Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 325 records · Page 18Linked to original sources

bioRxiv2024

Tonotopic organization of auditory cortex in awake marmosets revealed by multi-modal wide-field optical imaging

Tonotopic organization of the auditory cortex has been extensively studied in many mammalian species using various methodologies and physiological preparations. Tonotopy mapping in primates, however, is more limited due to constraints such as cortical folding, use of anesthetized subjects, and mapping methodology. Here we applied a combination of through-skull and through-window intrinsic optical signal imaging, wide-field calcium imaging, and neural probe recording techniques in awake marmosets (Callithrix jacchus), a New World monkey with most of its auditory cortex located on a flat brain surface. Coarse tonotopic gradients, including a recently described rostral-temporal (RT) to parabelt gradient, were revealed by the through-skull imaging of intrinsic optical signals and were subsequently validated by single-unit recording. Furthermore, these tonotopic gradients were observed with more details through chronically implanted cranial windows with additional verifications on the experimental design. Moreover, the tonotopy mapped by the intrinsic-signal imaging methods was verified by wide-field calcium imaging in an AAV-GCaMP labeled subject. After these validations and with the further effort to expand the field of view more anteroventrally in both windowed and through-skull subjects, an additional putative tonotopic gradient was observed more rostrally to the area RT, which has not been previously described by the standard model of tonotopic organization of the primate auditory cortex. Together, these results provide the most comprehensive data of tonotopy mapping in awake primate species with unprecedented coverage and details in the rostral proportion and supports a caudorostrally arranged mesoscale organization of at least three repeats of functional gradients in the primate auditory cortex, similar to the ventral stream of primate visual cortex.

neuroscience↗

bioRxiv2024

ROS Mediated the Photodynamic Antibacterial of Vibrio vulnificus by a DNA-Targeted Molecular Rotor Probe

Vibrio vulnificus, a highly pathogenic Gram-negative bacterium, is capable of inducing sepsis, necrotizing fasciitis, and skin and soft tissue infections through contact with wounds. Currently, the majority of V. vulnificus strains have developed resistance to multiple drugs, highlighting the critical necessity for the development of novel therapeutics capable of effectively targeting and eradicating this bacterium. In recent years, material molecules have emerged as promising antimicrobial agents. This study introduces a novel molecular fluorescent probe, BDTP, which demonstrates a wide-ranging antimicrobial effect against both Gram-negative and Gram-positive bacteria while exhibiting minimal toxicity to normal mammalian cells. Of particular significance is BDTPs ability to rapidly detect V. vulnificus, bind to bacterial DNA, and exhibit fluorescence monitoring behavior. Furthermore, BDTP displays enhanced photodynamic antibacterial activity when exposed to white light irradiation. Under a low dose of white light (15mW cm-2), the killing efficiency of V. vulnificus irradiated with 4uM for 10 minutes was more than 99.8%. Moreover, it could significantly inhibit and eliminate the biofilm formed by V. vulnificus. It can induce the production of reactive oxygen species (ROS) in V. vulnificus cells, leading to bacterial cell damage. More importantly, BDTP significantly promoted the healing of infected wounds in an animal model of V. vulnificus infection. Therefore, BDTP shows great promise as a potent antibacterial agent against V. vulnificus infection.

microbiology↗

bioRxiv2024

Extracellular electron transfer drives efficient H2-independent methylotrophic methanogenesis by Methanomassiliicoccus, a seventh order methanogen

Methylotrophic methanogenesis is achieved via methyl group dismutation or H2 reduction. This study reports extracellular electron droving efficient methylotrophic methanogenesis. The 7th order methanogen Methanomassiliicoccus luminyensis exclusively implements H2-dependent methylotrophic methanogenesis, but strain CZDD1 isolated from paddy soil possessed a higher methane-producing rate in coculture with Clostridium malenominatum CZB5 or the electrogenic Geobacter metallireducens. Chronoamperometry detected current production from CZB5, and current consumption accompanied CH4 production in a methanol-containing electrochemical culture of CZDD1. This demonstrated that M. luminyensis was capable of both direct species electron transfer (DIET) and extracellular electron transfer (EET) in methylotrophic methanogenesis. EET and DIET also enabled CZDD1 to produce methane from dimethyl arsenate. Differential transcriptomic analysis on H2-versus EET- and DIET-cocultures suggested that a membrane-bound Fpo-like complex and archaella of M. luminyensis CZDD1 could accept extracellular electrons. Given the ubiquitous environmental distribution of Methanomassiliicoccus strains, EET driven methylotrophic methanogenesis may contribute significantly to methane emission.

microbiology↗

bioRxiv2024

msCNVS: medium throughput single cell copy number variation sequencing with barcoded library construction free of preamplification toward clinical implementation

Single cell copy number variation sequencing (scCNV-seq) is valuable for genomic analysis of a variety of health and disease systems, yet the available methods either depend on either preamplification of the whole genome of each cell, special devices or untracable, which hinder scCNV-seq practice in clinics. Here we provide scalable multiplex scCNV-seq (msCNVS) that allows direct medium-throughput library construction for single cells, which are barcoded individually with Tn5 transposome in a microplate and immediately pooled for downstream processes, elevating the efficiency by orders of magnitude. An algorithm is developed on the distribution of segmented normalized read count density to identify the major peaks associating with integer copy numbers, further improving the accuracy for objective CNV calling. Here msCNVS faithfully distinguishes the unique CNV patterns of 5 cell lines. The individual msCNVS profiles of 70 individual K562 cells highly correlate with the profile of K562 bulk cells (R=0.90-0.98), and the triplicates of HeLa3 bulk cells correlated nearly perfect (R=0.99). The msCNVS CNV profiles of primary cell cultures of amniotic fluid are confirmed by G-banding karyotype analysis and chromosomal microarray analysis. Additionally, the coverage uniformity of msCNVS is superior to that of MDA and MALBAC and approaches what eMDA and DOP-PCR achieves. Furthermore, msCNVS detects CNV deletions in 2 stunted, abnormal blastocysts, one with CNV mosaicism, and uncovered variants of CNVs in circulated tumor cells, cancerous pleural effusion cells, and patient-derived xenograft nuclei. Thus, msCNVS promises a robust, reliable and highly efficient approach to genomic testing of precious and rare cells like those typically obtained in reproductive and cancer clinics. One-Sentence SummaryBy early pooling of multiple single cells individually barcoded with Tn5 transposome, msCNVS enables efficient CNV profiling of rare clinic samples

genomics↗

bioRxiv2024

Characterisation of cuticle mechanical properties: analysing stiffness in layered living systems to understand surface buckling patterns

Development of a living organism is a highly regulated process during which biological materials undergo constant change. De novo material synthesis and changes in mechanical properties of materials are key for organ development; however, few studies have attempted to produce quantitative measurements of the mechanical properties of biological materials during growth. Such quantitative analysis is particularly challenging where the material is layered, as is the case for the plant cuticle on top of the plant epidermal cell wall. Here, we focus on Hibiscus trionum flower petals, where buckling of the cuticle forms ridges, producing an iridescent effect. This ridge formation is hypothesised to be due to mechanical instability, which directly depends upon the mechanical properties of the individual layers within the epidermal cells. We present measurements of the mechanical properties of the surface layers of petal epidermal cells through atomic force microscopy (AFM) and the uniaxial tensile tester for ultrathin films (TUTTUT), across growth stages. We found that the wavelength of the surface ridges was set at the ridge formation stage, and this wavelength was preserved during further petal development, most likely because of the plasticity of the material. Our findings suggest that temporal changes in biological material properties are key to understanding the development of biological surface patterns.

plant biology↗

bioRxiv2024

Gene-language models are whole genome representation learners

The language of genetic code embodies a complex grammar and rich syntax of interacting molecular elements. Recent advances in self-supervision and feature learning suggest that statistical learning techniques can identify high-quality quantitative representations from inherent semantic structure. We present a gene-based language model that generates whole-genome vector representations from a population of 16 disease-causing bacterial species by leveraging natural contrastive characteristics between individuals. To achieve this, we developed a set-based learning objective, AB learning, that compares the annotated gene content of two population subsets for use in optimization. Using this foundational objective, we trained a Transformer model to backpropagate information into dense genome vector representations. The resulting bacterial representations, or embeddings, captured important population structure characteristics, like delineations across serotypes and host specificity preferences. Their vector quantities encoded the relevant functional information necessary to achieve state-of-the-art genomic supervised prediction accuracy in 11 out of 12 antibiotic resistance phenotypes. TeaserDeep transformers capture and encode gene language content to derive versatile latent embeddings of microbial genomes.

genomics↗

bioRxiv2024

Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging

The bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNA-Seq) to profile 29,325 enriched non-hematopoietic bone marrow cells and discover nine transcriptionally distinct subtypes. We next employed CO-detection by inDEXing (CODEX) multiplexed imaging of 18 individuals, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, niche for early hematopoietic stem and progenitor cells. We used our atlas to predict cell type labels in new bone marrow images and used these predictions to uncover mesenchymal stromal cell (MSC) expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. Our work represents the first comprehensive, spatially-resolved multiomic atlas of human bone marrow and will serve as a reference for future investigation of cellular interactions that drive hematopoiesis.

cell biology↗

bioRxiv2024

Structures of transcription-translation coupling complexes at each stage of the translation cycle

In the bacterium Escherichia coli, efficient expression of protein-coding genes is achieved through physical coupling of RNA polymerase (RNAP) synthesizing an mRNA and the first ribosome translating the mRNA, with transcription elongation factors NusG and NusA bridging RNAP and ribosome in a transcription-translation complex (TTC). Recent structural studies suggest that the flexibility in NusG and NusA accommodates the changes in ribosome conformation that occur during the translation cycle, but details have been unclear. Here, we report cryo-EM structures of TTCs at each stage of the translation cycle as an actively translating ribosome approaches to a halted transcription complex. We observe sequential conversion of a loosely coupled TTC (TTC-LC) to a tightly coupled TTC (TTC-B) to a collided TTC (TTC-A) as the ribosome approaches the transcription complex. We show that flexibility of the NusG linker and NusA "pantograph" enable TTC-LC and TTC-B to accommodate ribosome conformation at each stage of the translation cycle. We show that, in TTC-A, steric clash between ribosome and RNAP upon ribosome 30S head swiveling inhibits 30S head swiveling, consistent with translation slowdown, and applies mechanical force to the trailing edge of RNAP, causing transcription termination. Our results define the structures and properties of loosely coupled, tightly coupled, and collided TTCs at each stage of the translation cycle.

molecular biology↗

bioRxiv2024

Activation of locus coeruleus noradrenergic neuronsrapidly drives homeostatic sleep pressure

Homeostatic sleep regulation is essential for optimizing the amount and timing of sleep, but the underlying mechanism remains unclear. Optogenetic activation of locus coeruleus noradrenergic neurons immediately increased sleep propensity following transient wakefulness. Fiber photometry showed that repeated optogenetic or sensory stimulation caused rapid declines of locus coeruleus calcium activity and noradrenaline release. This suggests that functional fatigue of noradrenergic neurons, which reduces their wake-promoting capacity, contributes to sleep pressure.

neuroscience↗

bioRxiv2024

Brain preparedness: The cortisol awakening response proacts dynamic organization of large-scale brain networks across emotional and executive functions

Emotion and cognition involve an intricate crosstalk of neural and endocrine systems that support allostatic processes for maintenance of dynamic equilibrium and rapid adaptation for upcoming challenges. As a hallmark of human endocrine activity, the cortisol awakening response (CAR) is recognized to play a critical role in modulating emotional and executive functions. Yet, the underlying mechanisms of such effects remain elusive. By leveraging pharmacological neuroimaging technique and Hidden Markov Modeling of brain state dynamics, we show that the CAR proactively modulates rapid reconfigurations (state) of large-scale brain networks across multi-task demands. Behaviorally, suppression of CAR proactively and selectively impaired accuracy for emotional discrimination task but not for working memory (WM). In parallel, suppressed CAR led to a decrease in the occurrence rate of brain state dominant to emotional processing, but an increase in brain state linking to executive control under high WM demand. Further energy-based analyses revealed an increase in transition frequency and sequence complexity along with an increased entropy during emotional tasks when suppressed CAR, suggesting a decreased energy supply. Moreover, an increased transition frequency was observed when shifting from neutral to emotional conditions, but an opposite pattern during WM task, with n decreased transition frequency shifts from low to high-executive demands. Our findings establish a causal link between CAR and dynamic allocation of neural resources for emotional and executive functions, suggesting a cognitive neuroendocrine account for CAR-mediated proactive effects and human allostasis.

neuroscience↗

bioRxiv2024

Extracellular chemosymbiont populations in a shallow-water thyasirid clam potentially shaped by priority effect

Chemosynthetic animal symbioses are common in marine ecosystems but remain overlooked as contributors to global carbon fixation. We show that the shallow-water thyasirid clam Thyasira tokunagai, dominant in Yellow Sea sediments, harbors sulfur-oxidizing Sedimenticola symbionts with remarkably consistent genomic contents and functionality across the region, showing active Calvin cycle gene expression and close-knit host-symbiont metabolic integration. Field surveys demonstrated densities up to 2015 individuals{middle dot}m{square}2, while radiocarbon tracing revealed assimilation rate constants (0.002-0.005 day{square}{superscript 1}) peaking at 14.8{degrees}C. Spatial modelling combining abundance and temperature estimated a carbon fixation of 0.89 Tg C{middle dot}yr{square}{superscript 1} in Yellow Sea, equivalent to 43% of the annual sedimental C burial from the Chinese coast. The species complex that includes T. tokunagai is widely distributed and constitutes a globally significant, previously unaccounted blue carbon sink. Our findings underscore the crucial role of shallow-water chemosymbioses in carbon cycling, emphasising the importance of incorporating them into climate models and conservation strategies focused on carbon sequestration.

microbiology↗

bioRxiv2024

A site-wise reliability analysis of the ABCD diffusion fractional anisotropy data, impact of the scanner and analytical pipeline

The Adolescent Brain and Cognitive Development (ABCD) project is the largest study of adolescent brain development. ABCD longitudinally tracks 11,868 participants aged 9-10 years from 21 sites using standardized protocols for multi-site MRI data collection and analysis. While the multi-site and multi-scanner study design enhances the robustness and generalizability of analysis results, it may also introduce non-biological variances including scanner-related variations, subject motion, and deviations from protocols. ABCD imaging data were collected biennially within a period of ongoing maturation in cortical thickness and integrity of cerebral white matter. These changes can bias the classical test-retest methodologies, such as intraclass correlation coefficients (ICC). We developed a site-wise adaptive ICC (AICC) to evaluate the reliability of imaging-derived phenotypes while accounting for ongoing brain development. AICC iteratively estimates the population-level age-related brain development trajectory using a weighted mixed model and updates age-corrected site-wise reliability until convergence. We evaluated the test-retest reliability of regional fractional anisotropy (FA) measures from diffusion tensor imaging and cortical thickness (CT) from structural MRI data for each site. The mean AICC for 20 FA tracts across sites was 0.61{+/-}0.19, lower than the mean AICC for CT in 34 regions across sites, 0.76{+/-}0.12. Remarkably, sites using Siemens scanners consistently showed significantly higher AICC values compared to those using GE/Philips scanners for both FA (AICC=0.71{+/-}0.12 vs 0.46{+/-}0.17, p<0.001) and CT (AICC=0.80{+/-}0.10 vs 0.69{+/-}0.11, p<0.001). These findings demonstrate site-and-scanner related variations in data quality and underscore the necessity for meticulous data curation in subsequent association analyses.

neuroscience↗

bioRxiv2024

Lineage-tracing of Acta2+ cells in aged mice during lung fibrosis formation and resolution supports the lipofibroblasts to myofibroblast reversible switch

Idiopathic pulmonary fibrosis (IPF) develops mostly in old man and is characterized by the irreversible accumulation of excessive extracellular matrix components by activated myofibroblasts (aMYFs) leading to lung failure. Following bleomycin administration in young mice, fibrosis formation associated with efficient resolution takes place, the later limiting the clinical relevance of this model for IPF. In young mice, we previously reported that aMYFs captured during fibrosis formation differentiate towards a lipofibroblast (LIF)-like phenotype during resolution. In this study, we used aged mice in combination with bleomycin administration to trigger enhanced fibrosis formation and delayed resolution, as a more relevant model for IPF and examined the heterogeneity and fate of aMYFs at different time points. Alveolosphere assay were carried out to compare the alveolar resident mesenchymal niche activity for AT2 stem cells in young versus old mice. Lineage tracing of the Acta2+ aMYFs in old mice exposed to bleomycin followed by scRNAseq of the lineage-traced cells isolated during fibrosis formation and resolution was performed to delineate the heterogeneity of aMYFs during fibrosis formation and their fate during resolution. Data mining of human mesenchymal cells from IPF and control datasets were also performed to decipher the heterogeneity of aMYFs and investigate differentiation trajectories during fibrosis formation. Our results show that alveolar resident mesenchymal cells from old mice display decreased supporting activity for AT2 stem cells. We report that aMYFs consist of four subclusters displaying unique pro-alveologenic versus pro-fibrotic profiles. Alveolar fibroblasts displaying a high LIF-like signature largely constitute both the origin and fate of aMYFs during fibrosis formation and resolution, respectively. The heterogeneity of aMYFs is conserved in humans and a significant proportion of human aMYFs displays a high LIF signature. In conclusion, our data indicate that the cellular and molecular bases of aMYFs formation and differentiation towards the LIF phenotype are conserved between young and old mice. Importantly, our work identifies a subcluster of aMYFs that is potentially relevant for future management of IPF.

pathology↗

bioRxiv2024

Voice patches in the marmoset auditory cortex revealed by wide-field calcium imaging

Species-specific vocalizations are behaviorally critical sounds. Similar to faces, species-specific vocalizations are important for the survival and social interactions of both humans and vocal animals. Face patches have been found in the brains of both human and non-human primates. In humans, a voice patch system has been identified on the lateral superior temporal gurus (STG) that is selective to human voices over other sounds. In non-human primates, while vocalization-selective regions were found on the rostral portion of the temporal lobe outside of the auditory cortex in both macaques and marmosets using functional magnetic resonance imaging (fMRI), it is yet clear whether vocalization-selective regions are present in the auditory cortex. Using wide-field calcium imaging, a technique with both high temporal and high spatial resolution, we discovered two voice patches in the marmoset auditory cortex that preferentially respond to marmoset vocalizations over other sounds and carry call types and identity information. One patch is located on the posterior primary auditory cortex (A1), and the other one is located on the anterior non-core region of the auditory cortex. These voice patches are functionally connected and hierarchically organized as shown by latency and selectivity analyses. Our findings reveal the existence of voice patches in the auditory cortex of marmosets and support the notion that similar cortical architectures are adapted for recognizing communication signals for both vocalizations and faces in different primate species.

neuroscience↗

bioRxiv2024

DNA Prime-Protein Boost Targeting Conformational Non-RBD Region for Broad Cross-Neutralization

Preventing immune escape of SARS-CoV-2 variants is crucial in vaccine development to ensure broad protection against the virus. Conformational epitopes beyond the RBD region are vital components of the spike protein but have received limited attention in the development of broadly protective SARS-CoV-2 vaccines. In this study, we used a DNA prime-protein boost regimen to evaluate the broad cross-neutralization potential of immune response targeting conformational non-RBD region against SARS-CoV-2 viruses in mice. Mice with enhanced antibody responses targeting conformational non-RBD region show better performance in cross-neutralization against the Wuhan-01, Delta, and Omicron subvariants. Via analyzing the distribution of conformational epitopes, and quantifying epitope-specific binding antibodies, we verified a positive correlation between the proportion of binding antibodies against the N-terminal domain (NTD) supersite (a conformational non-RBD epitope) and SARS-CoV-2 neutralization potency. The current work highlights the importance of high ratio of conformational non-RBD-specific binding antibodies in mediating viral cross-neutralization and provides new insight into overcoming the immune escape of SARS-CoV-2 variants.

immunology↗

bioRxiv2024

OsNF-YB7 inactivates OsGLK1 to inhibit chlorophyll biosynthesis in rice embryo

As a master regulator of seed development, Leafy Cotyledon 1 (LEC1) promotes chlorophyll (Chl) biosynthesis in Arabidopsis, but the mechanism underlying this remains poorly understood. Here, we found that loss of function of OsNF-YB7, a LEC1 homolog of rice, leads to chlorophyllous embryo, indicating that OsNF-YB7 plays an opposite role in Chl biosynthesis in rice compared with that in Arabidopsis. OsNF-YB7 regulates the expression of a group of genes responsible for Chl biosynthesis and photosynthesis by directly binding to their promoters. In addition, OsNF-YB7 interacts with Golden 2-Like 1 (OsGLK1) to inhibit the transactivation activity of OsGLK1, a key regulator of Chl biosynthesis. Moreover, OsNF-YB7 can directly repress OsGLK1 expression by recognizing its promoter in vivo, indicating the involvement of OsNF-YB7 in multiple regulatory layers of Chl biosynthesis in rice embryo. We propose that OsNF-YB7 functions as a transcriptional repressor to regulate Chl biosynthesis in rice embryo.

plant biology↗

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

ARX regulates interneuron subtype differentiation and migration

Mutations in aristaless-related homeobox (ARX) are associated with neurodevelopmental disorders including developmental epilepsies, intellectual disabilities, and autism spectrum disorders, with or without brain malformations. Aspects of these disorders have been linked to abnormal cortical interneuron (cIN) development and function. To further understand ARXs role in cIN development, multiple Arx mutant mouse lines were interrogated. We found that ARX is critical for controlling cIN numbers and distribution, especially, in the developing marginal zone (MZ). Single cell transcriptomics and ChIP-seq, combined with functional studies, revealed ARX directly or indirectly regulates genes involved in proliferation and the cell cycle (e.g., Bub3, Cspr3), fate specification (e.g., Nkx2.1, Maf, Mef2c), and migration (e.g., Nkx2.1, Lmo1, Cxcr4, Nrg1, ErbB4). Our data suggest that the MZ stream defects primarily result from disordered cell-cell communication. Together our findings provide new insights into the mechanisms underlying cIN development and migration and how they are disrupted in several disorders.

neuroscience↗