Biology subjects

Zhang, R.

Publications and source records attributed to Zhang, R..

At least 199 records · Page 11Linked to original sources

bioRxiv2024

An Investigation into Mechanomyography for Signal Extraction and Classification of Human Lower Limb Activity

To mitigate the difficulties associated with the extraction of Mechanomyography (MMG) signals from raw Accelerometer (ACC) data and the subsequent classification of human lower limb activities based on MMG signals, the Feature Mode Decomposition (FMD) algorithm has been utilized for the isolation of the MMG signal. Simultaneously, surface Electromyography (sEMG) signals were recorded to perform correlation analyses, thereby validating the effectiveness of the extracted Mechanomyography (MMG) signals. The results demonstrate that the envelope entropy derived from the FMD was the lowest among the observed values, and the composite signal obtained via FMD displayed the highest correlation with the sEMG signal. This indicates that FMD is capable of efficiently isolating the MMG signal while maintaining the maximal quantity of muscle contraction data. To address the challenge of classifying human lower limb activities, a comprehensive feature extraction procedure was implemented, resulting in the derivation of 448 unique features from multi-channel mechanomyography (MMG) signals. Subsequently, Kernel Principal Component Analysis (KPCA) was employed to diminish the feature sets dimensionality. This was succeeded by the deployment of a Temporal Convolutional Network integrated with an Attention mechanism (TCN-Attention) to train the classification model. Additionally, an enhanced Northern Goshawk Optimization Algorithm was leveraged for optimization purposes. The findings indicate that FMD exhibited the minimum envelope entropy value of 8.13, concurrently attaining the maximum correlation coefficient of 0.87 between MMG and sEMG signals. Significantly, the SCNGO-TCN-Attention model demonstrated superior classification accuracy, attaining an exceptional accuracy rate of 98.44%.

bioengineering↗

bioRxiv2024

Dorsolateral prefrontal cortex drives strategic aborting by optimizing long-run policy extraction

Real world choices often involve balancing decisions that are optimized for the short-vs. long-term. Here, we reason that apparently sub-optimal single trial decisions in macaques may in fact reflect long-term, strategic planning. We demonstrate that macaques freely navigating in VR for sequentially presented targets will strategically abort offers, forgoing more immediate rewards on individual trials to maximize session-long returns. This behavior is highly specific to the individual, demonstrating that macaques reason about their own long-run performance. Reinforcement-learning (RL) models suggest this behavior is algorithmically supported by modular actor-critic networks with a policy module not only optimizing long-term value functions, but also informed of specific state-action values allowing for rapid policy optimization. The behavior of artificial networks suggests that changes in policy for a matched offer ought to be evident as soon as offers are made, even if the aborting behavior occurs much later. We confirm this prediction by demonstrating that single units and population dynamics in macaque dorsolateral prefrontal cortex (dlPFC), but not parietal area 7a or dorsomedial superior temporal area (MSTd), reflect the upcoming reward-maximizing aborting behavior upon offer presentation. These results cast dlPFC as a specialized policy module, and stand in contrast to recent work demonstrating the distributed and recurrent nature of belief-networks.

neuroscience↗

bioRxiv2024

scCompass: An integrated cross-species scRNA-seq database for AI-ready

Emerging single-cell sequencing technology has generated large amounts of data, allowing analysis of cellular dynamics and gene regulation at the single-cell resolution. Advances in artificial intelligence enhance life sciences research by delivering critical insights and optimizing data analysis processes. However, inconsistent data processing quality and standards remain to be a major challenge. Here we propose scCompass, which provides a data quality solution to build a large-scale, cross-species and model-friendly single-cell data collection. By applying standardized data pre-processing, scCompass integrates and curates transcriptomic data from 13 species and nearly 105 million single cells. Using this extensive dataset, we are able to archieve stable expression genes (SEGs) and organ-specific expression genes (OSGs) in human and mouse. We provide different scalable datasets that can be easily adapted for AI model training and the pretrained checkpoints with state-of-the-art (SOTA) single-cell foundataion models. In summary, the AI-readiness of scCompass, which combined with user-friendly data sharing, visualization and online analysis, greatly simplifies data access and exploitation for researchers in single cell biology(http://www.bdbe.cn/kun).

bioinformatics↗

bioRxiv2024

Butyrophilin 2A2 promotes T cell immunoregulation by enhancing CD45 phosphatase activity within the immune synapse

B7 costimulatory family member Butyrophilin 2A2 (BTN2A2) is predominantly expressed by antigen presenting cells and regulates T cell immunity, but molecular mechanisms are unclear. Using immunoblots analyzing TCR-initiated signaling intermediaries, co-immunoprecipitation studies, confocal microscopy, structural modeling-guided mutational analyses, and microscale thermophoresis, we demonstrate that BTN2A2 directly interacts with CD45RO, resulting in CD45 retention within the immune synapse during TCR activation. Recombinant BTN2A2 increased murine CD4+Foxp3+ regulatory T cells (Treg) and reduced T helper 17 (Th17) cells in vitro through mechanisms dependent on CD45 phosphatase activity. BTN2A2 treatment reduced clinical expression of two murine autoimmune disease models and increased Treg/Th17 ratios. Analyses of BTN2A2-deficient animals showed exacerbated disease associated with reduced Treg/Th17 ratios. Addition of BTN2A2 to human mixed lymphocyte responses similarly enhanced human Treg and suppressed Th17 cells and was CD45 phosphatase dependent. Together, our studies identify BTN2A2 as a physiological CD45RO ligand that enhances CD45 phosphatase activity in murine and human T cells, providing mechanisms for BTN2A2-mediated amelioration of autoimmunity. SummaryButyrophilin 2A2 ameliorates autoimmunity by binding to CD45RO on activated T cell surfaces leading to dampened TCR signaling which in turn leads to expansion of T regulatory cells and reduction of Th17 differentiation.

immunology↗

bioRxiv2024

Structural insights into SSNA1 self-assembly and its microtubule binding for centriole maintenance

SSNA-1 is a fibrillar protein localized at the area where dynamic microtubule remodeling occurs including centrosomes. Despite the important activities of SSNA1 to microtubules such as nucleation, co-polymerization, and lattice sharing microtubule branching, the underlying molecular mechanism have remained unclear due to a lack of structural information. Here, we determined the cryo-EM structure of C. elegans SSNA-1 at 4.55 [A] resolution and evaluated its role during embryonic development in C. elegans. We found that SSNA1 forms an anti-parallel coiled-coil, and its self-assembly is facilitated by the overhangs of 16 residues at its C-terminus, which dock on the adjacent coiled-coil to form a triple-stranded helical junction. Notably, the microtubule-binding region is within the triple-stranded junction, highlighting that self-assembly of SSNA-1 facilitates effective microtubule interaction by creating hubs along a fibril. Furthermore, our genetical analysis elucidated that deletion of SSNA-1 resulted in a significant reduction in embryonic viability and the formation of multipolar spindles during cell division. Interestingly, when the ability of SSNA-1 self-assembly was impaired, embryonic viability stayed low, comparable to that of the knockout strain. Our study provides molecular insights into the self-assembly mechanisms of SSNA-1, shedding light on its role in controlling microtubule binding and cell division through the regulation of centriole stability.

cell biology↗

bioRxiv2024

Distinct Binding Modes of Inter-Spike Cross-Linking Suggest a Supplementary Mechanism for SARS-CoV-2 Antibody Neutralization

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when bound fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, elucidate a potential molecular basis of Omicron immune escape, and expand our understanding on antibody evasion mechanisms.

immunology↗

bioRxiv2024

scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity by providing gene expression data at single-cell resolution, uncovering insights into rare cell populations, cell-cell interactions, and gene regulation. Foundation models pretrained on large-scale scRNA-seq datasets have shown great promise in analyzing such data, but existing approaches are often limited to modeling a small subset of highly expressed genes and lack the integration of external genespecific knowledge. To address these limitations, we present sc-Long, a billion-parameter foundation model pretrained on 48 million cells. sc-Long performs self-attention across the entire set of 28,000 genes in the human genome. This enables the model to capture long-range dependencies between all genes, including lowly expressed ones, which often play critical roles in cellular processes but are typically excluded by existing foundation models. Additionally, sc-Long integrates gene knowledge from the Gene Ontology using a graph convolutional network, enriching its contextual understanding of gene functions and relationships. In extensive evaluations, sc-Long surpasses both stateof-the-art scRNA-seq foundation models and task-specific models across diverse tasks, including predicting transcriptional responses to genetic and chemical perturbations, forecasting cancer drug responses, and inferring gene regulatory networks.

bioinformatics↗

bioRxiv2024

Corticonigral projections recruit substantia nigra pars lateralis dopaminergic neurons for auditory threat memories

Dopaminergic neurons (DANs) in the lateral substantia nigra project to the tail of striatum (TS), which is involved in threat conditioning. Auditory cortex also contributes to threatening behaviors, but whether it directly interacts with midbrain DANs and how these interactions might influence threat conditioning remain unclear. Here, functional mapping revealed robust excitatory input from auditory and temporal association cortexes to substantia nigra pars lateralis (SNL) DANs, but not to pars compacta (SNc) DANs. SNL DANs exhibited unique firing patterns, with irregular pacemaking and higher maximal firing, reflecting different channel complements than SNc DANs. Behaviorally, inhibiting cortex to SNL projections impaired memory retrieval during auditory threat conditioning. Thus, we demonstrate robust corticonigral projections to SNL DANs, contrasting with previous observations of sparse cortical input to substantia nigra DANs. These findings distinguish SNL DANs from other nigral populations, highlighting their role in threatening behaviors and expanding knowledge of cortex to midbrain interactions.

neuroscience↗

bioRxiv2024

Positive impact of Type-A and -C response regulator genes on growth and panicle architecture in rice

Cytokinin signal transduction occurs through a "two-component system." Type-A and -C response regulators (RRs) are groups of proteins of similar structures constituting significant components of cytokinin signal transduction. In rice, 13 (Type-A) and two (Type-C) RRs have been identified to date; however, their functions remain partially known. In this study, we examined the expression patterns of Type-A and Type-C RRs in rice using RNA-Seq and confirmed their functions by constructing mutants of the 15 genes with CRISPR/Cas9. Almost all Type-A RRs played positive roles in the development of secondary branches and secondary spikelets, particularly RR2 and RR4. Notably, rr1 rr2 and rr8 rr12 rr13 higher-order mutants displayed small panicle sizes and decreased plant height. Additionally, both Type-C RRs played positive roles in regulating heading date. RNA-seq revealed several genes with significantly altered expression in the rr2 and rr4 mutants, with almost half of the differentially expressed genes (DEGs) overlapping between the two mutants. Many of the DEGs were associated with the cytokinin and abscisic acid pathways. Our findings provide new insights into the functions of Type-A and -C RRs in rice growth and may serve as a foundation for future studies focusing on cytokinin signaling.

plant biology↗

bioRxiv2024

Multiplexed ultrasound imaging of gene expression

Acoustic reporter genes (ARGs) have enabled the imaging of gene expression with ultrasound, which provides high-resolution access to deep, optically opaque living tissues. However, unlike their fluorescent counterparts, ARGs have so far been limited to a single "color," preventing multiplexed imaging of cellular states or populations. Here, we use rational protein design and directed evolution to develop two novel ARGs that can be distinguished from each other based on their acoustic pressure response profiles, enabling "two-color" ultrasound imaging of gene expression. We demonstrate the utility of multiplexed ARGs for delineating bacterial cell species and cell states in vitro, and then apply them towards imaging distinct subpopulations of probiotics in the mouse gastrointestinal tract and in tumor-colonizing bacterial agents in vivo. Just as the first wavelength-shifted derivatives of fluorescent proteins opened a vivid world for optical microscopy, our next-generation acoustic proteins set the stage for a richer symphony of ultrasound signals from living subjects.

bioengineering↗

bioRxiv2024

Phase Separation to Resolve Growth-Related Circuit Failures

Fluctuations in host cell growth poses a significant challenge to synthetic gene circuits, often disrupting circuit function. Existing solutions typically rely on circuit redesign with alternative topologies or additional control elements, yet a broadly applicable approach remains elusive. Here, we introduce a new strategy based on liquid-liquid phase separation (LLPS) to stabilize circuit performance. By engineering a self-activating circuit with transcription factors (TF) fused to an intrinsically disordered region (IDR), we enable the formation of TF condensates at the promoter region, maintaining local TF concentration despite growth-mediated dilution. This condensate formation preserves bistable memory in the self-activating circuit, demonstrating that phase separation can robustly counteract growth fluctuations, offering a novel design principle for resilient synthetic circuits.

synthetic biology↗

bioRxiv2024

Revolutionizing large-scale DNA synthesis with microchip-based massive in parallel synthesis system

DNA synthesis serves as the fundamental enabling technology of engineering biology, aiming to provide DNA molecules of designed composition, length, and complexity at scale and low cost. Current high-throughput DNA synthesis technologies rely on intricate chip manufacturing and microfluidic systems to provide large-scale synthetic oligonucleotides, at the expense of low concentration and limited compatibility in the processing of longer DNA constructs assembly. Here, we report a microchip-based massive in parallel synthesis (mMPS), pioneering an "identification-sorting-synthesis-recycling" iteration mechanism to microchips for high throughput DNA synthesis. In comparison to microarray-based methods, we demonstrate that our method can increase the DNA product concentration by 4 magnitudes (to picomole-scale per sequence) and greatly simplifies the downstream processes for large-scale gene synthesis construction. By the construction of 1.97 million-diversity variant libraries that cover 1,254 human protein domains, we demonstrated the uniformity of the constructed variant libraries using mMPS-derived oligos is greatly improved, with amino acid distribution highly consistent as designed. In addition, by synthesizing 285 1kb-to-3kb genes with varying degrees of sequence complexity from previously reported strains A501 and 3DAC, potential ancestor of early archaea and bacteria, our result shows that the overall gene assembly success rate using mMPS-derived oligos is increased by 10-fold in comparison to other methods. Our mMPS technology holds the potential to close the gap between the quality and cost of writing DNA in increasing demand across many sectors of research and industrial activities.

synthetic biology↗

bioRxiv2024

Spatiotemporal coordination of actin regulators generates invasive protrusions in cell-cell fusion

Invasive membrane protrusions play a central role in a variety of cellular processes. Unlike filopodia, invasive protrusions are mechanically stiff and propelled by branched actin polymerization. However, how branched actin filaments are organized to create finger-like invasive protrusions is unclear. Here, by examining the mammalian fusogenic synapse, where invasive protrusions are generated to promote cell membrane juxtaposition and fusion, we have uncovered the mechanism underlying invasive protrusion formation. We show that two nucleation promoting factors (NPFs) for the Arp2/3 complex, WAVE and N-WASP, exhibit different localization patterns in the protrusions. While WAVE is closely associated with the plasma membrane at the leading edge of the protrusive structures, N-WASP is enriched with WIP along the actin bundles in the shafts of the protrusions. During protrusion initiation and growth, the Arp2/3 complex nucleates branched actin filaments to generate low density actin clouds, in which the large GTPase dynamin organizes the new branched actin filaments into bundles, followed by actin-bundle stabilization by WIP, the latter functioning as a novel actin-bundling protein. Disrupting any of these components results in defective protrusions and failed myoblast fusion in cultured cells and mouse embryos. Taken together, our study has revealed the intricate spatiotemporal coordination between two NPFs and two actin-bundling proteins in building invasive protrusions at the mammalian fusogenic synapse, and has general implications in understanding invasive protrusion formation in cellular processes beyond cell-cell fusion.

cell biology↗

bioRxiv2024

Birds migrate longitudinally in response to the resultant Asian monsoons of the Qinghai-Tibet Plateau uplift

The uplift of the Qinghai-Tibet Plateau is one of the greatest geological events on Earth, pivotally shaping biogeographic patterns across continents, especially for migratory species that need to overcome topographical barriers to fulfil their annual circle. However, how the uplift influences animal migration strategies remains largely unclear. We compare the current flyways of 50 avian species migrating across the plateau with those reconstructed before the uplift as a counterfactual. We find that the major effect of the plateau uplift is changing avian migratory directions from the latitudinal to the longitudinal. The monsoon system generated by the uplift rather than the high elevation per se shapes those changes. These findings unveil how an important global geological event has influenced biogeographic patterns of migratory birds, yielding testable hypotheses for how observed avian distributions emerge.

ecology↗

bioRxiv2024

Does Unfairness Evoke Anger or Disgust? A Quantitative Neurofunctional Dissection Based on 25 Years of Neuroimaging

Over the last decades, the traditional Homo economicus model has been increasingly challenged by convergent evidence underscoring the impact of emotions on decision-making. A classic example is the perception of unfairness operationalized in the Ultimatum Game where humans readily sacrifice personal gains to punish those who violate fairness norms. While the emotional mechanism underlying costly punishments has been widely acknowledged, the distinct contributions of moral emotions (anger or disgust) remain debated, partly due to methodological limitations of the conventional experiments. Here, we capitalize on a quantitative neurofunctional dissection approach by combining recent developments in neuroimaging meta-analyses, behavioral-level, network-level, and neurochemical-level decoding and data from 3,266 participants from functional neuroimaging studies to determine the common and distinct neural representations between unfairness and the two moral emotions. Experience of unfairness engaged a widespread bilateral network encompassing insular, cingulate, and frontal regions, with dorsal striatal regions mediating the decision to reject unfair offers. Disgust engaged a defensive-avoidance circuit encompassing amygdalar, occipital, and frontal regions, while anger engaged non-overlapping systems including mid-cingulate, thalamic, and frontal regions. Unfairness and anger or disgust respectively commonly engaged the anterior and mid-insula, while the latter additionally showed common recruitment of ventrolateral prefrontal and orbitofrontal cortices. Multimodal network, behavioral, and serotonergic decoding provided a more granular and convincing dissection of these results. Findings indicate a shared neuroaffective basis underlying the impact of emotions on unfairness-induced punishment behavior and suggest a common brain circuit has been evolutionarily shaped to protect individuals from personal harm and enforce societal norms.

neuroscience↗

bioRxiv2024

Cancer-associated adipocytes mediate CD8+T cell dysfunction via FGF21-driven lipolysis

Cancer-associated adipocytes (CAAs) reprogram metabolic status of tumor microenvironment (TME). The metabolic crosstalk between CAAs and CD8+T cells in TME remains unclear. Here we report that CAAs undergo lipolysis, releasing free fatty acids that promote lipid peroxidation and disturb mitochondrial homeostasis in CD8+T cells, leading to their functional exhaustion. Importantly, we uncover that fibroblast growth factor 21 (FGF21) autocrinally drives CAA lipolysis through upregulating adipose triglyceride lipase (ATGL) via FGFR1/KLB-p38 signaling. FGF21 deletion in adipose tissue or ATGL inhibition impedes CAA lipolysis, mitigates lipid peroxidation, normalizes mitochondrial dynamics of CD8+T cells, and restores their effector function, consequently blunting tumor growth. Moreover, combining ATGL inhibitor with anti-PD-1 therapy synergistically enhances the antitumor activity of CD8+T cells, yielding greater therapeutic efficacy. Our findings highlight the pivotal role of CAA lipol ysis in CD8+T cell dysfunction within TME, suggesting that targeting CAA lipolysis represents a valuable avenue for improving cancer immunotherapy.

cancer biology↗

bioRxiv2024

Fetal Liver-like Organoids Recapitulate Blood-Liver Niche Development and Multipotent Hematopoiesis from Human Pluripotent Stem Cells

The fetal liver is a hematopoietic organ, hosting a diverse and evolving progenitor population. While human liver organoids derived from pluripotent stem cells (PSCs) mimic aspects of embryonic and fetal development, they typically lack the complex hematopoietic niche and the interaction between hepatic and hematopoietic development. We describe the generation of human Fetal Liver-like Organoids (FLOs), that model human hepato-hematopoietic interactions previously characterized in mouse models. Developing FLOs first integrate a yolk sac-like hemogenic endothelium into hepatic endoderm and mesoderm specification. As the hepatic and hematopoietic lineages differentiate, the FLO culture model establishes an autonomous niche capable of driving subsequent progenitor differentiation without exogenous factors. Consistent with yolk sac-derived waves, hematopoietic progenitor cells (HPCs) within FLOs exhibit multipotency with a preference for myeloid lineage commitment, while retaining fetal B and T cell differentiation potential. We reconstruct in FLOs the embryonic monocyte-to-macrophage and granulocyte immune trajectories within the FLO microenvironment and assess their functional responses in the liver niche. In vivo, FLOs demonstrate a liver engraftment bias of hematopoietic cells, recapitulating a key phenomenon of human hematopoietic ontogeny. Our findings highlight the intrinsic capacity of liver organoids to support hematopoietic development, establishing FLOs as a platform for modeling and manipulating human blood-liver niche interactions during critical stages of development and disease.

developmental biology↗

bioRxiv2024

Giant virus creates subcellular environment to overcome codon-tRNA mismatch

Codon usage consonant with the cellular tRNA pool is important for efficient translation. However, many eukaryotic viruses, including amoeba-infecting mimiviruses, have codon usage that is largely deviated from that of their host, despite using the host machinery for translation. This raises the question of how these viruses cope with the mismatch between tRNA supply and demand. Here we show that Acanthamoeba castellanii mimivirus generates a subcellular area in the host cells to translate virus mRNAs. A combination of genome-wide ribosome profiling and RNA sequencing showed that ribosomes traversed along viral mRNAs with fewer pausing events than were observed on amoeba mRNAs. Frequently used codons in viral mRNAs had higher tRNA accessibility than the same type of codons in amoeba mRNAs. tRNA sequencing showed that the tRNA pool was not greatly altered during the infection even though the virus encodes tRNA genes. Instead, by in situ labelling, we found that viral mRNAs and newly synthesized proteins were localized at the periphery region of the viral factory, likely creating a unique environment to facilitate viral translation. Our data provide a perspective on how local translation assists the virus in overcoming the mismatch between tRNA supply and demand.

microbiology↗