Biology subjects

Quan, Y.

Publications and source records attributed to Quan, Y..

13 recordsLinked to original sources

bioRxiv2026

High Dimensional Immune Profiling Reveals CD39 as a Correlate of Tuberculosis Disease Severity

Immune biomarkers of tuberculosis (TB) disease severity present a challenging area of research that remains poorly understood. New technologies are able to perform larger, unbiased studies that can unravel the complex host-pathogen dynamics occurring during a Mycobacterium tuberculosis infection, the causative agent of TB. In this study, we designed a high dimensional approach combining viable bacterial burden (CFU, colony forming units) with time-of-flight mass cytometry (CyTOF) analysis to profile differences in cell-type abundance and cell-type specific protein expression during states of low, intermediate and high TB disease burden. Broadly, we segregated cell-type specific immune responses into those driven by bacterial burden and/or the mycobacterial infection strain. Interrogating these immune signatures allowed us to identify ATP-catabolizing protein CD39 as a correlate of disease severity. Treatment of mice with a small molecule inhibitor of CD39 promoted effector T cell functions and CD4 T cell expansion during Mtb infection. Collectively, our data defines the differential lung immune environment between various mycobacterial disease severity states and uncovers a potential immune biomarker of infection and therapeutic immunomodulating target to aid in the treatment of TB.

immunology↗

bioRxiv2026

Generalizable Finger Movement Decoding from Intracranial Recordings Across Static and Dynamic Actions

Reliable decoding of finger movements requires brain-computer interfaces (BCIs) that generalize across the diverse static and dynamic actions performed in daily life. Static postures and dynamic movement sequences rely on partially distinct neural representations, and the balance between these components varies widely across tasks. Yet most BCI decoding pipelines are optimized for a narrow task domain, limiting their ability to transfer to new scenarios. Here we show that standard intracranial decoding approaches show notable performance drops when applied to previously unseen finger tasks with different static-dynamic compositions, and that generalization critically depends on multiple elements of the decoding pipeline. High gamma features and short temporal windows yield the most robust cross task transfer. Although nonlinear models perform best when examples of all tasks are represented during training, linear decoders generalize better to novel, particularly dynamic, actions. We identify a consistent static-dynamic structure across tasks that may provide a useful basis for improving generalization. Finally, we show that anatomical heterogeneity between tasks also constrains generalization. Together, these results establish design principles for BCIs that generalize reliably across the rich repertoire of human finger movements.

neuroscience↗

bioRxiv2025

A gap-free telomere-to-telomere pig reference genome provides insight in centromere evolution and breed-specific selection

The domestic pig is a key agricultural species and biomedical model, yet its reference genome has remained incomplete. Using PacBio HiFi, Oxford Nanopore reads, and Hi-C sequencing, we assembled the first telomere-to-telomere (T2T), gap-free pig genome (T2T-Sscrofa). Importantly, this assembly derives from the same individual pig that provided the original reference genome, thereby completing the long-standing foundation of pig genomics. This assembly resolves 274.8 Mb of previously unassembled sequence, including centromeres, segmental duplications, and ribosomal DNA arrays, and identifies 255 new protein-coding genes. Comparative analyses reveal a Robertsonian translocation in the western European wild boar and extensive structural variation across global pig populations. T2T-Sscrofa provides a comprehensive genomic foundation for agricultural, evolutionary, and biomedical research.

zoology↗

bioRxiv2024

Concatemer Assisted Stoichiometry Analysis (CASA): a targeted mass spectrometry method for protein quantification

Large multi-protein machines are central to multiple biological processes. However, stoichiometric determination of protein complex subunits in their native states presents a significant challenge. This study addresses the limitations of current tools in accuracy and precision by introducing concatemer-assisted stoichiometry analysis (CASA). CASA leverages stable isotope-labeled concatemers and liquid chromatography parallel reaction monitoring mass spectrometry (LC-PRM-MS) to achieve robust quantification of proteins with sub-femtomole sensitivity. As a proof-of-concept, CASA was applied to study budding yeast kinetochores. Stoichiometries were determined for ex vivo reconstituted kinetochore components, including the canonical H3 nucleosomes, centromeric (Cse4CENP-A) nucleosomes, centromere proximal factors (Cbf1 and CBF3 complex), inner kinetochore proteins (Mif2CENP-C, Ctf19CCAN complex), and outer kinetochore proteins (KMN network). Absolute quantification by CASA revealed Cse4CENP-A as a cell-cycle controlled limiting factor for kinetochore assembly. These findings demonstrate that CASA is applicable for stoichiometry analysis of multi-protein assemblies. SummaryThis study presents Concatemer-Assisted Stoichiometry Analysis (CASA) to address a common challenge in cell biological research: quantifying the number of each protein subunit in a native protein complex.

molecular biology↗

bioRxiv2024

Description of new micro-colonial fungi species Neophaeococcomyces mojavensis, Coniosporium tulheliwenetii, and Taxawa tesnikishii cultured from biological soil crusts

Black yeasts and relatives comprise Micro-Colonial Fungi (MCFs) which are slow-growing stress-tolerant micro-eukaryotes that specialize in extreme environments. MCFs are paraphyletic and found in the Orders Chaetothyriales (Eurotiomycetes) and Dothideales (Dothidiomycetes). We have isolated and described three new MCFs species from desert biological soil crusts (BSCs) collected from two arid land regions: Joshua Tree National Park (Mojave Desert) and UC Natural Reserve at Boyd Deep Canyon (confluence of Mojave and Sonoran Deserts). BSCs are composite assemblages of cyanobacteria, eukaryotic algae, fungi, lichens, and bryophytes embedded into the surface of desert soils, providing a protective buffer against the harsh desert environment. Our work focused on one type of desert BSC, the cyanolichen crust dominated by Collema sp. Using culture-dependent protocols, three MCFs were axenically isolated from their respective samples along with the extracted DNA. Their genomes were sequenced using Illumina and Nanopore, and finally assembled and annotated using hybrid assembly approaches and established bioinformatics pipelines to conduct final taxonomic phylogenetic analysis and placement. The three species described here are unique specimen from desert BSCs, here we introduce, Neophaeococcomyces mojavensis (Chaetothyriales), Cladosporium tulheliwenetii (Dothideales), and Taxawa tesnikishii (Dothideales).

microbiology↗

bioRxiv2024

A novel mouse home cage lickometer system reveals sex- and housing-based influences on alcohol drinking

Alcohol use disorder (AUD) is a significant global health issue. Despite historically higher rates among men, AUD prevalence and negative alcohol-related outcomes in women are rising. Loneliness in humans has been associated with increased alcohol use, and traditional rodent drinking models involve single housing, presenting challenges for studying social enrichment. We developed LIQ PARTI (Lick Instance Quantifier with Poly-Animal RFID Tracking Integration), an open-source tool to examine home cage continuous access two-bottle choice drinking behavior in a group-housed setting, investigating the influence of sex and social isolation on ethanol consumption and bout microstructure in C57Bl/6J mice. LIQ PARTI, based on our previously developed single-housed LIQ HD system, accurately tracks drinking behavior using capacitive-based sensors and RFID technology. Group-housed female mice exhibited higher ethanol preference than males, while males displayed a unique undulating pattern of ethanol preference linked to cage changes, suggesting a potential stress-related response. Chronic ethanol intake distinctly altered bout microstructure between male and female mice, highlighting sex and social environmental influences on drinking behavior. Social isolation with the LIQ HD system amplified fluid intake and ethanol preference in both sexes, accompanied by sex- and fluid-dependent changes in bout microstructure. However, these efects largely reversed upon resocialization, indicating the plasticity of these behaviors in response to social context. Utilizing a novel group-housed home cage lickometer device, our findings illustrate the critical interplay of sex and housing conditions in voluntary alcohol drinking behaviors in C57Bl/6J mice, facilitating nuanced insights into the potential contributions to AUD etiology. Significance StatementLoneliness has been associated with increased alcohol use, and traditional rodent drinking models involve single housing, presenting challenges for studying social enrichment. Here we developed LIQ PARTI (Lick Instance Quantifier with Poly-Animal RFID Tracking Integration), an open-source group-housed lickometer system to investigate how social housing, isolation, and sex influence alcohol consumption patterns in C57Bl/6J mice. LIQ PARTI accurately identifies mouse drinking events and uncovered significant housing- and fluid-dependent diferences in ethanol consumption and bout microstructure between male and female mice. Social isolation-induced changes to ethanol drinking behavior and microstructure were highly plastic, as resocialization generally reversed these changes. These findings expand on the complex interplay between sex, social isolation, and alcohol use.

neuroscience↗

bioRxiv2024

Retrotransposon-mediated variation of a chitin synthase gene confers insect resistance to Bacillus thuringiensis Vip3Aa toxin

Bacillus thuringiensis (Bt) crops expressing Vip3Aa are highly efficacious in controlling major lepidopteran pests and delaying evolution of pest resistance. Although practical resistance to Vip3Aa in the field has not been reported, to proactively manage the pest resistance, there is an urgent need to better understand the genetic basis of resistance to Vip3Aa. This is particularly important for the fall armyworm (Spodoptera frugiperda), one of the most destructive pests around the world, which has evolved practical resistance to Bt crystal (Cry) toxins. Here, a highly Vip3Aa-resistant (resistance ratio: 5,562-fold) strain of S. frugiperda was selected in the laboratory. Results from bulked segregant analysis, fine-scale mapping, and genetic linkage analysis indicate that a mutation in the midgut-specific chitin synthase gene, SfCHS2, is strongly associated with high-level resistance to Vip3Aa. The resistance is ascribed to the transcriptional variation caused by retrotransposon insertion. The same variation of SfCHS2 was also detected in a field population. Importantly, knockout of SfCHS2 via CRISPR/Cas9 in susceptible S. frugiperda confers its complete resistance (>10,000-fold) to Vip3Aa. Also, we demonstrate that knockout of CHS2 can result in complete resistance to Vip3Aa in additional lepidopteran species, suggesting a general role of this gene in Vip3Aa resistance among lepidopteran pests. These results reported here would contribute to monitor and management of pest resistance to Vip3Aa.

genetics↗

bioRxiv2022

cGASylation by a bacterial E1-E2 fusion protein primes antiviral immune signaling

In all organisms, innate immune pathways sense viral infection and rapidly activate potent immune responses while maintaining a high degree of specificity to prevent inappropriate activation (autoimmunity). In humans, the innate-immune receptor cGAS detects viral infection to produce the nucleotide second messenger cGAMP, which initiates STING-dependent antiviral signaling. Bacteria encode predecessors of the cGAS-STING pathway, termed cyclic oliogonucleotide-based antiphage signaling systems (CBASS), and bacterial cGAS detects bacteriophage infection to produce cGAMP. How bacterial cGAS activation is controlled, however, remains unknown. Here, we show that the CBASS-associated protein Cap2 primes bacterial cGAS for activation through a ubiquitin transferase-like mechanism. A cryoelectron microscopy structure of the Cap2-cGAS complex reveals Cap2 as an all-in-one ubiquitin transferase-like protein, with distinct domains resembling the eukaryotic E1 protein ATG7 and the E2 proteins ATG10 and ATG3. The structure captures a reactive-intermediate state with the cGAS C-terminus extending into the Cap2 E1 active site and conjugated to AMP. We find that Cap2 ligates the cGAS C-terminus to a target molecule in cells, a process we call cGASylation. cGASylation primes cGAS for a [~]50-fold increase in cGAMP production. We further demonstrate that Cap2 activity is balanced by a specific endopeptidase, Cap3, which deconjugates cGAS and antagonizes antiviral signaling. Our data demonstrate that bacteria control immune signaling using an ancient, minimized ubiquitin transferase-like system and provide insight into the evolution of E1 and E2 machinery across the kingdoms of life.

microbiology↗

bioRxiv2021

Multi-site phosphorylation of yeast Mif2/CENP-C promotes inner kinetochore assembly

Kinetochores control eukaryotic chromosome segregation by connecting chromosomal centromeres to spindle microtubules. Duplication of centromeric DNA necessitates kinetochore disassembly and subsequent reassembly on the nascent sisters. To search for a regulatory mechanism that controls the earliest steps of kinetochore assembly, we studied Mif2/CENP-C, an essential basal component. We found that Polo-like kinase (Cdc5) and Dbf4-dependent kinase (DDK) phosphorylate the conserved PEST region of Mif2/CENP-C and that this phosphorylation directs inner kinetochore assembly. Mif2 phosphorylation promotes kinetochore assembly in a reconstituted biochemical system, and it strengthens Mif2 localization at centromeres in cells. Disrupting one or more phosphorylation sites in the Mif2-PEST region progressively impairs cellular fitness and sensitizes cells to microtubule poisons. The most severe Mif2-PEST mutations are lethal in cells lacking otherwise non-essential Ctf19 complex factors. These data suggest that multi-site phosphorylation of Mif2/CENP-C is a robust switch that controls inner kinetochore assembly, ensuring accurate chromosome segregation.

cell biology↗

bioRxiv2021

The structural basis for Ulp2 recruitment to the kinetochore

The step-by-step process of chromosome segregation defines the stages of the cell division cycle. In eukaryotes, signaling pathways that control these steps converge upon the kinetochore, a multiprotein assembly that connects spindle microtubules to the centromere of each chromosome. Kinetochores control and adapt to major chromosomal transactions, including replication of centromeric DNA, biorientation of sister centromeres on the metaphase spindle, and transit of sister chromatids into daughter cells during anaphase. Although the mechanisms that ensure tight microtubule coupling at anaphase are at least partly understood, kinetochore adaptations that support other cell cycle transitions are not. We report here a mechanism that enables regulated control of kinetochore sumoylation. A conserved surface of the Ctf3/CENP-I kinetochore protein provides a binding site for the SUMO protease, Ulp2. Ctf3 mutations that disable Ulp2 recruitment cause elevated inner kinetochore sumoylation and defective chromosome segregation. The location of the site within the assembled kinetochore suggests coordination between sumoylation and other cell cycle-regulated processes.

cell biology↗

bioRxiv2020

Colorectal cancer marker identification using the aging immune system-related blood cell DNA methylome

ObjectiveThere is a body of evidence that the aging immune system is linked to cancer. Here, we hypothesized that ubiquitination might play a key gatekeeper role in immune system aging and tumorigenesis in CRC. Therefore, we will systematically study the DNA methylation of ubiquitination genes and screen candidate CRC marker that are correlated with both aging and immune cell compositions. DesignThrough aging- and immune-related DNA methylation data, we investigated the DNA methylation regulation changes in promoters with other regions of genes during aging and their association with the immune cell proportion in the circulating whole blood of healthy individuals. Then, by collecting a cohort of 100 colon cancer patients and 50 healthy individuals, we used nucleic acid mass spectrometry to test whether ubiquitination genes can be used as candidate markers for the early screening of CRC. ResultsThe biological analyses for aging- and CD4 T cell proportion-derived differential genes showed that they are associated with ubiquitination. Among them, DZIP3 was significantly associated with both aging (P-value = 3.86E-06) and CD4 T cell proportion (P-value = 1.97E-05) in circulating blood. Then, we validated that the 1st exon DNA methylation of DZIP3 could predict the onset of early stage CRC (AUC = 0.833, OR = 8.82) and all pTNM stages of CRC (AUC = 0.782, OR = 5.70). ConclusionsThe epigenetically regulated ubiquitination plays an important role in immune aging and tumorigenesis. DNA methylation characteristic of DZIP3 can be used as a promising marker of CRC early screening. Summary boxO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIThe aging immune system is associated with cancer. C_LIO_LIUbiquitination plays potent roles in regulating a variety of signals in both innate and adaptive immune cells. C_LIO_LIThe abnormalities of ubiquitination are closely related to the occurrence of various tumors. C_LIO_LIBlood cell DNA methylome analysis provides a promising tool to probe the key components of immune cell dysregulation in aging and tumorigenesis. C_LI What are the new findings?O_LIThe aging- and immune cell proportion-derived differential genes are associated with ubiquitination. C_LIO_LIThe epigenetically regulated ubiquitination plays an important role in immune aging and tumorigenesis. C_LIO_LIDNA methylation characteristic of DZIP3, an E3 ubiquitin ligase with no reports on its function in immune cells and tumorigenesis, can be used as a promising markers of CRC early screening. C_LI How might it impact on clinical practice in the foreseeable future?O_LIThe in-depth study for DNA methylome of ubiquitination will open up a new path for the study of CRC pathogenesis, diagnosis and treatment. C_LIO_LIIn addition, DZIP3-focused screening technique only needs to extract the whole blood of individuals for MassARRAY analysis; the samples are easy to obtain, and the results are objective. Therefore, this method may have important applications in clinical CRC screening. C_LI

cancer biology↗

bioRxiv2018

Artesunate pErk up HepG2 cells to die through apoptosis in vitro

The dilemma between in vitro and in vivo drug screening results persisted to hinder preclinical anti-cancer drug development. In this study, drug screening was initially performed on monolayer cultures of HepG2 cells, whereas in vivo drug testing was performed on the subcutaneous xenograft mouse model of HepG2 cells in athymic nude mice. Results showed that Artesunate inhibited HepG2 cell growth in vitro, but was ineffective in vivo. Hence, we investigated the difference between in vitro and in vivo settings using this cell-drug combination as a model. Immuno-staining of hepatocellular carcinoma (HCC) biomarkers showed that -fetoprotein (AFP) was unaffected by Artesunate treatment in vitro or in vivo, suggesting that AFP was neither a biomarker nor response indicator. Alternatively, high albumin was detected in both monolayer and organoid cultures; contrariwise, the xenograft tumors prevailed low albumin, in consistency to human HCC with poor prognosis. Artesunate treatment reduced intracellular albumin expression in vitro; Artesunate did not alter tissue and serum albumin in xenograft mice, in coincidence with its irresponsiveness in vivo. However, Artesunate binding to albumin was undetectable. Instead, we observed a transient stimulation of Erk1/2 phosphorylation followed by DAPK1 dephosphorylation and apoptosis. Combined treatment of Artesunate with U0126 revoked Erk1/2-DAPK1 phosphorylation and exerted modest proliferative advantage at early time points, but eventually did not rescue HepG2 cells from death. U0126 induced multiploid formation independent of Artesunate, resulting in cell cycle arrest within 24 h post-treatment.\n\nSignificanceSystematic investigation of HCC biomarkers AFP and albumin among the in vitro models of monolayer and organoid cultures, and the in vivo models of subcutaneous and liver implantation xenograft mice was conducted.

cell biology↗

bioRxiv2016

The detection of covariation of mRNA levels of large sets of genes across multiple human populations

In this study, we analyse RNA-Seq data from panels of human lymphoblastoid cell lines (LCLs) to identify covariation in the mRNA levels of large numbers of genes. Such large scale covariation may have biological origin or be due to technical variation in analysis (generally referred to as batch effects). We show that batch effects cannot explain this covariation by demonstrating reproducibility across different human populations and across different methods of analysis. This view is also supported by enrichment of single and combinations of transcription factors (TFs) binding to cognate promoter regions, enrichment of genes shown to be sensitive to the knockdown of individual TFs, enrichment of functional pathways, and finally enrichment of protein-protein interactions in proteins encoded by groups of covarying genes. The properties of the groups of covarying genes are therefore most readily explained by the influence of cumulative variations in the effectors of gene expression that act in trans on cognate genes. We suggest that covariation has functional outcomes by showing that covariation of 83 genes involved in the spliceosome pathway accounts for 8-16% of the variation in the alternative splicing patterns of genes expressed in human LCLs.

genetics↗