations include the lack of 3D tracking, emerging optical technologies promise enhanced capabilities, paving the way for deeper understanding of microbial processes in aquatic ecosystems.

biophysics↗

bioRxiv2024

Bacterial stress granule protects mRNA through ribonucleases exclusion

Membraneless droplets formed through liquid-liquid phase separation of ribonucleoprotein particles contribute to mRNA storage in eukaryotic cells. How such aggresomes contribute to mRNA dynamics under stress, and their functional role, is less understood in bacteria. Here we used multiple approaches including live-cell imaging, polymer physics modelling and transcriptomics to show that prolonged stress leading to ATP depletion in Escherichia coli results in increased aggresome formation, compaction, and selective mRNA enrichment within these aggresomes. Longer transcripts accumulate more in aggresomes than in the cytosol. Mass spectrometry and mutagenesis studies showed that mRNA ribonucleases are excluded from aggresomes due to electrostatic repulsion arising from their negative surface charges. Experiments with fluorescent reporters and disruption of aggresome formation showed that mRNA storage within aggresomes promoted rapid translation reactivation and associated with reduced lag phases during growth after stress removal. Our findings suggest that mRNA storage within aggresomes confers an advantage for bacterial survival and recovery from stress.

biophysics↗

bioRxiv2023

Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines

Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.

microbiology↗

bioRxiv2019

Establishing the phenotypic basis of adherent-invasive Escherichia coli (AIEC) pathogenicity in intestinal inflammation

Background & AimsAdherent-invasive Escherichia coli (AIEC) are enriched in ileal Crohns disease patients and implicated in disease etiology. However, AIEC pathogenesis is poorly understood, and it is unclear if the expansion of these organisms contributes to inflammatory bowel disease (IBD). Questions also remain as to what extent the various in vitro phenotypes used to classify AIEC are pathologically relevant.\n\nMethodsWe utilized a combination of in vitro phenotyping and a murine model of intestinal inflammation to systematically relate AIEC phenotypes to pathogenicity for 30 mucosa-associated human-derived E. coli strains. In vitro assays used included survival/replication in and TNF- production by J774 macrophages as well as invasion/replication in Caco2 intestinal epithelial cells.\n\nResultsAIEC do not form a phenotypic group that is clearly separated from non-AIEC. However, E. coli strains displaying in vitro AIEC phenotypes caused, on average, more severe intestinal inflammation. Survival/replication of strains in J774 and Caco2 cells were positively correlated with disease in vivo, while adherence to Caco2 cells and TNF- production by J774 cells were not. Importantly, co-colonization with adherent non-AIEC strains ameliorated AIEC-mediated disease.\n\nConclusionOur findings do not support the existence of an AIEC pathovar that can be clearly separated from commensal E. coli. However, intracellular survival/replication phenotypes do contribute to murine intestinal inflammation, suggesting that the AIEC overgrowth observed in human IBD makes a causal contribution to disease. The ability to differentiate pathologically-relevant AIEC phenotypes from those that are not provides an important foundation for developing strategies to predict, diagnose and treat human IBD through characterizing and modulating patient E. coli populations.

microbiology↗