Biology subjects

Cai, D.

Publications and source records attributed to Cai, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin

TEA domain transcription factor 1 (TEAD1), a Hippo pathway transcription factor important in cellular homeostasis and development, is increasingly implicated in cancer biology. Here, we reveal a novel role for TEAD1 in organizing nuclear condensates, independent of active transcription. Using high-resolution imaging, ChIP-seq, RNA-seq and proximity-based proteomics, we demonstrate that in patient-derived renal cell carcinoma cells, TEAD1 forms micron-sized condensates by binding to the heterochromatic pericentromeric regions using its DNA-binding domain. TEAD-specific MCAT motifs selectively enrich and cluster in the pericentromeric region, specifically seeding TEAD1 condensates. TEAD1 condensates do not activate transcription but instead serve as depots for excess TEAD1, and disrupting TEAD1 condensates leads to increases in YAP/TEAD target gene expression. This organization of TEAD1 contrasts with that observed in other genomic regions of both RCC and normal kidney cells, in which TEAD1 associates with markers of active transcription. Our findings provide a mechanistic framework for TEAD1s dual regulatory roles, offering new insights into its contribution to transcriptional dysregulation and tumor progression.

cell biology↗

bioRxiv2025

A method for efficient, rapid, and minimally invasive implantation of individual non-functional motes with penetrating subcellular-diameter carbon fiber electrodes into rat cortex

ObjectiveDistributed arrays of wireless neural interfacing chips with 1-2 channels each, known as "neural dust", could enhance brain machine interfaces (BMIs) by removing the wired connection through the scalp and increasing biocompatibility with their submillimeter size. Although several approaches for neural dust have emerged, a procedure for implanting them in batches that builds upon the safety and performance of currently used electrodes remains to be demonstrated. ApproachHere, we demonstrate the feasibility of implanting batches of wireless motes that rest on the cortical surface with carbon fiber electrodes of subcellular diameter (6.8-8.4 {micro}m) that penetrate to a target brain depth of 1 mm without insertion aids. To simulate their implantation, we assembled more than 230 mechanically equivalent motes and affixed them to insertion tools with polyethylene glycol (PEG), a quickly dissolvable and biocompatible material. Then, we implanted mote grids of multiple configurations into rat cortex in vivo and evaluated insertion success and their arrangement on the brain surface using photos and videos captured during their implantation. Main ResultsWhen placing motes onto the insertion device, we found that they aggregated in molten PEG such that the array pitch was only 5% wider than the dimensions of the mote bases themselves (240 x 240 {micro}m). Overall, we found that motes with this arrangement could be inserted into rat cortex with a high success rate, as 171/186 (92%) motes in 4x4 (N=4) and 5x5 (N=5) square grid configurations were successfully inserted using the insertion device alone. After implantation, measurements of how much motes tilted (22{+/-}9{degrees}, [X]{+/-}S) and had been displaced relative to their original positions were smaller than those measured for devices implanted inside the brain in the literature. SignificanceCollectively, these data establish the viability of safely implementing motes with ultrasmall electrodes and epicortically-situated chips for use in future BMIs.

bioengineering↗

bioRxiv2024

The Landscape of Sex- and APOE Genotype-Specific Transcriptional Changes in Alzheimer's Disease at the Single Cell Level

Alzheimers disease (AD) is the most common form of dementia, with approximately two-thirds of AD patients are females. Basic and clinical research studies show evidence supporting sex-specific differences contributing to the complexity of AD. There is also strong evidence supporting sex-specific interaction between the primary genetic risk factor of AD, APOE4 and AD-associated neurodegenerative processes. Recent studies by us and others have identified sex and/or APOE4 specific differentially expressed genes in AD based on the bulk tissue RNA-sequencing data of postmortem human brain samples in AD. However, there lacks a comprehensive investigation of the interplay between sex and APOE genotypes at the single cell level. In the current study, we systematically explore sex and APOE genotype differences in single cell transcriptomics in AD. Our work provides a comprehensive overview of sex and APOE genotype-specific transcriptomic changes across 54 high-resolution cell types in AD and highlights individual genes and brain cell types that show significant differences between sexes and APOE genotypes. This study lays the groundwork for exploring the complex molecular mechanisms of AD and will inform the development of effective sex- and APOE-stratified interventions for AD.

genomics↗

bioRxiv2024

Axonal injury signaling is restrained by a spared synaptic branch

The intrinsic ability of injured neurons to degenerate and regenerate their axons facilitates nervous system repair, however this ability is not engaged in all neurons and injury locations. Here we investigate the regulation of a conserved axonal injury response pathway with respect to the location of damage in branched motoneuron axons in Drosophila larvae. The dileucine zipper kinase DLK, (also known as MAP3K12 in mammals and Wallenda (Wnd) in Drosophila), is a key regulator of diverse responses to axonal injury. In three different populations of motoneurons, we observed the same striking result that Wnd/DLK signaling becomes activated only in response to injuries that remove all synaptic terminals. Injuries that spare even a small part of a synaptic terminal fail to activate Wnd/DLK signaling, despite the presence of extensive axonal degeneration. The regulation of injury-induced Wnd/DLK signaling occurs independently of its previously known regulator, the Hiw/PHR ubiquitin ligase. We propose that Wnd/DLK signaling regulation is linked to the trafficking of a synapse-to-nucleus axonal cargo and that this mechanism enables neurons to respond to impairments in synaptic connectivity.

neuroscience↗

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

A browser-based platform for storage, visualization, and analysis of large-scale 3D images in HPC environments

High-throughput microscopy necessitates 3D image storage, visualization, and analysis in terabyte to petabyte scales. Centralized high-performance computing (HPC) infrastructure provides the resources, but interfacing software is limited. We developed an extensible platform with a scalable image storage format (SISF) and content delivery network (CDN) to enable fast, random access to compressed data. Additionally, we built a cloud-based nTracer2 software to annotate neuron morphology from SISF images in a web browser.

bioinformatics↗

bioRxiv2024

Steering cell-state and phenotype transitions by causal disentanglement learning

Understanding and manipulating cell-state and phenotype transitions is essential for advancing biological research and therapeutic treatment. We introduce CauFinder, an advanced framework designed to accurately identify causal regulators of these transitions and further precisely steer such transitions by integrating causal disentanglement modelling with network control based solely on observed data. By leveraging do-calculus and optimizing information flow metrics, CauFinder can distinguish causal factors from spurious ones, ensuring precise control over desired state transitions. One significant advantage of CauFinder is its ability to identify those variables causally affecting the cell-state/phenotype transitions among all observed variables, both theoretically and computationally, leading to the identification of their master regulators when combined with network control. Consequently, by employing a counterfactual algorithm, CauFinder is able effectively to facilitate desirable state transitions or steer these transitional trajectories/paths by modulating these causal drivers. Beyond its theoretical advantages, CauFinder outperforms existing approaches computationally in both simulated and real-world settings. CauFinder is able to not only reveal natural biological transition processes such as (a) cell differentiation, (b) lung adenocarcinoma (LUAD) to lung squamous cell carcinoma (LUSC) transdifferentiation and (c) drug-sensitive to drug-resistant transitions but also identify the causal regulators of their reverse transition processes, such as (A) cell dedifferentiation, (B) LUSC to LUAD transdifferentiation and (C) drug-resistant to drug-sensitive transitions. These findings highlight its superior ability to causally uncover essential regulatory mechanisms and accurately steer cell-state/phenotype transitions, thus providing novel therapeutic strategies.

bioinformatics↗

bioRxiv2024

Artifact-Minimized High-Ratio Image Compression with Preserved Analysis Fidelity

Recent advances in microscopy have pushed imaging data generation to an unprecedented scale. While scientists benefit from higher spatiotemporal resolutions and larger imaging volumes, the increasing data size presents significant storage, visualization, sharing, and analysis challenges. Lossless compression typically reduces the data size by <4 fold, whereas lossy compression trades smaller data size for the loss of a precise reconstruction of the original data. Here, we develop a novel quantization method and an artifact metric for automated compression parameter optimization that preserves information fidelity. We show that, when combined with the AV1 video codec, we achieve tens to ten thousand folds of data compression while introducing negligible visual defects or quantification errors in single-molecule localization and segmentation analyses. We developed an HDF5 filter with FFMPEG library support for convenient community adaptation. For instance, HDF5-enabled ImageJ plugins can now be seamlessly extended to support AV1 compression and visualization to handle terabyte-scale images.

bioinformatics↗

bioRxiv2024

Permissive and instructive Hox codes govern limb positioning

The positioning of limbs along the anterior-posterior axis varies widely across vertebrates. The mechanisms controlling this feature remain to be fully understood. For over 30 years, it has been speculated that Hox genes play a key role in this process but evidence supporting this hypothesis has been largely indirect. In this study, we employed loss- and gain-of-function Hox gene variants in chick embryos to address this issue. Using this approach, we found that Hox4/5 genes are necessary but insufficient for forelimb formation. Within the Hox4/5 expression domain, Hox6/7 genes are sufficient for reprogramming of neck lateral plate mesoderm to form an ectopic limb bud, thereby inducing forelimb formation anterior to the normal limb field. Our findings demonstrate that the forelimb program depends on the combinatorial actions of these Hox genes. We propose that during the evolutionary emergence of the neck, Hox4/5 provide permissive cues for forelimb formation throughout the neck region, while the final position of the forelimb is determined by the instructive cues of Hox6/7 in the lateral plate mesoderm. Impact statementElucidation of the Hox code defining forelimb positioning provides novel insights in lateral plate mesoderm patterning and the integration of vertebrate column structure and limb positioning.

developmental biology↗

bioRxiv2024

Encoding of interdependent features of head direction and angular head velocity in navigation

To comprehend the complex world around us, our brains are tasked with the remarkable job of integrating multiple features into a cohesive whole. While previous studies have primarily focused on the processing and integration of independent features, here we investigated the simultaneous encoding of the interdependent features, specifically head direction (HD) and its temporal derivative, angular head velocity (AHV), by first employing computational modeling on HD systems to explore emergent algorithms and then validated its biological plausibility with empirical data from mices HD systems. Our analysis revealed two distinct neuron populations: those with multiphasic tuning curves for HD compromised their HD encoding capacity to better capture AHV dynamics, while those with monophasic tuning curves primarily encoded HD. This pattern of functional dissociation was observed in both artificial HD systems and the cortical and subcortical regions upstream of biological HD systems, suggesting a general principle for encoding interdependent features. Further, exploration of the underlying mechanisms involved examining neural manifolds embedded within the representational space constructed by these neurons. We found that the manifold by neurons with multiphasic tuning curves was locally jagged and complex, which effectively expanded the dimensionality of the neural representation space and in turn facilitated a high-precision representation of AHV. Therefore, the encoding strategy for HD and AHV likely integrates characteristics of both dense and sparse coding schemes to achieve a balance between preserving specificity for individual features and maintaining their interdependency nature, marking a significant departure from the encoding of independent features and thus advocating future research delving into the encoding strategies of interdependent features.

neuroscience↗

bioRxiv2024

Thymidine Phosphorylase Promotes the Formation of Abdominal Aortic Aneurysm in Mice Fed a Western Diet

AimsThe precise molecular drivers of abdominal aortic aneurysm (AAA) remain unclear. Thymidine phosphorylase (TYMP) contributes to increased platelet activation, thrombosis, and inflammation, all of which are key factors in AAA development. Additionally, TYMP suppresses the proliferation of vascular smooth muscle cells (VSMCs), which are central to the development and progression of AAA. We hypothesize that TYMP plays a key role in AAA development. Methods and ResultsWe conducted a histological study using human AAA samples and normal abdominal aortas, revealing heightened levels of TYMP in human AAA vessel walls. To validate this observation, we utilized an Ang II perfusion-induced AAA model in wild-type C57BL/6J (WT) and Tymp-/-mice, feeding them a Western diet (TD.88137) starting from 4 weeks of age. We found that Tymp-/-mice were protected from Ang II perfusion-induced AAA formation. Furthermore, by using TYMP-expressing VSMCs as well as primarily cultured VSMCs from WT and Tymp-/- mice, we elucidated the essential role of TYMP in regulating MMP2 expression and activation. TYMP deficiency or inhibition by tipiracil, a selective TYMP inhibitor, led to reduced MMP2 production, release, and activation in VSMCs. Additionally, TYMP was found to promote pro-inflammatory cytokine expression systemically, and its absence attenuates TNF--stimulated activation of MMP2 and AKT. By co-culturing VSMCs and platelets, we observed that TYMP-deficient platelets had a reduced inhibitory effect on VSMC proliferation compared to WT platelets. Moreover, TYMP appeared to enhance the expression of activated TGF{beta}1 in cultured VSMCs in vitro and in human AAA vessel walls in vivo. TYMP also boosted the activation of thrombospondin-1 type 1 repeat domain-enhanced TGF{beta}1 signaling, resulting in increased connective tissue growth factor production. ConclusionOur findings collectively demonstrated that TYMP serves as a novel regulatory force in vascular biology, exerting influence over VSMC functionality and inflammatory responses that promote the development of AAA. Translational PerspectiveThymidine phosphorylase (TYMP) is increased in the vessel walls of patients with abdominal aortic aneurysm (AAA), and TYMP deficiency in mice reduces the incidence of AAA, suggesting that TYMP plays a crucial role in AAA development. This could be attributed to TYMPs role in enhancing systemic inflammation and thrombosis, inhibiting vascular smooth muscle cell function, increasing the activation of matrix metalloproteinase and AKT, as well as enhancing the expression of TGF{beta}1 and connective tissue growth factor. Tipiracil is an FDA-approved drug known to inhibit TYMP-enhanced thrombosis. Targeting TYMP with tipiracil could represent a promising new therapeutic strategy for AAA development.

cell biology↗

bioRxiv2024

A Dimerization-dependent Allosteric Activation for Receptor-like Kinase in Plants

Receptor-like kinases (RLKs) are essential in plants and phosphorylation is a critical step for their function. Interestingly, RLKs have many non-catalytic kinases/ pseudokinases and the biochemical basis for these pseudokinases remains unclear. FERONIA (FER) is an RLK with kinase activity, but the necessity of its kinase activity for genetic functions has been debated. Here, we uncovered that the kinase-deficient variant FERK565R can activate kinase activity in FER and its homologous through homo/heterodimerization-dependent allosteric activation. We further showed that reactive oxygen species (ROS) significantly promote the dimerization of FER family members. Next, we revealed that mutating the FER P740 within the G-H loop reduces FER dimerization and disrupts its allosteric activation, thus attenuating FERs transphosphorylation for its substrate. This disruption in allosteric activation abolishes the genetic function of FERK565R, impacting ROS production and ABA-mediated stomatal movements. Additionally, we found that MEDOS1 (MDS1), a member of the FER family, is incapable of catalyzing phosphotransfer, but can boost the kinase activity of FER and HERK1 through allosteric activation. These findings settle the debate on FERs inactivated forms, and reveal a new mechanism for allosteric activation of RLKs via redox signaling, enhancing our understanding of pseudokinases in plants. One-sentence summaryFER activates kinase activity of homologous family members through allosteric activation.

plant biology↗

bioRxiv2023

Sex Dependent Regional Differences in Dopamine Release Determined by Chronic Fast-Scan Cyclic Voltammetry in Nucleus Accumbens and Dorsal Striatum

We investigated sex differences in dopamine (DA) release in the nucleus accumbens (NAc) and dorsolateral striatum (DLS) using a chronic 16-channel carbon fiber electrode and fast-scan cyclic voltammetry (FSCV). Electrical stimulation (ES; 60Hz) induced DA release was recorded in the NAc of single or pair-housed male and female rats. When core (NAcC) and shell (NAcS) were recorded simultaneously, there was greater ES DA release in NAcC of pair-housed females compared with single females and males. Housing did not affect ES NAc DA release in males. In contrast, there was significantly more ES DA release from the DLS of female rats than male rats. This was true prior to and after treatment with methamphetamine. Furthermore, in castrated (CAST) males and ovariectomized (OVX) females, there were no sex differences in ES DA release from the DLS, demonstrating the hormone dependence of this sex difference. However, in the DLS of both intact and gonadectomized rats, DA reuptake was slower in females than in males. Finally, DA release following ES of the medial forebrain bundle at 60Hz was studied over four weeks. ES DA release increased over time for both CAST males and OVX females, demonstrating sensitization. Using this novel 16-channel chronic FSCV electrode, we found sex differences in the effects of social housing in the NAcS, sex differences in DA release from intact rats in DLS, sex differences in DA reuptake in DLS of intake and gonadectomized rats, and we report sensitization of ES-induced DA release in DLS in vivo. Significance StatementDopamine release is not uniform or fixed. In the nucleus accumbens, pair housing, compared with individual housing, is shown to differentially affect dopamine responsiveness to stimulation in a sex-dependent and region-specific way. There are also sex differences in stimulated dopamine release in the dorsolateral striatum of intact rats, which are not seen in gonadectomized rats, indicating the hormone dependence of this sex difference. However, reuptake of dopamine was slower in females than in males, independent of gonadal hormones. Importantly, the electrical stimulation-induced dopamine release in the dorsolateral striatum of gonadectomized rats demonstrated sensitization of dopamine release in vivo within animals for the first time. Thus, stimulated dopamine release exhibits sex-specific neuroplasticity that is modified in females by the housing conditions.

neuroscience↗

bioRxiv2023

Metabolomics-assisted mechanism analysis of gamma-PGA synthesis regulated by PhoP in B. licheniformis

Poly {gamma}-glutamic acid ({gamma}-PGA) is a widely used biopolymer whose synthesis relies on external nitrogen sources. PhoP is a global transcription factor that has been reported to be involved in regulation of phosphorus and nitrogen metabolisms, whether PhoP regulates {gamma}-PGA synthesis is worthy of further study. In this study, {gamma}-PGA yield was decreased by 19.4% in phoP deletion strain, while PhoP overexpression benefited {gamma}-PGA synthesis in Bacillus licheniformis, and the results of transcriptional level, electrophoretic mobility shift (EMSA) and GFP expression assays confirmed the direct positive regulation on {gamma}-PGA synthetase gene pgsB by PhoP. Furthermore, based on metabolomic and physiological analysis, we dissected three aspects that {gamma}-PGA synthesis indirectly regulated by PhoP. (i) PhoP influences glutamate transport through positively regulating glutamate transporter GltT. (ii) PhoP influences nitrogen source utilization through negatively regulating nitrogen metabolic repressor TnrA and positively regulating GlnR. (iii) PhoP influences ammonia assimilation through GlnR and TnrA. Together, our study improved metabolic regulatory network of {gamma}-PGA synthesis, and laid a foundation for PhoP regulation nitrogen metabolic network in Bacillus.

microbiology↗

bioRxiv2023

Surfactant protein A promotes atherosclerosis through mediating macrophage foam cell formation

BACKGROUNDAtherosclerosis is a progressive inflammatory disease where macrophage foam cells play a central role in the pathogenesis. Surfactant protein A (SPA) is a lipid-associating protein involved with regulating macrophage function in various inflammatory diseases. However, the role of SPA in atherosclerosis and macrophage foam cell formation has not been investigated. METHODSPrimary resident peritoneal macrophages were extracted from wildtype (WT) and SPA deficient (SPA-/-) mice to determine the functional effects of SPA in macrophage foam cell formation. SPA expression was assessed in healthy vessels and atherosclerotic aortic tissue from the human coronary artery and WT or apolipoprotein e-deficient (ApoE-/-) mice brachiocephalic arteries fed high fat diets (HFD) for 4 weeks. Hypercholesteremic WT and SPA-/- mice fed a HFD for 6 weeks were investigated for atherosclerotic lesions in vivo. RESULTSIn vitro experiments revealed that global SPA deficiency reduced intracellular cholesterol accumulation and macrophage foam cell formation. Mechanistically, SPA-/- dramatically decreased CD36 cellular and mRNA expression. SPA expression was increased in atherosclerotic lesions in humans and ApoE-/- mice. In vivo SPA deficiency attenuated atherosclerosis and reduced the number of lesion-associated macrophage foam cells. CONCLUSIONSOur results elucidate that SPA is a novel factor for atherosclerosis development. SPA enhances macrophage foam cell formation and atherosclerosis through increasing scavenger receptor cluster of differentiation antigen 36 (CD36) expression.

cell biology↗

bioRxiv2023

Optimizing the design of spatial genomic studies

Spatially-resolved genomic technologies have shown promise for studying the relationship between the structural arrangement of cells and their functional behavior. While numerous sequencing and imaging platforms exist for performing spatial transcriptomics and spatial proteomics profiling, these experiments remain expensive and labor-intensive. Thus, when performing spatial genomics experiments using multiple tissue slices, there is a need to select the tissue cross sections that will be maximally informative for the purposes of the experiment. In this work, we formalize the problem of experimental design for spatial genomics experiments, which we generalize into a problem class that we call structured batch experimental design. We propose approaches for optimizing these designs in two types of spatial genomics studies: one in which the goal is to construct a spatially-resolved genomic atlas of a tissue and another in which the goal is to localize a region of interest in a tissue, such as a tumor. We demonstrate the utility of these optimal designs, where each slice is a two-dimensional plane, on several spatial genomics datasets.

bioinformatics↗

bioRxiv2023

Hacking brain development to test models of sensory coding

Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations-- computations--that it makes, and what good these computations are for survival. A cardinal method in biology--and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the Drosophila melanogaster mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.

neuroscience↗

bioRxiv2023

A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications

Modern high-throughput microscopy methods such as light-sheet imaging and electron microscopy are capable of producing petabytes of data inside of a single experiment. Storage of these large images, however, is challenging because of the difficulty of moving, storing, and analyzing such vast amounts of data, which is often collected at very high data rates (>1GBps). In this report, we provide a comparison of the performance of several compression algorithms using a collection of published and unpublished datasets including confocal, fMOST, and pathology images. We also use simulated data to demonstrate the efficiency of each algorithm as image content or entropy increases. As a result of this work, we recommend the use of the BLOSC algorithm combined with ZSTD for various microscopy applications, as it produces the best compression ratio over a collection of conditions. CCS CONCEPTS* Applied computing [->] Bioinformatics; Imaging.

bioinformatics↗