Biology subjects

Ye, Z.

Publications and source records attributed to Ye, Z..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Optimizing linear ion trap data independent acquisition towards single cell proteomics

A linear ion trap (LIT) is an affordable, robust mass spectrometer that proves fast scanning speed and high sensitivity, where its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight (TOF) or orbitrap (OT) mass analyzers. Previous efforts to utilize the LIT for low-input proteomics analysis still rely on either built-in OTs for collecting precursor data or OT-based library generation. Here, we demonstrate the potential versatility of the LIT for low-input proteomics as a stand-alone mass analyzer for all mass spectrometry measurements, including library generation. To test this approach, we first optimized LIT data acquisition methods and performed library-free searches with and without entrapment peptides to evaluate both the detection and quantification accuracy. We then generated matrix-matched calibration curves to estimate the lower limit of quantification using only 10 ng of starting material. While LIT-MS1 measurements provided poor quantitative accuracy, LIT-MS2 measurements were quantitatively accurate down to 0.5 ng on column. Finally, we optimized a suitable strategy for spectral library generation from low-input material, which we used to analyze single-cell samples by LIT-DIA using LIT-based libraries generated from as few as 40 cells.

biochemistry↗

bioRxiv2023

TCF4 mutations disrupt synaptic function through dysregulation of RIMBP2 in patient-derived cortical neurons

Genetic variation in the transcription factor 4 (TCF4) gene is associated with risk for a variety of developmental and psychiatric conditions, which includes a syndromic form of ASD called Pitt Hopkins Syndrome (PTHS). TCF4 encodes an activity-dependent transcription factor that is highly expressed during cortical development and in animal models is shown to regulate various aspects of neuronal development and function. However, our understanding of how disease-causing mutations in TCF4 confer pathophysiology in a human context is lacking. Here we show that cortical neurons derived from patients with TCF4 mutations have deficits in spontaneous synaptic transmission, network excitability and homeostatic plasticity. Transcriptomic analysis indicates these phenotypes result from altered expression of genes involved in presynaptic neurotransmission and identifies the presynaptic binding protein, RIMBP2 as the most differentially expressed gene in PTHS neurons. Remarkably, TCF4-dependent deficits in spontaneous synaptic transmission and network excitability were rescued by increasing RIMBP2 expression in presynaptic neurons. Together, these results identify TCF4 as a critical transcriptional regulator of human synaptic development and plasticity and specifically identifies dysregulation of presynaptic function as an early pathophysiology in PTHS.

neuroscience↗

bioRxiv2023

Insm1 regulates the development of mTECs and immune tolerance

The Insm1 gene encodes a zinc finger protein with known functions in neuroendocrine cells and neurons. Here we characterized the expression and function of Insm1 in medullary thymic epithelial cells (mTECs). Insm1 is co-expressed with Aire in majority of Insm1 or Aire positive cells, while a few Insm1 positive cells did not express Aire. Mutation of Insm1 impair the expression of Aire and the generation of normal numbers of Aire-expressing mTECs during development. We detected downregulation of genes that expressed specifically in Aire-expressing mTEC and mimetic cells in Insm1 mutant mTECs. Conversely, when Insm1 was overexpressed in thymic epithelial cells in vivo, the size of the mTECs compartment was enlarged and the expression of Aire and genes expressed specifically in the neuroendocrine mimetic cells were increased. Mechanistically, Insm1 bound DNA in mTECs and the majority of the Insm1 binding sites were co-occupied by Aire. These Insm1 binding sites were enriched on super-enhancer regions and thus may contributed to remoted regulation. Both, mice with a thymus-specific mutation in Insm1 or nude mice transplanted with Insm1 mutant thymus, displayed autoimmune responses in multiple peripheral tissues. Together, our data demonstrate a role of Insm1 in development of mTECs and immune tolerance.

immunology↗

bioRxiv2022

Subtle Structural Translation Remarkably Modulates the Super-Resolution Imaging of Self-blinking Rhodamines

The evolution of super-resolution imaging techniques is benefited from the ongoing competition for optimal rhodamine fluorophores. Yet, it seems blinded to select the best one among different rhodamine derivatives for specific labeling and imaging, without the knowledge on imaging impact of even the minimum structural transform. Herein, we have designed a pair of self-blinking sulforhodamines (STMR, SRhB) with the bare distinction of methyl or ethyl substituents, and engineered them with Halo protein ligands. Although the two present similar spectral properties ({lambda}ab, {lambda}fl, {square}, etc.), they demonstrated unique single-molecule characteristics preferring to individual imaging applications. Experimentally, STMR with high emissive rates was qualified for imaging structures with rapid dynamics (endoplasmic reticulum, mitochondria), and SRhB with prolonged on-times and photostability was suited for relatively "static" nuclei and microtubules. Utilized this new knowledge, the mitochondrial morphology during apoptosis and ferroptosis was first super-resolved by STMR. Our study highlights the significance of even the smallest structural modification to the modulation of super-resolution imaging performance, and would provide insight for future fluorophore design.

biochemistry↗

bioRxiv2022

Voltage-gated sodium channel activity mediates sea urchin larval skeletal patterning through spatial regulation of Wnt5 expression

Defining pattern formation mechanisms during embryonic development is important for understanding the etiology of birth defects and to inform tissue engineering approaches. In this study, we used tricaine, a voltage-gated sodium channel (VGSC) inhibitor, to show that VGSC activity is required for normal skeletal patterning in Lytechinus variegatus sea urchin larvae. We demonstrate that tricaine-mediated patterning defects are rescued by an anesthetic-insensitive version of the VGSC LvScn5a. Expression of this channel is enriched in the ventrolateral ectoderm where it spatially overlaps with posterolaterally expressed Wnt5. We show that VGSC activity is required to spatially restrict Wnt5 expression to this ectodermal region that is adjacent and instructive to clusters of primary mesenchymal cells that initiate secretion of the larval skeleton as triradiates. Tricaine-mediated Wnt5 spatial expansion correlates with the formation of ectopic PMC clusters and triradiates. These defects are rescued by Wnt5 knock down, indicating that the spatial expansion Wnt5 is responsible for the patterning defects induced by VGSC inhibition. These results demonstrate a novel connection between bioelectrical status and the spatial control of patterning cue expression during embryonic pattern formation. Summary statementInhibition of voltage-gated sodium channels perturbs Wnt5-mediated patterning of the sea urchin larval skeleton

developmental biology↗

bioRxiv2022

Parallel Activation of Src and Hif1α Increases Localized Glycolytic ATP Generation for Re-assembly of Endothelial Adherens Junctions

Endothelial adherens junctions (AJs) are critical for the regulation of vascular barrier integrity and undergo dis-assembly during inflammatory injury, thus causing vascular leakiness. AJ re-assembly is thus necessary for restoration of the endothelial barrier following the initial injury. Here we examine the metabolic underpinnings that drive restoration of vascular integrity. In response to inflammatory stimuli, the glycolysis regulatory enzyme PFKFB3 is activated, resulting in a rapid and sustained increase of intracellular glycolytic ATP, especially in the proximity of AJs at the plasma membrane. We engineered a novel chemo-genetic construct (RapT) which allowed for precise temporal control of PFKFB3 recruitment to the plasma membrane. Activation of RapT by rapamycin during the barrier restoration phase increased regional ATP and accelerated AJ re-assembly. Mechanistically, we observed that PFKFB3 is activated through two modes. Src-mediated post-translational phosphorylation rapidly increases PFKFB3 activity. Using another chemo-genetic approach to temporally control Src activity, we found that Src activates PFKFB3 by binding to and phosphorylating it at residues Y175, Y334, and Y363. Tyrosine-phospho-deficient mutants of PFKFB3 at these residues block the glycolytic activation upon inflammatory stimuli. In parallel, elevated reactive oxygen species generated during inflammatory stimulation create pockets of regional hypoxia and allow for increased Hif1-mediated transcription of PFKFB3, leading to sustained glycolytic activation. Moreover, inhibition of PFKFB3 delays AJ reassembly and restoration of vascular integrity both in vitro and in vivo. In conclusion, we show that while inflammatory activation acutely compromises the endothelial barrier, inflammatory signaling also concomitantly generates a metabolic milieu in anticipation of the subsequent re-assembly of AJs and restoration of the vascular barrier.

cell biology↗

bioRxiv2022

MdrDB: Mutation-induced drug resistance DataBase

AO_SCPLOWBSTRACTC_SCPLOWMutation-induced drug resistance - where the efficacy of drugs is diminished by structural changes in proteins - presents a significant challenge to drug development and the clinical treatment of disease. Understanding the effects of mutation on protein-ligand binding affinities is a key step in developing more effective drugs and therapies, but as a research community we are currently hindered by the lack of a comprehensive database of relevant information. To address this issue, we have developed MdrDB, a database of information related to changes in protein-ligand affinity caused by mutations in protein structure. MdrDB combines data from seven publicly available datasets with calculated biochemical features, as well as 3D structures computed with PyMOL and AlphaFold 2.0, to form the largest database of its kind. With 3D structural information provided for all samples, MdrDB was specifically created to have the size, breadth, and complexity to be useful for practical protein mutation studies and drug resistance modeling. The database brings together wild type and mutant protein-ligand complexes, binding affinity changes upon mutation ({Delta}{Delta}G), and biochemical features calculated from complexes to advance our understanding of mutation-induced drug resistance, the development of combination therapies, and the discovery of novel chemicals. In total, MdrDB contains 100,537 samples generated from 240 proteins (5,119 total PDB structures), 2,503 mutations, and 440 drugs. Of the total samples, 95,971 are based on available PDB structures, with the remaining 4,566 based on AlphaFold 2.0 predicted structures.

bioinformatics↗

bioRxiv2022

Turn-on Rate Determines the Blinking Propensity of Rhodamine Fluorophores for Super-Resolution Imaging

Live-cell single-molecule localization microscopy has advanced with the development of self-blinking rhodamines. A pKcycling of <6 is recognized as the criterion for self-blinking, yet partial rhodamines matching the standard fail for super-resolution reconstruction. To resolve this controversy, we constructed two typical self-blinking rhodamines (pKcycling = 5.67, 5.35) and a tetramethylsulfonamide rhodamine with unfit pKcycling characteristic (7.00). Kinetic study uncovered slow equilibrium rates and limited blink numbers resulted in the reconstruction failure of partial rhodamines. From the kinetic disparity, a turn-on rate was abstracted to reveal the natural blinking frequency. The new parameter independent from applying laser satisfactorily explained the imaging failure, efficacious for determining the propensity of self-blinking from a kinetic perspective. Following the prediction from this parameter, the tetramethylsulfonamide rhodamine enabled live-cell super-resolution imaging of various organelles through Halo-tag technology. It is convinced that the turn-on rate would be a practical indicator of self-blinking and imaging performance.

biochemistry↗

bioRxiv2022

Improve the Protein Complex Prediction with Protein Language Models

AlphaFold-Multimer has greatly improved protein complex structure prediction, but its accuracy also depends on the quality of the multiple sequence alignment (MSA) formed by the interacting homologs (i.e., interologs) of the complex under prediction. Here we propose a novel method, denoted as ESMPair, that can identify interologs of a complex by making use of protein language models (PLMs). We show that ESMPair can generate better interologs than the default MSA generation method in AlphaFold-Multimer. Our method results in better complex structure prediction than AlphaFold-Multimer by a large margin (+10.7% in terms of the Top-5 best DockQ), especially when the predicted complex structures have low confidence. We further show that by combining several MSA generation methods, we may yield even better complex structure prediction accuracy than Alphafold-Multimer (+22% in terms of the Top-5 best DockQ). We systematically analyze the impact factors of our algorithm and find out the diversity of MSA of interologs significantly affects the prediction accuracy. Moreover, we show that ESMPair performs particularly well on complexes in eucaryotes.

bioinformatics↗

bioRxiv2022

Pink1-mediated mitophagy in the endothelium releases proteins encoded by mitochondrial DNA and activates neutrophil responses

Given their ancient evolutionary origins, eukaryotic mitochondria possess multiple vestiges of their prokaryotic ancestors. One such factor is the N-terminal formylation of proteins encoded by mitochondrial DNA. N-formylated proteins are also released by bacteria and trigger activation of immune cells such as neutrophils. Growing evidence indicate that circulating levels of mitochondrial formyl proteins are elevated in the serum of patients with excessive inflammatory responses and trigger neutrophil activation like their bacterial counterparts. However, the cellular source of these proteins, and the mechanism by which they are released into the circulation is not known. In this study, we have identified vascular endothelial cells as a source of mitophagy induced release of formyl proteins in response to inflammatory mediators in vitro. Mechanistically, endothelial mitophagy required activation of the Pink1 pathway. Using liposomal delivery of sgRNA targeting Pink1 in mice expressing endothelial-specific Cas9, we developed a mouse model in which Pink1 is specifically depleted in the endothelium. Deletion of endothelial Pink1 was remarkably protective in endotoxin-induced lung inflammation, resulting in reduced neutrophil infiltration and significantly reduced death in mice. We thus propose that endothelial cells upregulate pro-inflammatory mitophagy in response to inflammation, leading to release of mitochondrial formyl peptides and detrimental neutrophil recruitment into the lung.

cell biology↗

bioRxiv2022

DBP2Vec: Predicting DNA-binding proteins directly using pre-trained protein language model

DNA-binding proteins (DBPs) play a crucial role in numbers of biological processes and have received wide attention in recent years. Meanwhile, the rapid development of sequencing technologies lead to the explosive growth of new protein sequences, it is highly desired to develop a fast and accurate method for DNA-binding proteins prediction. Experimental methods such as chromatin immunoprecipitation on microarray (ChIP-chip) and X-ray crystallography are highly accurate but expensive and time-consuming. To address this issue, many computational methods have been proposed, they usually exploit multiple information about protein sequence, e.g., sequence composition information, physicochemical properties, evolutionary information, structural information, etc. Despite the effectiveness of these approaches, they heavily depend on prior biological knowledge and undergo a very complex process of feature extraction. In view of these shortcomings, here, we present a novel method, named DBP2Vec, to predict DNA-binding proteins directly from pre-trained protein language model (e.g., ESM-1b) which effectively encode biological properties without any prior knowledge by virtue of deep representation learning (e.g., BERT) on large protein sequences databases (e.g., UniParc). Tests on two DBPs benchmark datasets (e.g., PDB296, UniSwiss-Tst) demonstrate that our proposed method significantly outperforms existing state-of-the-art methods. The source code and the datasets used in the paper are publicly available at: https://github.com/hgcwei/DBP2Vec.

bioinformatics↗

bioRxiv2022

Multimodal electrocorticogram active electrode array based on zinc oxide-thin film transistors

Active electrocorticogram (ECoG) electrodes can amplify the weak electrophysiological signals and improve the anti-interference ability, but the traditional active electrodes are so opaque that cannot realize photoelectric collaborative observation. Here an active and fully-transparent ECoG array based on zinc oxide-thin film transistors (ZnO-TFTs) was developed as the local neural signal amplifier for electrophysiological monitoring. The transparency of the proposed ECoG array was up to 85% which is superior to previous reported active electrode array. Various electrical characterizations demonstrated its ability of electrophysiological signal recording, with a higher signal-to-noise ratio of 19.9 dB compared to the Au grid one (13.2 dB). The high transparency of ZnO-TFT electrode array allowed the collecting electrophysiological signals under direct light stimulation on optogenetic mice brain concurrently. The ECoG array could also work under 7-Tesla magnetic resonance imaging to record local brain signal without affecting brain tissue imaging. As the most transparent active ECoG array to date, it provides a powerful multimodal tool for brain observation, including recording brain activity under synchronized optical modulation and 7-Tesla magnetic resonance imaging.

bioengineering↗

bioRxiv2022

The essential role of disulfide bonds for the hierarchical self-assembly and wet-adhesion of CP20-derived peptides

Barnacles are typical fouling organisms which strongly adhere to immersed solid substrates by secreting proteinaceous adhesives called cement proteins (CPs). The self-assembly of the cement proteins forms a permanently bounded layer that binds barnacle to foreign surfaces. However, due to the abundance of cysteines in whole-length CP20, it is difficult to determine its natural structure and to properly describe its self-assembly properties. In this study, a putative functional motif of Balanus albicostatus CP20 (BalCP20) is identified and found to present distinctive self-assembly and wet-adhesion characteristics. The atomic force microscopy (AFM) and transmission electron microscope (TEM) investigations show that wildtype BalCP20-P3 forms grain-like spindles, which further assembly into fractal-like structures looks like ears of wheat. SDS-PAGE, AFM and LSCM show that DTT treatment opens up disulfide bonds between cysteines and disrupts the fractal-like structures (eras of wheat). Additionally, these morphologies are abolished when one of the BalCP20-P3 four cysteines is mutated by alanine. Circular dichroism (CD) results further suggest that the morphological diversity among BalCP20-P3 and its mutations lays on the proportion of -helix. The above results demonstrate that cysteines and disulfide bonds play a crucial role in the self-assembly of BalCP20-P3. This study provides new insights into BalCP20 underwater adhesion, and brings in new inspirations for the development of novel bionic underwater adhesive.

molecular biology↗

bioRxiv2022

Quantitative analysis of rabies virus-based synaptic connectivity tracing

Monosynaptically restricted rabies viruses have been used for more than a decade for synaptic connectivity tracing. However, the verisimilitude of quantitative conclusions drawn from these experiments is largely unknown. The primary reason is the simple metrics commonly used, which generally disregard the effect of starter cell numbers. Here we present an experimental dataset with a broad range of starter cell numbers and explore their relationship with the number of input cells across the brain using descriptive statistics and modelling. We show that starter cell numbers strongly affect input fraction and convergence index measures, making quantitative comparisons unreliable. Furthermore, we suggest a principled way to analyse rabies derived connectivity data by taking advantage of the starter vs input cell relationship that we describe and validate across independent datasets.

neuroscience↗

bioRxiv2022

A Unified Dynamic and Computational Mechanism for Persistent and Transient Neural Activity Patterns During Delayed-Response Tasks

Understanding how the brain preserves information despite intrinsic noise is a fundamental question in working memory. Typical working memory tasks consist of delay phase for maintaining information, and decoding phase for retrieving information. While previous works have focused on the delay neural dynamics, it is poorly understood whether and how the neural process during decoding phase reduces memory error. We studied this question by training recurrent neural networks (RNNs) on a color delayed-response task. We found that the trained RNNs reduce the memory error of high-probability-occurring colors (common colors) by decoding/attributing a broader range of neural states to them during decoding phase. This decoding strategy can be further explained by a continuing converging neural dynamics following delay phase and a non-dynamic biased readout process. Our findings highlight the role of the decoding phase in working memory, suggesting that neural systems deploy multiple strategies across different phases to reduce memory errors. SignificancePreserving information under noise is crucial in working memory. A typical working memory task consists of a delay phase for maintaining information, and a decoding phase for decoding the maintained into an output action. While the delay neural dynamics have been intensively studied, the impact of the decoding phase on memory error reduction remains unexplored. We trained recurrent neural networks (RNNs) on a color delayed-response task and found that RNNs reduce memory error of a color by decoding a larger portion of the neural state to that color. This strategy is supported both by a converging neural dynamic, and a non-dynamic readout process. Our results suggest that neural networks can utilize diverse strategies, beyond delay neural dynamics, to reduce memory errors.

neuroscience↗

bioRxiv2022

CPPVec: an accurate coding potential predictor based on adistributed representation of protein sequence

Long non-coding RNAs (lncRNAs) play a crucial role in numbers of biological processes and have received wide attention during the past years. Meanwhile, the rapid development of high-throughput transcriptome sequencing technologies (RNA-seq) lead to a large amount of RNA data, it is urgent to develop a fast and accurate coding potential predictor. Many computational methods have been proposed to alleviate this issue, they usually exploit information on open reading frame (ORF), k-mer, evolutionary signatures, or known protein databases. Despite the effectiveness, these methods still have much room to improve. Indeed, none of these methods exploit the context information of sequence, simple measures that are calculated with the continuous nucleotides are not enough to reflect global sequence order information. In view of this shortcoming, here, we present a novel alignment-free method, CPPVec, which exploits the global sequence order information of transcript for coding potential prediction for the first time, it can be easily implemented by distributed representation (e.g., doc2vec) of protein sequence translated from the longest ORF. Tests on human, mouse, zebrafish, fruit fly and Saccharomyces cerevisiae datasets demonstrate that CPPVec is an accurate coding potential predictor and significantly outperforms existing state-of-the-art methods.

bioinformatics↗

bioRxiv2022

Hippo pathway-mediated YAP1/TAZ inhibition is essential for proper pancreatic endocrine specification and differentiation

The Hippo pathway plays a central role in tissue development and homeostasis. However, the function of Hippo in pancreatic endocrine development remains obscure. Here, we examined the roles of Hippo pathway mediated YAP1/TAZ inhibition in the development stages of endocrine specification and differentiation. While YAP1 protein was localized to the nuclei in bipotent progenitor cells, Ngn3 expressing endocrine progenitors completely lost YAP1. Using genetic mouse models, we found that this inactivation of YAP1 requires both intact Hippo pathway and NGN3 protein. Deleting the Lats1 and 2 kinases (Lats1&2) in endocrine progenitor cells of developing mouse pancreas with Ngn3-Cre blocked endocrine progenitor cell differentiation and specification, resulting in reduced islets size and disorganized pancreas at birth. Loss of Lats1&2 in NGN3 expressing cells activated YAP1/TAZ transcriptional activity and recruited macrophages to the developing pancreas. These defects were rescued by deletion of YAP1/TAZ genes, suggesting that tight regulation of YAP1/TAZ by Hippo signaling is crucial for pancreatic endocrine specification. In contrast, deletion of Lats1&2 using beta-cell specific MIP1CreER resulted in a phenotypically normal pancreas, indicating that Lasts1&2 are dispensable for pancreatic beta-cell function. Our results demonstrate that YAP1/TAZ inhibition in the pancreatic endocrine compartment is not a passive consequence of endocrine specification. Rather, Hippo pathway-mediated YAP1/TAZ inhibition in endocrine progenitors is a prerequisite for endocrine specification and differentiation.

developmental biology↗

bioRxiv2022

Glucocorticoids Mediate Transcriptome-wide Alternative Polyadenylation: Mechanisms and Functional Implications

Alternative polyadenylation (APA) is a common genetic regulatory mechanism that generates distinct 3' ends for RNA transcripts. Changes in APA have been associated with multiple biological processes and disease phenotypes. However, the role of hormones and their drug analogs in APA remains largely unknown. In this study, we investigated transcriptome-wide the impact of glucocorticoids on APA in 30 human B-lymphoblastoid cell lines. We found that glucocorticoids could regulate APA of a subset of genes, possibly by changing the expression of 142 RNA-binding proteins, some with known APA-regulating properties. Interestingly, genes with glucocorticoid-mediated APA were enriched in viral translation-related pathways, while genes with glucocorticoid-mediated expression were enriched in interferon and interleukin pathways, suggesting that glucocorticoid-mediated APA might result in functional consequences distinct from gene expression. Glucocorticoid-mediated APA was also cell-type-specific, suggesting an action of glucocorticoids that may be unique to immune regulation. We also observed evidence for genotype-dependent glucocorticoid-mediated APA, providing potential functional mechanisms for a series of common genetic variants that had previously been associated with immune disorders, but without a clear mechanism. In summary, this study reports a series of novel observations regarding the impact of glucocorticoids on APA, suggesting novel avenues for mechanistic studies of hormonal biology.

genomics↗