Biology subjects

Wen, Q.

Publications and source records attributed to Wen, Q..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

The roles of DDR2 and substrate stiffness on cancer cell transcriptome and proliferation

The interactions between cancer cells and the ECM regulate carcinogenesis. The collagen receptor kinase DDR2 is dysregulated in certain cancer cells, but its precise role in these malignancies remains unclear. In this study, we perform RNA-seq to determine how DDR2 and the biomechanical environment regulate cancer cell behaviors. We show that DDR2 knockdown in SH-SY5Y neuroblastoma cells inhibits proliferation and promotes senescence by regulating relevant genes. Increasing substrate stiffness reduces proliferation and promotes cell spreading but does not change senescence or transcriptome. Furthermore, DDR2 knockdown modulates cellular responses to substrate stiffness changes, unraveling a crosstalk between DDR2 and mechanosensing. These findings indicate DDR2 and ECM biomechanics regulate cancer cell behavior through distinct mechanisms, providing new mechanistic insights of cancer progression.

biochemistry↗

bioRxiv2023

All-optical interrogation of brain-wide activity in freely swimming larval zebrafish

We introduce an all-optical technique that enables volumetric imaging of brain-wide calcium activity and targeted optogenetic stimulation of specific brain regions in freely swimming larval zebrafish. The system consists of three main components: a 3D tracking module, a dual color fluorescence imaging module, and a real-time activity manipulation module. Our approach uses a sensitive genetically encoded calcium indicator in combination with a long Stokes shift red fluorescence protein as a reference channel, allowing the extraction of Ca2+ activity from signals contaminated by motion artifacts. The method also incorporates rapid 3D image reconstruction and registration, facilitating real-time selective optogenetic stimulation of different regions of the brain. By demonstrating that selective light activation of the midbrain regions in larval zebrafish could reliably trigger biased turning behavior and changes of brain-wide neural activity, we present a valuable tool for investigating the causal relationship between distributed neural circuit dynamics and naturalistic behavior. HighlightsO_LIWe develop an all-optical technique that enables simultaneous whole brain imaging and optogenetic manipulation of selective brain regions in freely behaving larval zebrafish. C_LIO_LIA combination of a genetically encoded calcium indicator and a long Stokes-shift red fluorescence protein, together with the adaptive filter algorithm, enables us to reliably distinguish calcium activity from motion-induced signal contamination. C_LIO_LIRapid 3D image reconstruction and registration enables real-time targeted optogenetic stimulation of distinct brain regions in a freely swimming larval zebrafish. C_LI

neuroscience↗

bioRxiv2023

Hierarchical behavior control by a single class of interneurons

Animal behavior is organized into nested temporal patterns that span multiple timescales. This behavior hierarchy is believed to arise from a hierarchical neural architecture: neurons near the top of the hierarchy are involved in planning, selecting, initiating, and maintaining motor programs, whereas those near the bottom of the hierarchy act in concert to produce fine spatiotemporal motor activity. In Caenorhabditis elegans, behavior on a long timescale emerges from ordered and flexible transitions between different behavioral states, such as forward, reversal, and turn. On a short timescale, different parts of the animal body coordinate fast rhythmic bending sequences to produce directional movements. Here, we show that SAA, a class of interneurons that enable cross-communication between dorsal and ventral head motor neurons, play a dual role in shaping behavioral dynamics on different timescales. On a short timescale, SAA regulate and stabilize rhythmic bending activity during forward movements. On a long timescale, the same neurons suppress spontaneous reversals and facilitate reversal termination by inhibiting RIM, an integrating neuron that helps maintain a behavioral state. These results suggest that feedback from a lower-level cell assembly to a higher-level command center is essential for bridging behavioral dynamics at different levels. Significance StatementIn this study, we reveal the dual role of SAA interneurons in C. elegans, demonstrating their influence over diverse behavior timescales. These neurons not only stabilize short-term rhythmic activities during forward movements, but also modulate long-term behavioral transitions between motor states. This indicates the essential role of feedback from low-level neural assemblies to command centers in a hierarchical neural architecture, emphasizing its significance in orchestrating behavior across scales. Our study offers critical insights into the intricate neural interactions behind organized and adaptive behavior.

neuroscience↗

bioRxiv2023

The scale-invariant covariance spectrum of brain-wide activity

Understanding neural activity organization is vital for deciphering brain function. By recording whole-brain calcium activity in larval zebrafish during hunting and spontaneous behaviors, we find that the shape of the neural activity space, described by the neural covariance spectrum, is scale-invariant: a smaller, randomly sampled cell assembly resembles the entire brain. This phenomenon can be explained by Euclidean Random Matrix theory, where neurons are reorganized from anatomical to functional positions based on their correlations. Three factors contribute to the observed scale invariance: slow neural correlation decay, higher functional space dimension, and neural activity heterogeneity. In addition to matching data from zebrafish and mice, our theory and analysis demonstrate how the geometry of neural activity space evolves with population sizes and sampling methods, thus revealing an organizing principle of brain-wide activity.

neuroscience↗

bioRxiv2023

Analysis of Biodeterioration on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing and Conventional Culturing Methods

AbstractWooden buildings are facing biodeterioration due to natural weathering. Ancestral halls are traditional Chinese wooden architecture with high artistic value. The research analyzed the microbial diversity of nine ancestral halls in Guangdong Province under subtropical monsoon climates. With amplicon sequencing, we found a common core microorganism group, including Bacillus, Pseudomonas, Paenibacillus, Acinetobacter, Toxicocladosporium, Cladosporium, Aspergillus, and Epicoccum. A total of 8 different species of bacteria and 7 different species of fungi were isolated from Chen Clan Ancestral halls, most of which were proven to be capable of degrading cellulose or lignin. The comparison between damaged and undamaged sites (whether the paint coating is flaked off) revealed similar microbial compositions but with differing abundances. Firmicutes and Ascomycota dominated damaged surfaces, while Proteobacteria and Actinobacteria prevailed in undamaged ones. Notably, Cladosporium, widely present in both sites, emerged as the primary cellulose-degrading genus. Given the similar microbial compositions between damaged and undamaged sites, it is suggested that using paint alone as the exclusive means to protect bare wood is insufficient. Apparent correlation between microorganisms on wooden surfaces and humans showed that the increase of visitor flow rates might impact the microbiota composition on cultural relics. We evaluated the effect of four representative biocides and determined the feasibility of low-concentration Isothiazolinone. This research facilitates a basic understanding of the microbial weathering of ancestral halls and add significant reference for preserving wooden structures.

microbiology↗

bioRxiv2022

Analysis of the mechanism of castor tolerance to Cd metal based on proteomics and metabolomics

The pollution of soil with heavy metals is an increasingly serious worldwide problem, and cadmium (Cd) has attracted attention because of its high toxicity to almost all plants. Since castor tolerates the accumulation of heavy metals, it has the potential for heavy metal soil remediation. We studied the mechanism of the tolerance of castor to Cd stress treatments at three doses: 300 mg/L, 700 mg/L, and 1,000 mg/L. Our research provides new ideas for revealing the defense and detoxification mechanisms of Cd-stressed castor. By combining the results of physiology, differential proteomics and comparative metabolomics, we conducted a comprehensive analysis of the networks that regulate the response of castor to Cd stress. The physiological results mainly emphasize the super-sensitive responses of castor plant roots to Cd stress and the effects of Cd stress on plants antioxidant system, ATP synthesis and ion homeostasis. We confirmed these results at the protein and metabolite levels. At the same time, proteomics and metabolomics show that castor plants mainly block the root systems absorption of Cd2+ by enhancing the strength of the cell wall, and inducing programmed cell death in response to the three different doses of Cd stress. In addition, the plasma membrane ATPase encoding gene (RcHA4), which was significantly upregulated in our differential proteomics and RT-qPCR studies, was transgenically overexpressed in wild type Arabidopsis thaliana for functional verification. The results indicated that this gene plays an important role in improving plant Cd tolerance.

molecular biology↗

bioRxiv2022

Multicellular Aligned Bands Disrupt Global Collective Cell Behavior

Mechanical stress patterns emerging from collective cell behavior have been shown to play critical roles in morphogenesis, tissue repair, and cancer metastasis. In our previous work utilizing microcontact printing to geometrically constrain valvular interstitial cell monolayers into specific shapes, we demonstrated that the general patterns of observed cell alignment, size, and apoptosis correlate with predicted mechanical stress fields if nonuniform cell properties are used in the computational models. However, these radially symmetric models did not predict the substantial heterogeneity in cell behavior observed in individual circular aggregates. The goal of this study is to determine how the heterogeneities in cell behavior emerge over time and diverge from the predicted collective cell behavior. Cell-cell interactions in circular multicellular aggregates of valvular interstitial cells were studied with time-lapse imaging ranging from hours to days, and migration, proliferation, and traction stresses were measured. Our results indicate that individual elongated cells create strong local alignment within pre-confluent cell populations on the microcontact printed protein islands. These cells influence the alignment of additional cells to create dense, locally aligned bands of cells which disrupt the global behavior. Cells are highly elongated at the endpoints of the bands yet have decreased spread area in the middle and reduced mobility. Although traction stresses at the endpoints of bands are enhanced, even to the point of detaching aggregates from the culture surface, the cells in dense bands exhibit reduced proliferation, less nuclear YAP, and increased apoptotic rates indicating a low stress environment. These findings suggest that strong local cell-cell interactions between primary fibroblastic cells can disrupt the global collective cellular behavior leading to substantial heterogeneity of cell behaviors in constrained monolayers. This local emergent behavior within aggregated fibroblasts may play an important role in development and disease of connective tissues.

bioengineering↗

bioRxiv2022

A descending interneuron with depolarized resting membrane potential controls C. elegans motor states

Continuity of behaviors requires animals to make smooth transitions between successive and mutually exclusive behavioral states. Neural principles that govern these transitions are not well understood. C. elegans spontaneously switch between two opposite motor states, forward and backward movement, a phenomenon long thought to reflect the reciprocal inhibition between two interneurons that separately gate the forward and backward motor circuits, AVB and AVA. Combining experimental data and mathematical modeling, we report that spontaneous forward and backward locomotion and their corresponding motor circuits are not separately controlled. AVA and AVB are neither functionally equivalent nor strictly reciprocally inhibitory. Instead, while AVA phasically inhibits the forward promoting interneuron AVB at a fast timescale, it maintains a tonic, extrasynaptic excitation on AVB over the longer timescale. AVAs depolarized spontaneous membrane potential is necessary for this tonic excitation. We propose a new, master neuron model for locomotion. AVA, with tonic and phasic activity of opposite polarities on different time scales, acts as a master neuron to break the symmetry between the underlying forward and backward motor circuits. This offers a parsimonious solution for sustained locomotion consisted of mutually exclusive motor states. TeaserA tonically active C. elegans premotor interneuron functions as the master neuron that underlies continuous modulation of forward and backward movement to ensure smooth transitions between the two opposing motor states.

neuroscience↗

bioRxiv2022

Development of visual cortex in human neonates are selectively modified by postnatal experience

Experience-dependent cortical plasticity is a pivotal process of human brain development and essential for the formation of most cognitive functions. Although studies found that early visual experience could influence the endogenous development of visual cortex in animals, little is known about such impact on human infants. Using the multi-modal MRI data from developing human connectome project, we revealed the early structural and functional maps in the ventral visual cortex and their development across the first month of age. Particularly, we found the postnatal experience could modulate both the cortical morphology in ventral visual cortex and the functional circuit between bilateral primary visual cortices. But the cortical myelination and overall functional circuits of ventral cortex, particularly that of the high-order visual cortex, developed without significant influence of postnatal experience in such early period. These experience-dependent cortical properties were further validated in the preterm-born infants who have longer postnatal time but immature cortical development at birth. The results confirmed that the development of cortical thickness was dominated by the postnatal experience but the functional circuit might be determined by the overall maturity of visual cortex. These data suggest in human newborns that early postnatal experience shapes the structural and functional development of the visual cortex in selective and organized pattern.

neuroscience↗

bioRxiv2022

Denoising diffusion weighted imaging data using convolutional neural networks

Diffusion weighted imaging (DWI) with multiple, high b-values is critical for extracting tissue microstructure measurements; however, high b-value DWI images contain high noise levels that can overwhelm the signal of interest and bias microstructural measurements. Here, we propose a simple denoising method that can be applied to any dataset, provided a low-noise, single-subject dataset is acquired using the same DWI sequence. The denoising method uses a one-dimensional convolutional neural network (1D-CNN) and deep learning to learn from a low-noise dataset, voxel-by-voxel. The trained model can then be applied to high-noise datasets from other subjects. We validated the 1D-CNN denoising method by first demonstrating that 1D-CNN denoising resulted in DWI images that were more similar to the noise-free ground truth than comparable denoising methods, e.g., MP-PCA, using simulated DWI data. Using the same DWI acquisition but reconstructed with two common reconstruction methods, i.e. SENSE1 and sum-of-square, to generate a pair of low-noise and high-noise datasets, we then demonstrated that 1D-CNN denoising of high-noise DWI data collected from human subjects showed promising results in three domains: DWI images, diffusion metrics, and tractography. In particular, the denoised images were very similar to a low-noise reference image of that subject, more than the similarity between repeated low-noise images (i.e. computational reproducibility). Finally, we demonstrated the use of the 1D-CNN method in two practical examples to reduce noise from parallel imaging and simultaneous multi-slice acquisition. We conclude that the 1D-CNN denoising method is a simple, effective denoising method for DWI images that overcomes some of the limitations of current state-of-the-art denoising methods, such as the need for a large number of subjects for training and accounting for the rectified noise floor.

neuroscience↗

bioRxiv2022

TrpA1 is a shear stress mechanosensing channel regulating intestinal homeostasis in Drosophila

Adult stem cells are essential for maintaining normal tissue homeostasis and supporting tissue repair. Although genetic and biochemical programs controlling adult stem cell behavior have been extensively investigated, how mechanosensing regulates stem cells and tissue homeostasis is not well understood. Here, we show that shear stress can activate enteroendocrine cells, but not other gut epithelial cell types, to regulate intestine stem cell-mediated gut homeostasis. This shear stress sensing is mediated by transient receptor potential A1 (TrpA1), a Ca2+-permeable ion channel that expressed only in enteroendocrine cells among all gut epithelial cells. Genetic depletion of TrpA1 or modification of its shear stress sensing function causes reduced intestine stem cell proliferation and intestine growth. We further show that among the TrpA1 splice variants, only select isoforms are activated by shear stress. Altogether, our results suggest the naturally occurring mechanical force such as fluid passing generated shear stress regulates intestinal stem cell-mediated tissue growth by activating enteroendocrine cells, and Drosophila TrpA1 as a new shear stress sensor.

developmental biology↗

bioRxiv2021

Extrasynaptic signaling enables an asymmetric juvenile motor circuit to produce a symmetric mature gait.

In many animals, there is a direct correspondence between the motor patterns that drive locomotion and the motor neuron innervation onto the muscle groups. For example, the adult C. elegans moves with symmetric and alternating dorsal-ventral bending waves arising from symmetric motor neuron input onto the dorsal and ventral muscles. In contrast to the adult, the C. elegans motor circuit at the juvenile larval stage has asymmetric wiring between motor neurons and muscles, but still generates adult-like bending waves with dorsal-ventral symmetry. We show that in the juvenile circuit, wiring between excitatory and inhibitory motor neurons coordinates the contraction of dorsal muscles with relaxation of ventral muscles, producing dorsal bends. However, ventral bending is not driven by analogous wiring. Instead, ventral muscles are excited uniformly by premotor interneurons through extrasynaptic signaling. Ventral bends occur in anti-phasic entrainment to activity of the same motor neurons that drive dorsal bends. During maturation, the juvenile motor circuit is replaced by two motor subcircuits that separately drive dorsal and ventral bending. Modeling reveals that the juveniles immature motor circuit is an adequate solution to generate adult-like dorsal-ventral bending before the animal matures. Developmental rewiring between functionally degenerate circuit solutions, that both generate symmetric bending patterns, minimizes behavioral disruption across maturation. HighlightsO_LIC. elegans larvae generate symmetric motor pattern with an asymmetrically wired motor circuit. C_LIO_LISynaptic wiring between excitatory and inhibitory motor neurons drives dorsal bending. C_LIO_LIExtrasynaptic excitation by premotor interneurons entrains ventral muscles for anti-phasic ventral bending. C_LIO_LIA developmental strategy to enable mature motor pattern before the circuit structurally matures. C_LI

neuroscience↗

bioRxiv2021

Defining proximity proteomics of post-translationally modified proteins by antibody-mediated protein A-APEX2 labeling

Proximity labeling catalyzed by promiscuous enzymes, such as APEX2, has emerged as a powerful approach to characterize multiprotein complexes and protein-protein interactions. However, current methods depend on the expression of exogenous fusion proteins and cannot be applied to post-translational modifications. To address this limitation, we developed a new method to label proximal proteins of interest by antibody-mediated protein A-APEX2 labeling (AMAPEX). In this method, a modified protein is bound in situ by a specific antibody, which then tethers a protein A-APEX2 (pA-APEX2) fusion protein. Activation of APEX2 labels the nearby proteins with biotin; these proteins are then purified using streptavidin beads and are identified by mass spectrometry. We demonstrate the utility of this approach by profiling the binding proteins of histone modifications including H3K27me3, H3K9me3, H3K4me3, H4K5ac and H4K12ac, and we verified the genome-wide colocalization of these identified proteins with bait proteins by published ChIP-seq analysis. Overall, AMAPEX is an efficient tool to identify proteins that interact with modified proteins.

molecular biology↗

bioRxiv2021

Regeneration of spinal motor axons: Negative regulation by Celsr2 implicating Cdc42/Rac1 and JNK/c-Jun signaling

During development, cadherins Celsr2 and Celsr3 control axon navigation. Unlike Celsr3, Celsr2 remains expressed in the adult, suggesting unexplored roles in maintenance and repair. Here we show that Celsr2 knockdown promotes motor axon regeneration in mouse and human spinal cord explants and cultured motor neurons. Celsr2 downregulation is accompanied by increased levels of GTP-bound Rac1 and Cdc42, and of JNK and c-Jun proteins. Using a branchial plexus injury model, we show that forelimb functional recovery is improved in Celsr2 mutant versus control mice. Compared to controls, in mutant mice, reinnervated biceps muscles are less atrophic, contain more newly formed neuromuscular junctions, and generate larger electromyographic potentials, while motor neuron survival and axon regeneration are improved. GTP-bound Rac1 and Cdc42, JNK and c-Jun are upregulated in injured mutant versus control spinal cord. In conclusion, Celsr2 negatively regulates motor axon regeneration via Cdc42/Rac1/JNK/c-Jun signaling and is a target for neural repair.

neuroscience↗

bioRxiv2020

Microbiota in milk from healthy and mastitis cows varies greatly in diversity, species richness and composition, as revealed by PacBio sequencing

Mastitis is the most economically important disease of dairy cows. This study used PacBio single-molecule real-time sequencing technology to sequence the full-length of the l6S rRNA from the microbiota in 27 milk samples (18 from mastitis and 9 from healthy cows; the cows were at different stages of lactation). We observed that healthy or late stage milk microbiota had significantly higher microbial diversity and richness. The community composition of the microbiota from different groups also varied greatly. In milk from healthy cows the microbiota was predominantly comprised of Lactococcus lactis, Acinetobacter johnsonii and Bacteroides dorei, while from mastitis cows it was predominantly comprised of Bacillus cereus, Clostridium cadaveris and Streptococcus suis. The prevalence of La. lactis and B. cereus in milk from healthy and mastitis cows was confirmed by digital droplets PCR. Differences in milk microbiota composition could suggest an important role for these microbes in protecting the host from mastitis. Based on the milk microbiota profiles, the Udder Health Index was constructed to predict the risk of bovine mastitis. Application of this predictive model could aid early identification and prevention of mastitis in dairy cows, though the model requires further optimisation using a larger dataset.

microbiology↗

bioRxiv2020

Autophagy-associated Production of Antimicrobial Peptides hBD1 and LL37 Exhibits Anti-Bacillus Calmette-Guerin Effects in Lung Epithelial Cells.

Antimicrobial peptides (AMPs) constitute important groups of bactericidal polypeptides against various microorganisms that exhibit their anti-bacteria activity through cleavage of precursor peptides into the active form of 50-100 amino acids in length. Various AMP cleavage mechanisms have been reported in different cell types; however, those in Mycobacterium tuberculosis (MTB)-infected lung epithelial cells remain unknown. In the present study, we found that MTB-infected lung epithelial cells expressed high level of the AMPs hBD1 and LL37 to kill intracellular MTB as the first-line immune barrier against MTB infection. Notably, their production in the lung epithelial cells was closely related to the function of autophagosomes and lysosomes. Experimental induction of autophagy in lung epithelial cells could enhance the expression of active hBD1 and LL37 at the post-transcriptional level, whereas silencing of these two active AMPs could decrease the bactericidal effect of autophagy. These findings indicated that cleavage of peptide precursors to form active AMPs might constitute a previously unrecognized antibacterial mechanism of autophagy. Author summaryLM and RW conceived and designed the experiments; RW performed the experiments and analyzed the data; QW analyzed the data and contributed reagents/materials/analysis tools; HL performed the experiments; XZ, JY, YL and ZH analyzed the data. LM and RW drafted the manuscript.

immunology↗

bioRxiv2020

Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA

1Protected areas are central to meeting biodiversity conservation goals, but measuring their effectiveness is challenging. We address this challenge by using DNA from leech-ingested bloodmeals to estimate vertebrate occupancies across the 677 km2 Ailaoshan reserve in Yunnan, China. 163 park rangers collected 30,468 leeches from 172 patrol areas. We identified 86 vertebrate species, including amphibians, mammals, birds, and squamates. Multi-species occupancy modelling showed that species richness increased with elevation and distance to reserve edge, including the distributions of most of the large mammals (e.g. sambar, black bear, serow, tufted deer). The exceptions were the three domestic mammal species (cows, sheep, goats) and muntjak deer, which were more common at lower elevations. eDNA-estimated vertebrate occupancies are Granular, Repeatable, Auditable, Direct, Efficient, and Simple-to-understand measures that can be used to assess conservation effectiveness and thus to improve the contributions that protected areas make to achieving global biodiversity goals.

ecology↗

bioRxiv2019

Genomic profiling of circulating tumor DNA reveals genetics and residual disease in NK/T lymphoma

BackgroundExtranodal NK/T-cell lymphoma, nasal type (ENTKL), is an aggressive hematological malignancy with poor prognosis. Early detection of tumors at initial diagnosis or during routine surveillance is important for improving survival outcomes. Molecular profiling of circulating tumor DNA (ctDNA) is a promising noninvasive tool for monitoring disease status. Here, we investigated the feasible of ctDNA detection in ENTKL. MethodsPlasma ctDNA was assessment were based on blood specimens that were collected from 65 patients recently diagnosed with ENKTL at the hematology medical center of Xinqiao Hospital, longitudinal samples collected under chemotherapy also included. Gene mutation spectrum of ENKTL was analyzed via cancer personalized profiling sequencing (CAPP-Seq). This study is registered with ClinicalTrials.gov (ChiCTR1800014813) ResultsFrom February 2017 to September 2019, 65 patients were enrolled, we found that the most frequently mutated genes were KMT2D (23.1%), APC (12.3%), ATM (10.8%), ASXL3 (9.2%), JAK3 (9.2%), SETD2 (9.2%), TP53 (9.2%), NOTCH1 (7.7%). The mutation frequencies of KMT2D was significantly higher in stage III-IV, and mutations in KMT2D, ASXL3 and JAK3 were significantly correlated with the metabolic tumor burden of the patients. Compared with tumor tissue DNA, ctDNA profiling showed good concordance. Serial ctDNA analysis showed that treatment with chemotherapy could decrease the number and mutation allele frequency of genes. Compared with PET/CT, ctDNA has more advantages for tracking residual disease in patients. In addition, we also found that mutated KMT2D predicted poor prognosis in patients. ConclusionCollectively, our results provide evidence that ctDNA may serve as a novel precision medicine biomarker in ENKTL.

genomics↗