Biology subjects

Du, X.

Publications and source records attributed to Du, X..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

StomaVision: stomatal trait analysis through deep learning

StomaVision is an automated tool designed for high-throughput detection and measurement of stomatal traits, such as stomatal number, pore size, and closure rate. It provides insights into plant responses to environmental cues, streamlining the analysis of micrographs from field-grown plants across various species, including monocots and dicots. Enhanced by a novel collection method that utilizes video recording, StomaVision increases the number of captured images for robust statistical analysis. Accessible via an intuitive web interface at and available for local use in a containerized environment at , this tool ensures long-term usability by minimizing the impact of software updates and maintaining functionality with minimal setup requirements. The application of StomaVision has provided significant physiological insights, such as variations in stomatal density, opening rates, and total pore area under heat stress. These traits correlate with critical physiological processes, including gas exchange, carbon assimilation, and water use efficiency, demonstrating the tools utility in advancing our understanding of plant physiology. The ability of StomaVision to identify differences in responses to varying durations of heat treatment highlights its value in plant science research. Plain language summaryStomaVision is a tool that automatically counts and measures tiny openings on plant leaves, helping us learn how plants deal with their surroundings. It is easy to use and works well with various plant species. This tool helps scientists see how plants change under stress, making plant research easier and more accurate.

plant biology↗

bioRxiv2024

A method for recognizing motor imagery EEG signals based on high-quality lead selection

In the application of motor imagery brain-computer interface system, high-density leads bring redundant noise, which leads to time-consuming system operation and poor performance. A channel selection strategy based on brain function network is proposed. This method introduces Synchronization likelihood was used as a connection index to construct a motor imagery brain functional network, and the centrality analysis of the constructed network was used to select the combination of strong motor-related leads. Experiments were carried out on the EEG datasets dataset IVa of the 3rd International Brain-Computer Interface Competition and dataset I of the 4th International Brain-Computer Interface Competition, and 27 high-quality channels were selected from the 118 channels of dataset IVa, as well as 16 high-quality channels were selected from the 59 channels of dataset I. Finally, the CSP algorithm and support vector machine are used to extract features and classify. The experimental results show that the proposed channel selection strategy can greatly reduce the number of channels while obtaining higher recognition accuracy, which verifies the practicability and effectiveness of the proposed method.

bioengineering↗

bioRxiv2024

Matrimeres are systemic nanoscale mediators of tissue integrity and function

Tissue barriers must be rapidly restored after injury to promote regeneration. However, the mechanism behind this process is unclear, particularly in cases where the underlying extracellular matrix is still compromised. Here, we report the discovery of matrimeres as constitutive nanoscale mediators of tissue integrity and function. We define matrimeres as non-vesicular nanoparticles secreted by cells, distinguished by a primary composition comprising at least one matrix protein and DNA molecules serving as scaffolds. Mesenchymal stromal cells assemble matrimeres from fibronectin and DNA within acidic intracellular compartments. Drawing inspiration from this biological process, we have achieved the successful reconstitution of matrimeres without cells. This was accomplished by using purified matrix proteins, including fibronectin and vitronectin, and DNA molecules under optimal acidic pH conditions, guided by the heparin-binding domain and phosphate backbone, respectively. Plasma fibronectin matrimeres circulate in the blood at homeostasis but exhibit a 10-fold decrease during systemic inflammatory injury in vivo. Exogenous matrimeres rapidly restore vascular integrity by actively reannealing endothelial cells post-injury and remain persistent in the host tissue matrix. The scalable production of matrimeres holds promise as a biologically inspired platform for regenerative nanomedicine.

bioengineering↗

bioRxiv2024

Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm

The BonnMu resource is a transposon-tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator (Mu) line with dent (B73, Co125) and flint (DK105, EP1 and F7) germplasm, resulting in the generation of 8,064 mutagenized BonnMu F2-families. Sequencing of these Mu-tagged families revealed 425,924 heritable Mu insertions affecting 36,612 (83%) of the 44,303 high-confidence gene models of maize (B73v5). On average, we observed 12 Mu insertions per gene (425,924 total insertions/ 36,612 affected genes) and 53 insertions per BonnMu F2-family (425,924 total insertions/ 8,064 families). Mu insertions and photos of seedling phenotypes from segregating BonnMu F2-families can be accessed through the Maize Genetics and Genomics Database (MaizeGDB). Downstream examination via the automated Mutant-seq Workflow Utility (MuWU) identified 94% of the germinal insertion sites in genic regions and only a small fraction of 6% inserting in non-coding intergenic sequences of the genome. Consistently, Mu insertions aligned with gene-dense chromosomal arms. In total, 42% of all BonnMu insertions were located in the 5 untranslated region (UTR) of genes, corresponding to accessible chromatin. Furthermore, for 38% of the insertions (163,843 of 425,924 total insertions) Mu1, Mu8 and MuDR were confirmed to be the causal Mu elements. Our publicly accessible European BonnMu resource has archived insertions covering two major germplasm groups, thus facilitating both forward and reverse genetics studies.

genomics↗

bioRxiv2024

Insights into Human Epileptogenesis with Proteomic Profiling

Epilepsy affects millions globally, and drug-resistant epilepsy remains a challenge. Molecular mechanisms underlying epilepsy remain elusive. Protein profiling through proteomics offers insight into biomarkers and therapeutic targets. Human brain tissue from epilepsy surgeries was analyzed using data-independent acquisition (DIA) proteomics. Samples were categorized into Core (epileptogenic focus), Border (marginal excision tissue), and Nonepileptic control groups. Differential expression proteins (DEPs) were identified and shared proteins were analyzed. 163 DEPs were identified which may has potential roles in the initiation of epileptic electrical firing, 412 DEPs which indicating the difference between epilepsy and Nonepilepsy patients and 10 DEPs consistently altered in Core which indicating potential roles in epileptogenesis. Notably, P35754/GLRX, O75335/PPFIA4, and Q96KP4/CNDP2 were consistently expressed differently in all group pairs. From validation experiments, the expression of Kv3.2 significant reduced in the Core group compare to border group by immunohistochemistry and knockdown of Kv3.2 increased seizure susceptibility and altered neuronal excitability through our cellular and animal experimentation.

neuroscience↗

bioRxiv2023

Species-specific design of artificial promoters by transfer-learning based generative deep-learning model

Native prokaryotic promoters share common sequence patterns, but are species dependent. For understudied species with limited data, it is challenging to predict the strength of existing promoters and generate novel promoters. Here, we developed PromoGen, a collection of nucleotide language models to generate species-specific functional promoters, across dozens of species in a data and parameter efficient way. Twenty-seven species-specific models in this collection were finetuned from the pretrained model which was trained on multi-species promoters. When systematically compared with native promoters, the Escherichia coli- and Bacillus subtilis-specific artificial PromoGen-generated promoters (PGPs) were demonstrated to hold all distribution patterns of native promoters. A regression model was developed to score generated either by PromoGen or by another competitive neural network, and the overall score of PGPs is higher. Encouraged by in silico analysis, we further experimentally characterized twenty-two B. subtilis PGPs, results showed that four of tested PGPs reached the strong promoter level while all were active. Furthermore, we developed a user-friendly website to generate species-specific promoters for 27 different species by PromoGen. This work presented an efficient deep-learning strategy for de novo species-specific promoter generation even with limited datasets, providing valuable promoter toolboxes especially for the metabolic engineering of understudied microorganisms.

synthetic biology↗

bioRxiv2023

Peripheral gating of pain by glial endozepine

We report that diazepam binding inhibitor (DBI) is a glial messenger mediating satellite glia-sensory neuron crosstalk in the dorsal root ganglion (DRG). DBI is highly and specifically expressed in satellite glia cells (SGCs) of mice, rat and human, but not in sensory neurons or other DRG-resident cells. Knockdown of DBI results in a robust mechanical hypersensitivity without significant effects on other sensory modalities. In vivo overexpression of DBI in SGCs reduces sensitivity to mechanical stimulation and alleviates mechanical allodynia in neuropathic and inflammatory pain models. We further show that DBI acts as a partial agonist and positive allosteric modulator at the neuronal GABAA receptors, particularly strongly effecting those with a high-affinity benzodiazepine binding site. Such receptors are selectively expressed by a subpopulation of mechanosensitive DRG neurons and these are also more enwrapped with DBI-expressing glia, as compared to other DRG neurons, suggesting a mechanism for specific effect of DBI on mechanosensation. These findings identified a new, peripheral neuron-glia communication mechanism modulating pain signalling, which can be targeted therapeutically.

neuroscience↗

bioRxiv2023

Super-Resolution Imaging of Fast Morphological Dynamics of Neurons in Behaving Animals

Neurons are best studied in their native working states in which their functional and morphological dynamics support animals natural behaviors. Super-resolution microscopy can potentially reveal these dynamics in much higher details but has been challenging in behaving animals due to severe motion artifacts. Here, we report multiplexed line-scanning structured illumination microscopy, which could tolerate motions of up to 50 m/s while achieving 150 and 100 nm lateral resolutions in its linear and nonlinear forms respectively over large fields-of-view. We continuously imaged the dynamics of spinules in dendritic spines and axonal boutons volumetrically over thousands of frames and tens of minutes in mouse brains during sleep-wake cycles. Super-resolution imaging of axonal boutons revealed their prevalent spinule dynamics on a scale of seconds. Simultaneous two-color imaging further enabled analyses of the correlation between the spatial distributions of diverse PSD-95 clusters and the structural dynamics of dendrites in the brains of awake mice.

neuroscience↗

bioRxiv2023

A small molecule inhibitor of PTP1B and PTPN2 enhances T cell anti-tumor immunity

The inhibition of protein tyrosine phosphatases 1B (PTP1B) and N2 (PTPN2) has emerged as an exciting approach for bolstering T cell anti-tumor immunity. ABBV-CLS-484 is a PTP1B/PTPN2 inhibitor in clinical trials for solid tumors. Here we have explored the therapeutic potential of a related small-molecule-inhibitor, Compound-182. We demonstrate that Compound-182 is a highly potent and selective active site competitive inhibitor of PTP1B and PTPN2 that enhances T cell recruitment and activation and represses the growth of tumors in mice, without promoting overt immune-related toxicities. The enhanced anti-tumor immunity in immunogenic tumors could be ascribed to the inhibition of PTP1B/PTPN2 in T cells, whereas in cold tumors, Compound-182 elicited direct effects on both tumor cells and T cells. Importantly, treatment with Compound-182 rendered otherwise resistant tumors sensitive to -PD1 therapy. Our findings establish the potential for small molecule inhibitors of PTP1B and PTPN2 to enhance anti-tumor immunity and combat cancer.

cancer biology↗

bioRxiv2023

NG2 Glia Reprogramming Induces Robust Axonal Regeneration After Spinal Cord Injury

Spinal cord injury (SCI) often leads to neuronal loss, axonal degeneration and behavioral dysfunction. We recently show that in vivo reprogramming of NG2 glia produces new neurons, reduces glial scaring, and ultimately leads to improved function after SCI. By examining endogenous neurons, we here unexpectedly uncover that NG2 glia reprogramming also induces robust axonal regeneration of the corticospinal tract and serotonergic neurons. Such reprogramming-induced axonal regeneration may contribute to the reconstruction of neural networks essential for behavioral recovery.

neuroscience↗

bioRxiv2023

Nunchaku: Optimally partitioning data into piece-wise linear segments

When analysing two-dimensional data sets, scientists are often interested in regions where one variable depends linearly on the other. Typically they use an ad hoc method to do so. Here we develop a statistically rigorous, Bayesian approach to infer the optimal partitioning of a data set into contiguous piece-wise linear segments. Our nunchaku algorithm is freely available. Focusing on microbial growth, we use nunchaku to identify the range of optical density where the density is linearly proportional to the number of cells and to automatically find the regions of exponential growth for both Escherichia coli and Saccharomyces cerevisiae. For budding yeast, we consequently are able to infer the Monod constant for growth on fructose. Our algorithm lends itself to automation and high throughput studies, increases reproducibility, and will facilitate data analysis for a broad range of scientists.

bioinformatics↗

bioRxiv2023

Deciphering molecular heterogeneity and dynamics of neural stem cells in human hippocampal development, aging, and injury

While accumulated publications support the existence of neurogenesis in the adult human hippocampus, the homeostasis and developmental potentials of neural stem cells (NSCs) under different contexts remain unclear. Based on our generated single-nucleus atlas of the human hippocampus across neonatal, adult, aging and injury, we dissected the molecular heterogeneity and transcriptional dynamics of human hippocampal NSCs under different contexts. We further identified new specific neurogenic lineage markers that overcome the lack of specificity found in some well-known markers. Based on developmental trajectory and molecular signatures, we found that a subset of NSCs exhibit quiescent properties after birth, and most NSCs become deep quiescence during aging. Furthermore, certain deep quiescent NSCs are re-activated following stroke injury. Together, our findings provide valuable insights into the development, aging, and re-activation of the human hippocampal NSCs, and help to explain why adult hippocampal neurogenesis is infrequently observed in humans.

neuroscience↗

bioRxiv2023

A parabrachial-hypothalamic parallel circuit governs cold defense in mice

Thermal homeostasis is vital for mammals and is controlled by brain neurocircuits. Remarkable advances have been made in understanding how neurocircuits centered in the hypothalamic preoptic area (POA), the brains thermoregulation center, control warm defense, whereas mechanisms by which the POA regulates cold defense remain unclear. Here, we confirmed that the pathway from the lateral parabrachial nucleus (LPB) to the POA, is critical for cold defense. Parallel to this pathway, we uncovered that a pathway from the LPB to the dorsomedial hypothalamus (DMH), namely the LPB[->]DMH pathway, is also essential for cold defense. Projection-specific blockings revealed that both pathways provide an equivalent and cumulative contribution to cold defense, forming a parallel circuit. Specifically, activation of the LPB[->]DMH pathway induced strong cold-defense responses, including increases in thermogenesis of brown adipose tissue (BAT), muscle shivering, heart rate, and physical activity. Further, we identified a subpopulation of somatostatin+ neurons in the LPB that target the DMH to promote BAT thermogenesis. Therefore, we reveal a parabrachial-hypothalamic parallel circuit in governing cold defense in mice. This not only enables resilience to hypothermia but also provides a scalable and robust network in heat production, reshaping our understanding of how neural circuits regulate essential homeostatic behaviors.

neuroscience↗

bioRxiv2023

Reprogramming of lipid secretome in senescent synovial fibroblasts ameliorate osteoarthritis development

Osteoarthritis (OA) is one of the most common causes of physical disability among older people and its incidence increases with age. Removal of the senescent cells (SNCs) delays OA pathologies, but little is known about the SNCs in OA synovium and their roles in OA pathogenesis. Here, we reported that RCAN1+IL1+ double-positive cells represent a senescent subset of synovial fibroblasts which accelerate cartilage degeneration via saturated fatty acids (SFAs). Using single-cell RNA sequencing and synovial organoids, we found that IL1+ senescent synovial fibroblasts mainly located at lining layer of human OA synovium and promote cartilage degeneration. We performed genome-wide CRISPR/Cas9 screens to identify novel regulators of cell-surface bounded IL1 in senescent cells. RCAN1, which was a hit as positive regulator of IL1, governs the cellular senescence and pro-degenerative senescence-associated secretory phenotype (SASP). Mechanistically, we found that RCAN1 mediated the secretion of SFAs from senescent synovial fibroblasts, which promote chondrocytes senescence and cartilage matrix degradation. Intra-articular delivery of synovium-targeted anti-Rcan1 siRNA ameliorates the development of post-traumatic OA in mice, while reducing of SNCs accumulation in synovium and increasing cartilage regeneration. Last, co-culture experiments of human OA cartilage explant with synovial organoids confirmed that RCAN1 silencing in human synovial fibroblasts suppressed chondrocyte senescence and cartilage degradation. Thus, our study revealed a pro-degenerative interaction between RCAN1+IL1+ senescent synovial fibroblasts and chondrocytes through secreted lipid mediators in OA progression. And targeted RCAN1 inhibition in senescent synovium is a promising approach for restore the joint homeostasis.

pathology↗

bioRxiv2023

The cation channel mechanisms of subthreshold inward depolarizing currents in the VTA dopaminergic neurons and their roles in the depression-like behavior

The slow-intrinsic-pacemaker dopaminergic (DA) neurons originating in the ventral tegmental area (VTA) are implicated in various mood- and emotion-related disorders, such as anxiety, fear, stress and depression. Abnormal activity of projection-specific VTA DA neurons is the key factor in the development of these disorders. Here, we describe the crucial role for the NALCN and TRPC6, non-selective cation channels in mediating the subthreshold inward depolarizing current and driving the firing of action potentials of VTA DA neurons in physiological condition. Furthermore, we demonstrate that down-regulation of TRPC6 protein expression in the VTA DA neurons likely contributes to the reduced activity of projection-specific VTA DA neuron in chronic mild unpredictable stress (CMUS) depressive mice. In consistent with these, selective knockdown of TRPC6 channels in the VTA DA neurons conferred mice with depression-like behavior. This current study suggests down-regulation of TRPC6 expression/function is involved in reduced VTA DA neuron firing and chronic stress-induced depression-like behavior of mice.

neuroscience↗

bioRxiv2023

3D-Printed LEGO(R)-inspired Titanium Scaffolds for Patient-Specific Regenerative Medicine

Despite the recent advances in 3D-printing, it is difficult to fabricate implants that optimally fit a defect size/shape. There are some approaches to resolve this issue, such as patient-specific implant based on CT images, however, it is labor-intensive and costly. Especially in developing countries, affordable treatments are required, while still not excluding these patient groups from manufacturing advances. Here, a SLM 3D-printing strategy was used to fabricate a hierarchical, Assemblable Titanium Scaffold(ATS), which can be manually assembled in any shape or size with ease. A surgeon can create a scaffold that would fit to the defect right before the implantation during the surgery. Additionally, the direct inclusion of micro- and macroporous structures via 3D-printing, as well as a double acid-etched surface treatment(ST) in the ATS, ensure improved nutrient flow and cellular activity. Different structures were designed, 3D-printed and then surface treated for the ST groups. Both individual and stacked ATS have sufficient mechanical properties to withstand physiological loading, and the porous groups resulted enhanced cell proliferation, mineralizaton and osteogenesis compared to non-porous group. Furthermore, successful cell attachment and migration between the assembled ATS were observed. Finally, we demonstrate possible medical applications that reveal the potential of the ATS through assembly.

bioengineering↗

bioRxiv2023

CTLA-4 antibody-drug conjugate reveals autologous destruction of B-lymphocytes associated with regulatory T cell impairment

Germline CTLA-4 deficiency causes severe autoimmune diseases characterized by dysregulation of Foxp3+ Tregs, hyper-activation of effector memory T cells, and variable forms autoimmune cytopenia including gradual loss of B cells. Cancer patients with severe immune-related adverse events (irAE) after receiving anti-CTLA-4/PD-1 combination immunotherapy also have markedly reduced peripheral B cells. The immunological basis for B cell loss remains unexplained. Here we probe the decline of B cells in human CTLA-4 knock-in mice by using anti-human CTLA-4 antibody Ipilimumab conjugated to a drug payload emtansine (Anti-CTLA-4 ADC). The anti-CTLA-4 ADC-treated mice have T cell hyper-proliferation and their differentiation into effector cells which results in B cell depletion. B cell depletion is mediated by both CD4 and CD8 T cells and at least partially rescued by anti-TNF-alpha antibody. These data revealed an unexpected antagonism between T and B cells and the importance of regulatory T cells in preserving B cells.

immunology↗

bioRxiv2023

The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study

Untargeted lipidomics allows analysis of a broader range of lipids than targeted methods and permits discovery of unknown compounds. Previous ring trials have evaluated the reproducibility of targeted lipidomics methods, but inter-laboratory comparison of compound identification and unknown feature detection in untargeted lipidomics has not been attempted. To address this gap, five laboratories analyzed a set of mammalian tissue and biofluid reference samples using both their own untargeted lipidomics procedures and a common chromatographic and data analysis method. While both methods yielded informative data, the common method improved chromatographic reproducibility and resulted in detection of more shared features between labs. Spectral search against the LipidBlast in silico library enabled identification of over 2,000 unique lipids. Further examination of LC-MS/MS and ion mobility data, aided by hybrid search and spectral networking analysis, revealed spectral and chromatographic patterns useful for classification of unknown features, a subset of which were highly reproducible between labs. Overall, our method offers enhanced compound identification performance compared to targeted lipidomics, demonstrates the potential of harmonized methods to improve inter-site reproducibility for quantitation and feature alignment, and can serve as a reference to aid future annotation of untargeted lipidomics data.

systems biology↗