Biology subjects

Li, C.

Publications and source records attributed to Li, C..

At least 523 records · Page 29Linked to original sources

bioRxiv2024

Robust Neutralization of SARS-CoV-2 Variants Including JN.1 and BA.2.87.1 by Trivalent XBB Vaccine-Induced Antibodies

Newly emerged SARS-CoV-2 variants like JN.1, and more recently, the hypermutated BA.2.87.1, have raised global concern. We recruited two groups of participants who had BA.5/BF.7 breakthrough infection post three doses of inactivated vaccines: one group experienced subsequent XBB reinfection, while the other received the XBB-containing trivalent WSK-V102C vaccine. Our comparative analysis of their serum neutralization activities revealed that the WSK-V102C vaccine induced stronger antibody responses against a wide range of variants, notably including JN.1 and the highly escaped BA.2.87.1. Furthermore, our investigation into specific mutations revealed that fragment deletions in NTD significantly contribute to the immune evasion of the BA.2.87.1 variant. Our findings emphasize the necessity for ongoing vaccine development and adaptation to address the dynamic nature of SARS-CoV-2 variants.

microbiology↗

bioRxiv2024

Mapping Cell Fate Transition in Space and Time

Cell fate transition is fundamentally a spatiotemporal process, but previous work has largely neglected the spatial dimension. Incorporating both space and time into models of cell fate transition would be a key step toward characterizing how interactions among neighboring cells, the presence of local niche factors, and physical migration of cells contribute to tissue development. To realize this potential, we propose topological velocity inference (TopoVelo), a model for jointly inferring spatial and temporal dynamics of cell fate transition from spatial transcriptomic data. TopoVelo extends the RNA velocity framework to model single-cell gene expression dynamics of an entire tissue with spatially coupled differential equations. Our principled probabilistic approach enables the incorporation of time point labels and multiple slices. We further introduce the idea of cell velocity, which is defined as the physical direction of cell maturation and migration. Simulated data analysis indicates that incorporating spatial coordinates significantly improves the accuracy of velocity and time inference. When evaluated on real Slide-Seq and Stereo-Seq data, TopoVelo significantly improves the spatial coherence of inferred cell ordering compared to previous methods. Furthermore, TopoVelo accurately recovers the expected directions of cell differentiation and migration in the embryonic mouse cerebral cortex, gut, and lung. Our work introduces a new dimension into the study of cell fate transitions and lays a foundation for modeling the collective dynamics of cells comprising an entire tissue.

bioinformatics↗

bioRxiv2024

Intrinsic diving reflex induces potent antioxidative response by activation of NRF2 signaling

AimsThis study aims to elucidate the underlying mechanisms of diving reflex, a powerful endogenous mechanism supporting underwater mammalian survival. Antioxidative responses, observed in marine mammals, may be contributing factors. Using a multi-organ approach, this study assesses whether acute and chronic diving reflex activate nuclear factor-erythroid-2-related factor 2 (NRF2) signaling pathways, which regulate cellular antioxidant responses. MethodsMale Sprague-Dawley rats (n=38) underwent either a single diving session to elicit acute diving reflex, or daily diving sessions for 4-weeks to produce chronic diving reflex. NRF2 (total, nuclear, phosphorylated), NRF2-downstream genes, and malondialdehyde were assessed via Western blot, immunofluorescence, RT-PCR, and ELISA in brain, lung, kidney, and serum. ResultsDiving reflex increased nuclear NRF2, phosphorylated NRF2, and antioxidative gene expression, in an organ-specific and exposure time-specific manner. Comparing organs, the brain had the highest increase of phosphorylated NRF2 expression, while kidney had the highest degree of nuclear NRF2 expression. Comparing acute and chronic sessions, phosphorylated NRF2 increased the most with chronic diving reflex, but acute diving reflex had the highest antioxidative gene expression. Notably, calcitonin gene-related peptide appears to mediate diving reflex effects on NRF2 activation. ConclusionsAcute and chronic diving reflex activate potent NRF2 signaling in the brain and peripheral organs. Interestingly, acute diving reflex induces higher expression of downstream antioxidative genes compared to chronic diving reflex. This result contradicts previous assumptions requiring chronic exposure to diving for induction of antioxidative effects and implies that the diving reflex has a strong translational potential during preconditioning and postconditioning therapies. Key PointsO_LIDiving reflex activates potent NRF2 signaling via multiple mechanisms, including phosphorylation, nuclear translocation, and KEAP1 downregulation with both acute and chronic exposure. C_LIO_LIDiving reflex activates NRF2 via differential pathways in the brain and other organs; phosphorylated NRF2 increases more in the brain, while nuclear NRF2 increases more in the peripheral organs. C_LIO_LIAcute diving reflex exposure induces a more pronounced antioxidative effect than chronic diving reflex exposure, indicating that the antioxidative response activated by diving reflex is not dependent upon chronic adaptive responses and supports diving reflex as both a preconditioning and postconditioning treatment. C_LI

physiology↗

bioRxiv2024

Chronic alcohol exposure induces cerebral microbleeds by TGF-β1/Smad signaling pathway mediated remodeling of cerebral small vessels

BackgroundLong-term heavy drinking is a major risk factor for cerebral microbleeds(CMBs), which are increasingly gaining attention as a pathological phenotype of cerebral small vessel diseases(CSVD). Under pathological conditions, remodeling of the extracellular matrix(ECM) on the walls of small vessels causes disarray in the structure and function of these vessels, leading to cerebral small vessel sclerosis and consequent rupture and bleeding. This can result in cognitive and emotional disorders, abnormal gait and increased risk of falling. However, the mechanisms underlying how long-term alcohol consumption leads to CMBs and decline in motor function remain unknown. MethodsWe constructed a chronic alcohol exposure mouse model and measured the deposition of ECMs on the small vessels in motor-related brain regions. The presence of microbleeds was confirmed through Prussian blue staining and Magnetic Resonance Imaging. We also extracted primary cerebral microvascular smooth muscle cells (CMVSMCs) from the newborn mice and explored the effects of alcohol on the phenotypic transformation and substance synthesis function. Additionally, we conducted interventional experiments on the cell and animal models with an anti-fibrotic drugs Pirfenidone(PFD). ResultsWe found that mice with long-term alcohol exposure showed decreased motor function. In their motor-related brain regions, such as the motor cortex(MC), thalamus/basal ganglia(Tha/BG), and cerebellum(CB), we observed microbleeds. On the small vessels in these areas, we detected excessive deposited ECM proteins. In vitro experiments with primary CMVSMCs revealed that after alcohol treatment, the cells underwent a transformation into fibroblast-like phenotypes, and excessive production of the aforementioned ECM proteins, which is regulated by upstream TGF{beta}1/Smad signaling pathway. Additionally, PFD applied on cell and animal models could reverse the above processes to some extent. ConclusionsOur study found that the remodeling of ECM accompanied by activation of TGF-{beta}1/Smad signaling pathway may be involved in alcohol-induced CMBs. It could be a potential therapeutic target for CMBs or CSVD.

molecular biology↗

bioRxiv2024

Differential mitochondrial bioenergetics and cellular resilience in astrocytes, hepatocytes, and fibroblasts from aging baboons

Biological resilience, broadly defined as ability to recover from acute challenge and return to homeostasis, is of growing importance to the biology of aging. At the cellular level, there is variability across tissue types in resilience and these differences likely to contribute to tissue aging rate disparities. However, there are challenges in addressing these cell-type differences at regional, tissue and subject level. To address this question, we established primary cells from aged male and female baboons between 13.3-17.8 years spanning across different tissues, tissue regions, and cell types including: (1) fibroblasts from skin and from heart separated into left ventricle (LV), right ventricle (RV), left atrium (LA) and right atrium (RA), (2) astrocytes from the prefrontal cortex and hippocampus and (3) hepatocytes. Primary cells were characterized by their cell surface markers and their cellular respiration assessed with Seahorse XFe96. Cellular resilience was assessed by modifying a live-cell imaging approach we previously reported that monitors proliferation of dividing cells following response and recovery to oxidative (50{micro}M-H2O2), metabolic (1mM-glucose) and proteostasis (0.1{micro}M-thapsigargin) stress. We noted significant differences even among similar cell types that are dependent on tissue source and the diversity in cellular response is stressor specific. For example, astrocytes were more energetic and exhibited greater resilience to oxidative stress (OS) than both fibroblasts and hepatocytes. RV and RA fibroblasts were less resilient to OS compared with LV and LA respectively. Skin fibroblasts were less impacted by proteostasis stress compared to astrocytes and cardiac fibroblasts. Future studies will test the functional relationship of these outcomes to age and developmental status of donors as potential predictive markers.

cell biology↗

bioRxiv2024

The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars - Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States

The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved six Salmonella clusters carrying the pESI plasmid. Four were emergent Salmonella Infantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carrying blaCTX-M-65 gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries the blaCTX-M-65 gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containing blaCTX-M-65 gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid in Salmonella in poultry and humans.

genomics↗

bioRxiv2024

Selective degradation of multimeric proteins via chemically induced proximity to TRIM21

Targeted protein degradation (TPD) has emerged as an effective strategy to eliminate disease-causing proteins by inducing their interactions with the protein degradation machinery. First-generation TPD agents exploit a limited set of broadly expressed E3 ubiquitin ligases with constitutive activity, forbidding their application to proteins requiring higher levels of targeting selectivity. Here, by phenotype-based screening, we discovered that the antipsychotic drug acepromazine possesses interferon-enhanced cytotoxicity towards cancer cell lines expressing high levels of aldo-keto reductases 1C. These enzymes convert acepromazine into its stereo-selective metabolite (S)-hydroxyl-acepromazine, which recruits the interferon-induced E3 ubiquitin ligase TRIM21 to the vicinity of the nuclear pore complex, resulting in the degradation of nuclear pore proteins. Co-crystal structures of acepromazine and derivatives in complex with the PRYSPRY domain of TRIM21 revealed a ligandable pocket, which was exploited for designing heterobifunctional degraders. The resulting chemicals selectively degrade multimeric proteins-- such as those in biomolecular condensates--without affecting monomeric proteins, consistent with the requirement of substrate-induced clustering for TRIM21 activation. As aberrant protein assemblies have been causally linked to diseases such as neurodegeneration, autoimmunity, and cancer, our findings highlight the potential of TRIM21-based multimer-selective degraders as a strategy to tackle the direct causes of these diseases.

pharmacology and toxicology↗

bioRxiv2024

IL-1beta-induced epithelial cell and fibroblast transdifferentiation fuels neutrophil recruitment in chronic rhinosinusitis with nasal polyps

Neutrophilic inflammation contributes to multiple chronic inflammatory airway diseases, including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated with an unfavorable prognosis. Here, using single-cell RNA sequencing (scRNA-seq) to profile human nasal mucosa obtained from the inferior turbinates, middle turbinates, and nasal polyps of CRSwNP patients, we identified two IL-1 signaling-induced cell subsets--LY6D+ club cells and IDO1+ fibroblasts--that promote neutrophil recruitment by respectively releasing S100A8/A9 and CXCL1/2/3/5/6/8 into inflammatory regions. IL-1{beta}, a pro-inflammatory cytokine involved in IL-1 signaling, induces the transdifferentiation of LY6D+ club cells and IDO1+ fibroblasts from primary epithelial cells and fibroblasts, respectively. In an LPS-induced neutrophilic CRSwNP mouse model, blocking IL-1{beta} activity with a receptor antagonist significantly reduced the numbers of LY6D+ club cells and IDO1+ fibroblasts and mitigated nasal inflammation. This study reveals the roles of two cell subsets in neutrophil recruitment and demonstrates an IL-1-based intervention for mitigating neutrophilic inflammation in CRSwNP.

immunology↗

bioRxiv2024

Deciphering the molecular mechanism of DNA-protein interactive co-condensates

Nucleic acid and protein co-condensates exhibit diverse morphologies crucial for fundamental cellular processes. Despite their significance, the molecular mechanisms governing morphology transitions remain poorly understood. To address this gap in knowledge, we investigated DNA and the human transcription factor p53 as a model system, specifically focusing on DNA-protein interactive co-condensates (DPICs)--a scenario where neither dsDNA nor the protein demonstrates phase-separation behavior individually. Through a combination of experimental assays and theoretical approaches, we elucidated: (i) the phase diagram of DPICs, identifying two distinct transition phenomena--a phase transition between viscoelastic fluid and viscoelastic solid states, and a morphology transition from droplet-like to "pearl chain"-like DPICs; (ii) the growth dynamics of DPICs. Droplet-like and "pearl chain"-like DPICs, although with dramatically distinct final morphologies and material properties, share a common initial critical microscopic cluster (CMC) size at the nanometer scale during the early stage of phase separation. These findings provide novel insights into the biophysical mechanisms underlying multi-component phase separations within cellular environments. Significance StatementNucleic acids and proteins have the capacity to form co-condensates, exhibiting various morphologies, including droplet-like and "pearl chains" formations. Despite this observation, the underlying biophysical mechanisms remain poorly understood. In this study, we employed DNA and the protein p53 as a model system. Our investigation revealed that the strength of the DNA-p53 interactions dictates the material properties of the co-condensates, leading to a transition from a viscoelastic fluid to a viscoelastic solid phase. This transition is accompanied by a morphological shift from droplet-like formations to structures resembling "pearl chains". Additionally, we explored the growth dynamics of these co-condensates and demonstrated that the strength of p53-DNA interactions influences the relaxation time of the co-condensates, thereby potentially determining their morphological features.

biophysics↗

bioRxiv2024

scMulan: a multitask generative pre-trained language model for single-cell analysis

Cells can be viewed as complex stories written by coordinated expression of genes. The success of AI large language models (LLMs) in mastering the human language inspired us to develop a large AI model scMulan with 368 million parameters to generate cell transcriptomics with designated attributes by learning the cell language. We defined a unified c-sentence to incorporate cell transcriptomics and meta-attributes, and pre-trained scMulan on the equivalence of 100 million human cells. Experiments showed that scMulan can generate designated pseudo transcriptomics, predict missing attributes of cells, reconstruct unobserved cells along functional gradients, and can help to identify driving regulators of cell fates. The generated data passed tests of current tools and can reflect the underlying biology.

bioinformatics↗

bioRxiv2024

In vitro neutrophil-bacteria assay in whole blood microenvironments with single-cell confinement

Blood is a common medium through which invasive bacterial infections disseminate in the human body. In vitro neutrophil-bacteria assays allow flexible mechanistic studies and screening of interventional strategies. In standard neutrophil-bacteria assays, both the immune cells and microorganisms are typically interrogated in an exogenous, homogeneous, bulk fluid environment (e.g., culture media or bacterial broth in microtiter plates), lacking the relevant physicochemical factors in the heterogenous blood-tissue microenvironment (e.g., capillary bed) with single-cell confinement. Here we present an in vitro neutrophil-bacteria assay by leveraging an open microfluidic model known as "-Blood" that supports sub-microliter liquid microchannels with single-cell confinement. In this study we compare the exogenous and endogenous fluids including neutrophils in RPMI (standard suspension cell culture media) and whole blood in response to Staphylococcus aureus (S. aureus, a gram-positive, non-motile bacterium) in phosphate buffered saline (PBS), Mueller Hinton Broth (MHB), and human serum. Our results reveal a significant disparity between the exogenous and endogenous fluid microenvironments in the growth kinetics of bacteria, the spontaneous generation of capillary (i.e., Marangoni) flow, and the outcome of neutrophil intervention on the spreading bacteria.

biophysics↗

bioRxiv2024

Defining cell type-specific immune responses in a mouse model of allergic contact dermatitis by single-cell transcriptomics

Allergic contact dermatitis (ACD), a prevalent inflammatory skin disease, is elicited upon repeated skin contact with protein-reactive chemicals through a complex and poorly characterized cellular network between immune cells and skin resident cells. Here, single-cell transcriptomic analysis of the murine hapten-elicited model of ACD reveals that upon elicitation of ACD, infiltrated CD4+ or CD8+ lymphocytes were primarily the IFN{gamma}-producing type 1 central memory phenotype. In contrast, type 2 cytokines (IL4 and IL13) were dominantly expressed by basophils, IL17A was primarily expressed by {delta}{gamma} T cells, and IL1{beta} was identified as the primary cytokine expressed by activated neutrophils/monocytes and macrophages. Furthermore, analysis of skin resident cells identified a sub-cluster of dermal fibroblasts with preadipocyte signature as a prominent target for IFN{gamma}+ lymphocytes and dermal source for key T cell chemokines CXCL9/10. IFN{gamma} treatment shifted dermal fibroblasts from collagen-producing to CXCL9/10-producing, which promoted T cell polarization toward the type-1 phenotype through a CXCR3-dependent mechanism. Furthermore, targeted deletion of Ifngr1 in dermal fibroblasts in mice reduced Cxcl9/10 expression, dermal infiltration of CD8+ T cell, and alleviated ACD inflammation in mice. Finally, we showed that IFN{gamma}+ CD8+ T cells and CXCL10-producing dermal fibroblasts co-enriched in the dermis of human ACD skin. Together, our results define the cell type-specific immune responses in ACD, and recognize an indispensable role of dermal fibroblasts in shaping the development of type-1 skin inflammation through the IFNGR-CXCR3 signaling circuit during ACD pathogenesis.

immunology↗

bioRxiv2024

Contrasting Phyllosphere Mycobiome in two Lycopodiaceae Plant Species: Unraveling Potential HupA-Producing Fungi and Fungal Interactions

BackgroundHuperzine A (HupA) is a natural lycopodium alkaloid renowned for its efficacy in treating neurodegenerative diseases such as Alzheimers disease. It specifically occurs in the Huperzioideae subfamily of Lycopodiaceae. Fungi associated with Huperzioideae species are potential contributors to HupA biosynthesis, offering promising prospects for HupA production. However, limited knowledge of fungal diversity in lycophytes, coupled with decreased HupA production over time of fungal strains, has impeded the discovery and applications of HupA-producing fungi. Here, we investigated huperzine concentrations and the mycobiome across various tissues of two Lycopodiaceae species, Huperzia asiatica (a HupA producer) and Diphasiastrum complanatum (a non-HupA producer). Our objectives across the tissues of the two species are to unveil the distribution of potential HupA-producing fungi and elucidate fungal interactions within the mycobiome, aiming to uncover the role of HupA-producing fungi and pinpoint their potential fungal facilitators. ResultsAmong the tissues, H. asiatica exhibited the highest HupA concentration in apical shoots (360.27 g/ml) whereas D. complanatum showed no HupA presence in any tissue. We obtained 441 Amplicon Sequence Variants (ASVs) from H. asiatica and 497 ASVs from D. complanatum. The fungal communities in bulbils and apical shoots of H. asiatica were low in diversity and dominated by Sordariomycetes, a fungal class harboring the majority of reported HupA-producing fungi. Integrating bioinformatics with published experimental reports, we identified 27 potential HupA-producing fungal ASVs, primarily in H. asiatica, with 12 ASVs identified as hubs in the fungal interaction network, underscoring their pivotal roles in mycobiome stability. Members of certain fungal genera, such as Penicillium, Trichoderma, Dioszegia, Exobasidium, Lycoperdon and Cladosporium exhibited strong connections with the potential HupA producers in H. asiaticas network rather than in D. complanatums, implying their prospects as fungal facilitators in enhancing HupA production. ConclusionsThis study advances our knowledge of fungal diversity in Lycopodiaceae and provides insights into the search for potential HupA-producing fungi and fungal facilitators. It highlights the importance of exploring young tissues, and emphasizes the ecological interactions that promote the fungi-mediated production of complex bioactive compounds, offering new directions for research in fungal ecology and secondary metabolite production.

microbiology↗

bioRxiv2024

Delineation of signaling routes that underlie differences in macrophage phenotypic states

Macrophages represent a major immune cell type in tumor microenvironments, they exist in multiple functional states and are of a strong interest for therapeutic reprogramming. While signaling cascades defining pro-inflammatory macrophages are better characterized, pathways that drive polarization in immunosuppressive macrophages are incompletely mapped. Here, we performed an in-depth characterization of signaling events in primary human macrophages in different functional states using mass spectrometry-based proteomic and phosphoproteomic profiling. Analysis of direct and indirect footprints of kinase activities has suggested PAK2 and PKC kinases as important regulators of in vitro immunosuppressive macrophages (IL-4/IL-13 or IL-10 stimulated). Network integration of these data with the corresesponding transcriptome profiles has further highlighted FOS and NCOR2 as central transcription regulators in immunosuppressive states. Furthermore, we retrieved single cell sequencing datasets for tumors from cancer patients and found that the unbiased signatures identified here through proteomic analysis were able to successfully separate pro-inflammatory macrophage populations in a clinical setting and could thus be used to expand state-specific markers. This study contributes to in-depth multi-omics characterizations of macrophage phenotypic landscapes, which could be valuable for assisting future interventions that therapeutically alter immune cell compartments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/574349v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1234713org.highwire.dtl.DTLVardef@10f4999org.highwire.dtl.DTLVardef@a8dd60org.highwire.dtl.DTLVardef@5dfb33_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGlobal proteomic characterization of primary human macrophages in different states C_LIO_LIMapping of main signaling events through in-depth data analysis C_LIO_LIPKC and PAK2 kinases are important regulators of immunosuppressive macrophages C_LIO_LIProteomic signatures enable accurate detection of pro-inflammatory macrophages in patient tumors C_LI

bioinformatics↗

bioRxiv2024

Skeletal Muscle Stem Cells Modulate Niche Function in Duchenne Muscular Dystrophy through YY1-CCL5 Axis

Stem cell activity is known to be tightly regulated by both intrinsic and extrinsic pathways but less is known about whether and how stem cells modulate their niche microenvironment. Adult skeletal muscle stem cells (MuSCs) are indispensable for muscle regeneration and also tightly regulated by macrophages (MPs) and fibro-adipogenic progenitors (FAPs) in the niche. Deregulated MuSC/MP/FAP interactions and the ensuing inflammation and fibrosis are hallmarks of dystrophic muscle. Here in this study we demonstrate that intrinsic deletion of transcription factor YY1 in MuSCs exacerbates dystrophic pathologies by altering the cellular composition and heterogeneity of MPs and FAPs. Further analysis reveals that the YY1 loss induces the expression of immune genes in MuSCs, including Ccl5. Augmented secretion of CCL5 from MuSCs promotes the recruitment of MPs via CCL5/CCR5 mediated crosstalk, which subsequently hinders the apoptosis and clearance of FAPs through elevated TGF{beta}1 accumulation. Maraviroc mediated pharmacological blockade of the CCL5/CCR5 axis effectively mitigates muscle dystrophy and improves muscle performance. Lastly, we further demonstrate that YY1 represses Ccl5 transcription in MuSCs by directly binding to its enhancer thus facilitating promoter-enhancer looping. Altogether, our study has demonstrated the previously unappreciated role of MuSCs in actively shaping their niche microenvironment through secreting immunomodulatory cytokines, and has also provided novel insight into the therapeutic intervention of muscle dystrophy.

cell biology↗

bioRxiv2024

A removable and cosmopolitan dsRNA Toti-like virus causes latent infection in a model diatom strain

Diatoms contribute to 20% of global primary productivity. Although some diatom viruses have been identified, the molecular mechanisms underlying their interactions with the host remain poorly understood. In this study, we report the discovery of an RNA molecule in the DNA extracts of the Phaeodactylum tricornutum strain Pt1, which possesses a well-annotated genome and has been used as a diatom model system since 1956. We confirmed this molecule to be a double-stranded linear RNA molecule and, through sequencing, demonstrated it to be a virus in the Totiviridae family that is prevalent among marine stramenopiles. We also detected this virus in Phaeodactylum tricornutum strain Pt3, which was collected in 1930s from a similar geographic location to Pt1, suggesting its prevalence within the region. By employing various inhibitors of the viral RNA-dependent RNA polymerase, we successfully generated a virus-free line isogenic to Pt1, establishing a model system to investigate the impact of RNA viruses on diatom physiology. The virus-free lines did not display obvious growth advantages or defects, indicating a tendency of the virus towards latent infection. Furthermore, we generated a robust antibody against the coat protein of this virus. By performing immunoprecipitation coupled with mass spectrometry, we found that translation-related proteins are enriched as potential interacting partners of the coat protein. Our results suggest that potential viral impacts in molecular research should be considered when Pt1 and Pt3 are used for studying translation-related processes. Additionally, our study unveiled a temperate mode of interaction between viruses and marine algal hosts that differs from the commonly-reported virulent, lytic infections. HighlightsO_LIprevalent dsRNA virus belonging to the Totiviridae family was discovered in the Pt1 and Pt3 strains of the model diatom Phaeodactylum tricornutum. C_LIO_LIvirus is absent in eight other strains of P. tricornutum, highlighting the importance of studying multiple accessions. C_LIO_LIvirus can be eliminated using a nucleotide analogue, resulting in a virus-free isogenic strain that allows us to investigate how viruses may affect diatom physiology. C_LIO_LIrobust antibody against the coat protein of this virus was developed to assist mechanistic studies of diatom-virus interactions. C_LI

microbiology↗

bioRxiv2024

Kernel-smoothed permutation for extreme P-value estimation in genetic association studies

In genetic studies, permutation tests serve as a cornerstone to estimate P-values. This is because researchers may design new test statistics without a known closed-form distribution, or the assumption of a well-established test may not hold. However, permutation tests require vast number of permutations which is proportional to the magnitude of the actual P-values. When it comes to genome-wide association studies where multiple-test corrections are routinely conducted, the actual P-values are extremely small, requiring a daunting number of permutations that may be beyond the available computational resources. Existing models that reduce the required number of permutations all assume a specific format of the test statistic to exploit its specific statistical properties. We propose Kernel-smoothed permutation which is a model-free method universally applicable to any statistic. Our tool forms the null distribution of test statistics using a kurtosis-driven transformation, followed by a kernel-based density estimation (KDE). We compared our Kernel-smoothed permutation to Naive permutation using statistics from known closed-form null distributions. Based on three frequently used test statistics in association studies, i.e., t-test, sequence kernel association test (SKAT), and chi-squared test, we demonstrated that our model reduced the required number of permutations by a magnitude with the same or higher accuracy.

bioinformatics↗

bioRxiv2024

Enhancement of Mediodorsal Thalamus Rescues Aberrant Belief Dynamics in a Novel Mouse Model for Schizophrenia

Optimizing behavioral strategy requires belief updating based on new evidence, a process that engages higher cognition. In schizophrenia, aberrant belief dynamics may lead to psychosis, but the mechanisms underlying this process are unknown, in part, due to lack of appropriate animal models and behavior readouts. Here, we address this challenge by taking two synergistic approaches. First, we generate a mouse model bearing patient-derived point mutation in Grin2a (Grin2aY700X+/-), a gene that confers high-risk for schizophrenia and recently identified by large-scale exome sequencing. Second, we develop a computationally trackable foraging task, in which mice form and update belief-driven strategies in a dynamic environment. We found that Grin2aY700X+/- mice perform less optimally than their wild-type (WT) littermates, showing unstable behavioral states and a slower belief update rate. Using functional ultrasound imaging, we identified the mediodorsal (MD) thalamus as hypofunctional in Grin2aY700X+/- mice, and in vivo task recordings showed that MD neurons encoded dynamic values and behavioral states in WT mice. Optogenetic inhibition of MD neurons in WT mice phenocopied Grin2aY700X+/- mice, and enhancing MD activity rescued task deficits in Grin2aY700X+/- mice. Together, our study identifies the MD thalamus as a key node for schizophrenia-relevant cognitive dysfunction, and a potential target for future therapeutics.

neuroscience↗