Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 937 records · Page 52Linked to original sources

bioRxiv2024

Soft biocompatible polymer optical fiber tapers for implantable neural devices

Optical fibers are between the most common implantable devices for delivering light in the nervous system for optogenetics and infrared neural stimulation applications. Tapered optical fibers, in particular, can offer homogeneous light delivery to a large volume and spatially resolved illumination compared to standard flat-cleaved fibers while being minimally invasive. However, the use of tapers for neural applications has up to now been limited to silica optical fibers, whose large Youngs modulus can cause detrimental foreign body response in chronic settings. Here, we present the fabrication and optimization of tapered fiber implants based on polymer optical fibers (POFs). After numerically determining the optimal materials and taper geometry, we fabricated two types of POFs by thermal fiber drawing. The fabrication of the taper was achieved by chemical etching of the fibers, for which several solvents previously reported in literature have been tested. The influence of different parameters on the etching process and on the quality of the obtained tapers was also investigated. The large illumination volume of the produced high-quality taper-based implants was finally tested in vitro in a brain phantom.

neuroscience↗

bioRxiv2024

Genome Analyses of A Worldwide Multisource Collection of Klebsiella variicola Reveal Adaptation Relevant for Human Infection

AO_SCPLOWBSTRACTC_SCPLOWKlebsiella variicola (K.var), part of the Klebsiella pneumoniae (K.pne) species complex, is an emerging human pathogen originally associated with plants. Phylogenomic analyses of a global dataset of isolates categorised as human, animal, plant, or environmental strains suggest that K.var are broadly disseminated regardless of hosts or habitats and exhibit genomic variability that is relevant for occupying and transmitting within and across multiple sources. Ancestral state analyses confirm that K.var are originally derived from non-human sources. Genome-wide association analyses of human versus non-human isolates of K.var indicate isolates from human origins are linked to the loss of cold-shock response genes such as lpxP and cspB. Importantly, human K.var isolates also showed enriched antimicrobial resistance gene content and diversity acquired through mobile genetic elements, horizontal gene transfer and mutations within the chromosomal loci which underscore the impact of antimicrobial exposure and proximity to antibiotic resistant K.pne in nosocomial environments. Capsular profiles of K.var suggest high levels of variability in gene composition and indicate that gene functionality for wcaJ in capsule formation differs between K.var and K.pne. Although capsular specialisation was not observed in a host/habitat or lineage-dependent manner, human isolates harbour, on average, a higher siderophore gene content in addition to mrkD mutations which impact on fimbriae and biofilm formation. There is limited evidence of any specific K.var lineages exhibiting convergence of both virulence and antimicrobial resistance genotypes which suggest that these attributes are evolving independently in clinical strains. Our work highlights that gene attrition and acquisition provide a basis for adaptation of K.var as human pathogens. The broad distribution and evolution of K.var highlight the need for improved diagnostic precision and surveillance under a One Health framework.

microbiology↗

bioRxiv2024

Synaptic composition, activity, mRNA translation and dynamics in combined single-synapse profiling using multimodal imaging

Complex neuronal circuit functions emerge from local, actively regulated synaptic protein levels that interplay with synaptic neurotransmission across heterogenous synapse populations. Understanding the mechanisms by which chemical and disease-associated genetic perturbations impact neuronal circuit functions requires simultaneous measurement of these factors with single-synapse resolution at population scale. Here, we combine in situ multimodal imaging of local mRNA translation, synaptic multiprotein composition, and synapse activity measured via calcium or glutamate fluxes, within the same spatially resolved synapses. We apply this approach of multimodal synapse profiling to study ketamine plasticity. Results map a causal network of NR2A-depletion-induced changes to synaptic scaffolding and receptor proteins, driven by synaptic activity and local mRNA translation, which translates to Grin2a models of schizophrenia in vitro and in vivo. Thus, multimodal synaptomics can reveal mechanistic neurobiology that underlies chemical and genetic perturbations within the context of scalable neuronal cultures, which can serve as models for human disease and therapeutic development.

neuroscience↗

bioRxiv2024

CD90 identifies distinct fractions of muscle stem cells with different modalities of activation and quiescence maintenance

Stem cell transition from quiescence to activation is crucial to guarantee productive tissue regeneration. Here we show that CD90 diversifies quiescent muscle stem cells (MuSCs) in murine and human muscle into two subpopulations differing in the kinetics of activation, CD90+ve MuSCs exhibiting a faster exit quiescence and predominating the initial phases of regeneration compared to CD90-ve MuSCs. In the absence of injury, the CD90+ve fraction is primed toward activation through an active CD90-AMPK axis but is maintained in quiescence through signals from the extracellular matrix. Our studies show that Collagen VI, which is preferentially expressed by CD90+ve MuSCs, binds to the Calcitonin receptor and plays a role in this context. Moreover, while the number of CD90+ve and CD90-ve subpopulations is similar in healthy muscles, the CD90-ve fraction predominates in the muscles of murine models of Duchenne and Ullrich congenital muscular dystrophies. These findings provide novel insights into the mechanistic determinants of MuSCs functional heterogeneity and have implications for understanding the stimulation of repair in dystrophic muscle.

cell biology↗

bioRxiv2024

Dissociable Default Mode Network Connectivity Patterns Underlie Distinct Symptoms in Psychosis Risk

The Clinical High Risk (CHR) stage of psychosis is characterized by subthreshold symptoms of schizophrenia including negative symptoms, dysphoric mood, and functional deterioration. Hyperconnectivity of the default-mode network (DMN) has been observed in early schizophrenia, but the extent to which hyperconnectivity is present in CHR, and the extent to which such hyperconnectivity may underlie transdiagnostic symptoms, is not clear. As part of the Shanghai At-Risk for Psychosis (SHARP) program, resting-state fMRI data were collected from 251 young adults (158 CHR and 93 controls, M = 18.72, SD = 4.68, 129 male). We examined functional connectivity of the DMN by performing a whole-brain seed-to-voxel analysis with the MPFC as the seed. Symptom severity across a number of dimensions, including negative symptoms, positive symptoms, and affective symptoms were assessed. Compared to controls, CHRs exhibited significantly greater functional connectivity (p < 0.001 uncorrected) between the MPFC and 1) other DMN nodes including the posterior cingulate cortex (PCC), and 2) auditory cortices (superior and middle temporal gyri, STG/MTG). Furthermore, these two patterns of hyperconnectivity were differentially associated with distinct symptom clusters. Within CHR, MPFC-PCC connectivity was significantly correlated with anxiety (r= 0.23, p=0.006), while MPFC-STG/MTG connectivity was significantly correlated with negative symptom severity (r=0.26, p=0.001). Secondary analyses using item-level symptom scores confirmed a similar dissociation. These results demonstrate that two dissociable patterns of DMN hyperconnectivity found in the CHR stage may underlie distinct dimensions of symptomatology.

neuroscience↗

bioRxiv2024

Single-Cell Resolution DESI Mass Spectrometry Imaging through 10-Fold Sample Expansion

Desorption electrospray ionization mass spectrometry imaging (DESI MSI) is a valuable tool for label-free, spatially resolved molecular analysis of biological tissues. However, its spatial resolution has been limited to tens of micrometers due to constraints in spray geometry and solvent flow, hindering single-cell imaging. Inspired by expansion microscopy, we developed a tenfold DESI expansion MSI (10x-DESI ExMSI) technique to achieve cellular-level resolution. In this study, tissue sections were embedded in a swellable polyelectrolyte gel, and physically enlarged by approximately tenfold without compromising molecular integrity. After drying of the sample, mass spectrometry imaging was performed using a custom-built DESI ion source coupled with an Orbitrap mass spectrometer. Using mouse brain tissues as representative samples, 10x-DESI ExMSI achieved a spatial resolution of approximately 5 {micro}m, comparable to the highest levels attained by advanced commercial MALDI-MSI systems. Enhanced resolution allowed clear visualization of fine structural details, such as the granule cell layer of the dentate gyrus and the pyramidal layer of the Cornu Ammonis, which were unresolved in unexpanded samples under a 100 m step size. Lipid profiling demonstrated high retention and detection efficiency, confirming the techniques suitability for comprehensive molecular imaging. The 10x-DESI ExMSI significantly advances DESI MSI by enabling single-cell level resolution without modifying existing mass spectrometers. The method is simple, cost-effective, and easily implementable in most laboratories, making high-resolution DESI MSI accessible for a wide range of biological applications. This approach overcomes longstanding limitations of DESI imaging and holds great potential for detailed molecular studies at the cellular level.

biochemistry↗

bioRxiv2024

Ten-Fold Expansion MALDI Mass Spectrometry Imaging of Tissues and Cells at 500 nm Resolution

Achieving high spatial resolution in matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is crucial for detailed molecular mapping in biological tissues and cells. However, conventional MALDI-MSI platforms are typically limited to spatial resolutions of 5-20 m, restricting their ability to visualize fine subcellular structures. Here, we present a novel ten-fold expansion MALDI-MSI (10X ExMSI) method that attains 500 nm spatial resolution without the need for specialized optics or customized instrumentation. By physically expanding biological samples using a swellable hydrogel matrix, our method maintains high retention and broadens the detection range of lipids, ensuring comprehensive lipid profiling. We demonstrated the effectiveness of 10X ExMSI by visualizing intricate subcellular structures within mouse brain tissues, including individual nuclei, astrocytes, Purkinje cells, and, notably, dendritic arborizations-features previously unresolvable using mass spectrometry imaging. Applying 10X ExMSI to single-cell analysis of cultured cells revealed detailed spatial distributions of lipids at the subcellular to organelle level. Notably, the method is fully compatible with standard commercial MALDI-MSI platforms, enabling widespread adoption without significant additional investment. The 10X ExMSI offers a transformative tool for high-resolution molecular imaging, opening new avenues for molecular analysis in diverse biological and biomedical fields, including neuroscience, pathology, and cellular biology.

biochemistry↗

bioRxiv2024

Parkinsonism disrupts neuronal modulation in the pre-supplementary motor area during movement preparation

Multiple studies suggest that Parkinsons disease (PD) is associated with changes in neuronal activity throughout the basal ganglia-thalamocortical motor circuit. There are limited electrophysiological data, however, describing how parkinsonism impacts neuronal activity in the pre-supplementary motor area (pre-SMA), an area in medial frontal cortex involved in movement planning and motor control. In this study, single unit activity was recorded in the pre-SMA of two non-human primates during a visually cued reaching task in both the naive and parkinsonian state using the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of parkinsonism. In the naive state neuronal discharge rates were dynamically modulated prior to the presentation of the instructional go-cue. In a subset of these modulated cells, the magnitude of modulation correlated linearly with reaction time (RT). In the parkinsonian state, however, modulation of discharge rates in the pre-SMA was disrupted and the predictive encoding of RT was significantly diminished. These findings add to our understanding of the role of pre-SMA in motor behavior and suggest that disrupted encoding in this cortical area contributes to the alteration of early preparatory and pre-movement processes that are present in Parkinsons disease. SIGNIFICANCE STATEMENTGoal-directed movements, such as reaching for an object, necessitate temporal preparation and organization of information processing within the basal ganglia-thalamocortical motor network. Impaired movement in people with Parkinsons disease is thought to be the result of pathophysiological activity disrupting information flow within this network. This work provides neurophysiological evidence linking altered motor preplanning processes encoded in pre-supplementary motor area (pre-SMA) neuronal firing to the pathogenesis of motor disturbances in parkinsonism.

neuroscience↗

bioRxiv2024

AnimalMotionViz: an interactive software tool for tracking and visualizing animal motion patterns using computer vision

Monitoring the movement patterns of dairy cattle can provide important insight into space utilization or space occupancy in a barn. Although several precision livestock technologies have been developed to record dairy cattle movements, there is a lack of open source tools to track and visualize cattle movement patterns. Therefore, we developed an open-source computer vision software tool, AnimalMotionViz, that allows users to track and visualize dairy cattle movement patterns using a motion heatmap. The software comes with an easy-to-use web-based graphical user interface built with the Python Dash package. It implements a set of background subtraction algorithms in the OpenCV package to track animal motion patterns in real time. The software processes each frame of the input video and identifies the background and foreground using these algorithms. Foreground objects are then subtracted from the background across all frames and cumulatively overlaid on an empty mask image created with the first frame of the input video to visualize the intensity or frequency of motion across different regions. The user can generate motion heatmaps in an image and video, and also track specific regional motion with a custom mask. The software also returns the top three peak intensity locations, the total percentage of regions used, and the within-quadrant percentage of regions used. In four 5 min sample videos, quadrants with peak intensity of space use, as identified using the software, aligned with quadrants where calves spent the greatest duration of time, according to continuous recording of behavior from video. The motion heatmaps generated by AnimalMotionViz can be used to understand space utilization or space occupation by animals, as well as to assess how space allocation affects dairy cow movement. We conclude that the newly developed AnimalMotionViz is a user-friendly and efficient tool to support research developments in precision livestock farming towards enhancing cattle management practices and improving pen designs.

animal behavior and cognition↗

bioRxiv2024

Impairment of Neuronal Activity in the Dorsolateral Prefrontal Cortex Occurs Early in Parkinsonism

BackgroundParkinsons disease (PD) is often characterized by altered rates and patterns of neuronal activity in the sensorimotor regions of the basal ganglia thalamocortical network. Little is known, however, regarding how neuronal activity in the executive control network of the brain changes in the parkinsonian condition. ObjectiveInvestigate the impact of parkinsonism on neuronal activity in the dorsolateral prefrontal cortex (DLPFC), a key region in executive control, during a go/nogo reaching task. MethodsUsing a within-subject design, single and multi-unit neuronal activity was recorded in the DLPFC of a nonhuman primate before and after the induction of mild parkinsonism using the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). ResultsCoincident with development of mild parkinsonian motor signs, there was a marked reduction in the percentage of DLPFC cells with significant task-related firing rate modulation during go and nogo conditions. ConclusionsThese results suggest that DLPFC dysfunction may occur early in parkinsonism and contribute to cognitive impairments and disrupted executive function often observed in PD patients.

neuroscience↗

bioRxiv2024

Superimposed inhibitory surrounds underlying Saliency-based Stimulus Selection in avian Midbrain isthmi pars magnocellularis

In the avian midbrain network, bottom-up spatial attention is directed by saliency-based stimulus selection. However, it remains unclear whether the isthmi pars magnocellularis (Imc), the first site in the midbrain network to represent stimulus selection, can represent stimulus salience and what is the mechanism by which the midbrain network computes salience. Here, we used two separate translational motion stimuli as the main stimulation protocols and conducted in vivo electrophysiological experiments in the pigeons Imc. By combining bio-plausible model validation, we found two types of inhibitory surrounds of the Imc neuron receptive field, homogenous inhibitory surrounds (HIS) and non-homogenous inhibitory surrounds (non-HIS), and elucidated the mechanism by which both arise. While HIS is local and depends on stimulus feature similarity, which can be used to compute stimulus saliency, non-HIS is global and doesnt depend on stimulus feature similarity, which can be used to compute stimulus selection. Moreover, the superimposition of HIS and non-HIS modulates the neural response of Imc. The two inhibitory surrounds of Imc identified in this study more clearly elucidate the full process of achieving bottom-up stimulus selection based on saliency in the midbrain network and show that Imc is a nucleus that can represent both stimulus saliency and stimulus selection.

neuroscience↗

bioRxiv2024

Citalopram exhibits immune-dependent anti-tumor effects by modulating C5aR1+ TAMs and CD8+ T cells

Administration of selective serotonin reuptake inhibitors (SSRIs) is associated with a reduced cancer risk and shows significant anti-tumor effects across multiple tumor types, suggesting the potential for repurposing SSRIs in cancer therapy. Nonetheless, the specific molecular target and mechanism of action of SSRIs remain to be fully elucidated. Here, we reveal that citalopram exerts an immune-dependent anti-tumor effects in hepatocellular carcinoma (HCC). Interestingly, the anti-HCC effects of citalopram are not reliant on its conventional target, the serotonin transporter. Through various drug repurposing approaches, including global reverse gene expression profiling, drug affinity responsive target stability assay, and molecular docking, the complement component 5a receptor 1 (C5aR1) is identified as a new target of citalopram. C5aR1 is predominantly expressed by tumor-associated macrophages (TAMs), and citalopram treatment enhances local macrophage phagocytosis and elicits CD8+ T anti-tumor immunity. C5aR1 deficiency or depletion of CD8+ T cells hinders the anti-HCC effects of citalopram. Collectively, our study reveals the immunomodulatory roles of citalopram in inducing anti-tumor immunity, and provides a basis for considering the repurposing of SSRIs as promising anticancer agents for HCC treatment.

cancer biology↗

bioRxiv2024

Integrated temporal profiling of iPSCs-derived motor neurons from ALS patients carrying C9orf72, FUS, TARDBP, and SOD1 mutations

Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease that damages motor neurons in the central nervous system, causing progressive muscle weakness that ultimately leads to death. However, its underlying mechanisms still need to be fully understood, particularly the heterogeneity and similarity between various gene mutants during disease progression. In this study, we conducted temporal RNA-seq profiling in human induced pluripotent stem cells (hiPSCs) and iPSC-derived motor neurons (iMNs) carrying the C9orf72, FUS, TARDBP, and SOD1 mutations from both ALS patients and healthy individuals. We discovered dysregulated gene expression and alternative splicing (AS) throughout iMN development and maturation, and ALS iMNs display enrichment of cytoskeletal defects and synaptic alterations from premature stage to mature iMNs. Our findings indicate that synaptic gene dysfunction is the common molecular hallmark of fALS, which might result in neuronal susceptibility and progressive motor neuron degeneration. Analysis of upstream splicing factors revealed that differentially expressed RNA-binding proteins (RBPs) in ALS iMNs may cause abnormal AS events, suggesting the importance of studying RBP defects in ALS research. Overall, our research provides a comprehensive and valuable resource for gaining insights into the shared mechanisms of ALS pathogenesis during motor neuron development and maturation in iMN models.

neuroscience↗

bioRxiv2024

ECM-free patient-derived organoids preserve diverse prostate cancer lineages and uncover in vitro-enriched cell types

Patient-derived organoids (PDOs) offer new opportunities to model various cancers. However, their application in prostate cancer (PCa) has been hampered by poor success rates and overgrowth of cell types which are not representative of the patient samples. By exploiting a cohort of 164 PCa patient samples and tuning several culture parameters, we show that an extracellular matrix-free (ECM)-free culture system increases the take-rate of PDOs with luminal-like and PCa features. Single-cell RNA sequencing (scRNA-seq) reveals that ECM-free PDOs comprise cell populations associated with known PCa signatures and exhibit transcriptomic resemblance with their respective parental tumors. In addition, we define organoid-associated cell type signatures and identify markers discriminating tumors versus benign cells ex vivo and in situ. Furthermore, we generate the first prostate PDO single-cell atlas integrating previously-published scRNA-seq datasets and our newly- generated data. We show that Matrigel-based organoid cultures derived from primary PCa are essentially composed of benign-like epithelial cells, irrespective of the dataset or the malignant nature of the tissue of origin. In contrast, ECM-free conditions maintain heterogenous patient-specific luminal tumor cell populations and enrich in intermediate cell types. Ultimately, our work will significantly enhance the potential of PDOs in basic and translational PCa research.

cancer biology↗

bioRxiv2024

Astrocytic Ryk signaling coordinates scarring and wound healing after spinal cord injury

Wound healing after spinal cord injury involves highly coordinated interactions among multiple cell types, which is poorly understood. Astrocytes play a central role in creating a border against the non-neural lesion core. To do so, astrocytes undergo dramatic morphological changes by first thickening the processes and then elongating and overlap them. We show here show that the expression of a cell-surface receptor, Ryk, is induced in astrocytes after injury in both rodent and human spinal cord. Astrocyte-specific knockout of Ryk dramatically elongated the reactive astrocytes and accelerated the formation of the border and reduced the size of the scar. Astrocyte-specific knockout of Ryk also accelerated the injury responses of multiple cell types, including the resolution of neuroinflammation. Single cell transcriptomics analyses revealed a broad range of changes cell signaling among astrocytes, microglia, fibroblasts, endothelial cell, etc, after astrocyte-specific Ryk knockout, suggesting that Ryk not only regulates the injury response of astrocytes but may also regulate signals which coordinate the responses of multiple cell types. The elongation is mediated by NrCAM, a cell adhesion molecule induced by astrocyte-specific conditional knockout of Ryk after spinal cord injury. Our findings suggest a promising therapeutic target to accelerate wound healing and promote neuronal survival and enhance functional recovery.

neuroscience↗

bioRxiv2024

Simple models of non-random mating and environmental transmission bias standard human genetics statistical methods

There is recognition among human complex-trait geneticists that not only are many common assumptions made for the sake of statistical tractability (e.g., random mating, independence of parent/offspring environments) unlikely to apply in many contexts, but that methods reliant on such assumptions can yield misleading results, even in large samples. Investigations of the consequences of violating these assumptions so far have focused on individual perturbations operating in isolation. Here, we analyze widely used estimators of genetic architectural parameters, including LD-score regression and both population-based and within-family GWAS, across a broad array of perturbations to classical assumptions, such as multivariate assortative mating and vertical transmission (parental effects on offspring phenotypes not mediated by genetic inheritance). We find that widely-used statistical approaches are unreliable across a broad range of perturbations, and that structural sources of confounding often operate synergistically to distort conclusions. For example, mild multivariate assortative mating and vertical transmission together can dramatically inflate heritability estimates and GWAS false positive rates. Further, GWAS will become progressively more polluted by off-target associations as sample sizes increase. Given these challenges, we introduce xftsim, a forward time simulation library capable of modeling a wide range of genetic architectures, mating regimes, and transmission dynamics, to facilitate the systematic comparison of existing approaches and the development of robust methods. Together, our findings illustrate the importance of comprehensive sensitivity analysis and present a valuable tool for future research.

genetics↗

bioRxiv2024

Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges

Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated Molecular Dynamics (GaMD) simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity-relationship (SAR) studies and transverse relaxation measurements by NMR spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Strikingly, small structure perturbations on these key contributors, such as the addition of a methyl group that disrupts the planarity of the ligand resulted in > 100-fold reduction in the binding affinity. Our work deepened the understanding of RNA-small molecule interactions and integrated a new generalizable platform for the rational design of selective small-molecule RNA binders.

biochemistry↗

bioRxiv2024

DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing

Nanopore direct RNA sequencing (DRS) advances RNA biology but is limited by relatively low basecalling accuracy, low throughput, yet high RNA input and costs. Here we introduce a novel DRS toolkit, DEMINERS, which integrates an RNA multiplexing experimental workflow, a machine-learning barcode classifier based on Random Forest and a novel basecaller built on an optimized convolutional neural network providing an additional species-specific training module. With the increased accuracy in barcode classification and basecalling, DEMINERS can demultiplex up to 24 samples and the required RNA input and running time are both substantially reduced. We demonstrated the applications of DEMINERS in clinical metagenomics, cancer transcriptomics and parallel comparison of transcriptomic features in different biological conditions, revealing altered airway microbial diversity in COVID-19 and a potential role of m6A in increasing transcriptomic diversity in glioma and the mature blood-stage of malaria parasites. Overall, DEMINERS is a simple, robust, high-throughput DRS method for accurately estimating transcript levels, poly(A) lengths, and mutation and RNA modification heterogeneity at single-read level, with minimal sequencing biases.

bioinformatics↗