Biology subjects

Xiao, K.

Publications and source records attributed to Xiao, K..

30 records · Page 2Linked to original sources

bioRxiv2024

Biophysical modeling of membrane curvature generation and curvature sensing by the glycocalyx

Generation of membrane curvature is fundamental to cellular function. Recent studies have established that the glycocalyx, a sugar-rich polymer layer at the cell surface, can generate membrane curvature. While there have been some theoretical efforts to understand the interplay between the glycocalyx and membrane bending, there remain open questions about how the properties of the glycocalyx affect membrane bending. For example, the relationship between membrane curvature and the density of glycosylated proteins on its surface remains unclear. In this work, we use polymer brush theory to develop a detailed biophysical model of the energetic interactions of the glycocalyx with the membrane. Using this model, we identify the conditions under which the glycocalyx can both generate and sense curvature. Our model predicts that the extent of membrane curvature generated depends on the grafting density of the glycocalyx and the length of the polymers constituting the glycocalyx. Furthermore, when coupled with the intrinsic membrane properties such as spontaneous curvature and a line tension along the membrane, the curvature generation properties of the glycocalyx are enhanced. These predictions were tested experimentally by examining the propensity of glycosylated transmembrane proteins to drive the assembly of highly-curved filopodial protrusions at the plasma membrane of adherent mammalian cells. Our model also predicts that the glycocalyx has curvature sensing capabilities, in agreement with the results of our experiments. Thus, our study develops a quantitative framework for mapping the properties of the glycocalyx to the curvature generation capability of the membrane. Significance StatementThe glycocalyx is a dense layer of glycosylated transmembrane proteins and lipids distributed on the extracellular surface of eukaryotic cells. It is known to mediate cell-cell interactions and protect cells from invasion by pathogens. However, recently it has been found to play a role in generating membrane curvature, which is essential to diverse cellular functions spanning from endocytosis to cell division. Experiments have revealed that different membrane shapes: spherical vesicles, pearls, and tubes are regulated by the glycocalyx. However, currently, we lack a quantitative physical explanation of how glycocalyx properties determine membrane geometries. Here we develop a polymer brush theory-based model, which suggests that the interplay between glycocalyx polymers and membrane bending captures the wide variety of membrane shapes from spherical buds to elongated pearl-like shapes found in previously published experiments. We predict that the physical properties of glycocalyx polymers, line tension, and membrane elastic parameters play significant roles in regulating membrane morphologies. We find that the glycocalyx prefers higher local membrane curvature indicating that the glycocalyx can sense local curvature.

biophysics↗

bioRxiv2024

Polaris Neurosense: A General-Purpose Non-invasive Neurotechnology Research Platform

This article describes our initial work toward a general-purpose platform for non-invasive neurotechnology research. This platform consists of a multi-modal wireless recording device, an associated software API, and full integration into BCI2000 software. The device is placed on the forehead and features two electroencephalographic (EEG) sensors, an inertial movement sensor (IMU), a photoplethysmogram (PPG) sensor, a microphone, and vibration-based feedback. Herein, we demonstrate different technical characteristics of our platform and its use in the context of sleep monitoring/modulation, simultaneous and synchronized recordings from different hardware, and evoked potentials. With further development and widespread dissemination, our platform could become an important tool for research into new non-invasive neurotechnology protocols in humans.

bioengineering↗

bioRxiv2023

HOXB13 alters chromatin accessibility in prostate cancer through interactions with the SWI/SNF complex

HOXB13 is a posterior homeobox protein that is associated with the initiation and growth of prostate cancer (PCa). While most research has focused on the role of HOXB13 on androgen receptor (AR) activity, we demonstrate that HOXB13 is essential to the proliferation of both AR-positive and -negative PCa. Strikingly, HOXB13 is remarkably selective and has almost no effect on non-prostatic tissues. Despite this common essentiality in PCa, HOXB13 activity is markedly different in AR-negative PCa, where interactions with the AP-1 change the HOXB13 cistrome in stem-cell like castration-resistant prostate cancer. We show that HOXB13 activity is commonly mediated by SMARCD2, a member of the mSWI/SNF chromatin remodeling complex. Despite the distinct transcription factor interactions in AR-positive and -negative PCa the HOXB13/SMARCD2 commonly alters chromatin accessibility at HOXB13 binding sites that causes increased proliferation in PCa. Overall, this work demonstrates a novel mechanism of action for HOXB13 and highlights its critical role in AR-negative castration-resistant prostate cancer.

cancer biology↗

bioRxiv2023

Whole genome sequencing reveals autooctoploidy in the Chinese sturgeon and its evolutionary trajectories

The Order Acipenseriformes, which include sturgeons and paddlefishes, represent "living fossils" with complex genomes that are good models for understanding whole genome duplication (WGD) and ploidy evolution in fishes. Here we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8 n), a hexavalent (6 n), two tetravalents (4 n), and a divalent (2 n). We propose based on an analysis taking into account delayed rediploidization that its octoploid genome composition results from two rounds of homologous whole genome duplications (WGDs), and further provide insight into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy composition and evolutionary trajectories of polyploidy fishes.

genomics↗

bioRxiv2023

A critical role for CaMKII in behavioral timescale synaptic plasticity in hippocampal CA1 pyramidal neurons.

Behavioral timescale synaptic plasticity (BTSP) is a type of non-Hebbian synaptic plasticity reported to underlie place field formation in the hippocampal CA1 neurons. Despite this important function, the molecular mechanisms underlying BTSP are poorly understood. The -Calcium-calmodulin-dependent protein kinase II (CaMKII) is activated by synaptic transmission-mediated calcium influx and its subsequent phosphorylation is central to synaptic plasticity. Because the activity of CaMKII is known to outlast the event triggering phosphorylation, we hypothesized it could be involved in the extended timescale of the BTSP process. To examine the role of CaMKII in BTSP, we performed whole-cell in-vivo and in-vitro recordings in CA1 pyramidal neurons from mice engineered to have a point mutation at the autophosphorylation site (T286A) causing accelerated signaling kinetics. Here we demonstrate a profound deficit in synaptic plasticity, strongly suggesting that CaMKII signaling is required for BTSP. This study elucidates part of the molecular mechanism of BTSP and provides insight into the function of CaMKII in place cell formation and ultimately learning and memory. TeaserThe molecular mechanisms of BTSP have been revealed to require the autophosphorylation of CaMKII.

neuroscience↗

bioRxiv2022

in vivo RNA structural probing of guanine and uracil nucleotides in yeast

RNAs have critical catalytic or regulatory functions in the cell and play significant roles in many steps of gene expression regulation. RNA structure can be essential for its cellular function. Therefore, methods to investigate the structure of RNA in vivo are of great importance for understanding the role of cellular RNAs. RNA structural probing is an indirect method to probe the three-dimensional structure of RNA by analyzing the reactivity of different nucleotides to chemical modifications. The chemical modifications can target either the RNA backbone or the Watson-Crick face of nucleotides. The selective 2-hydroxyl acylation analyzed by primer extension (SHAPE) can probe the ribose sugar in all unpaired RNA nucleotides. In contrast, Dimethyl sulfate (DMS) alkylates adenine and cytosine and reports on base pairing context but is not reactive to guanine (G) or uracil (U). Recently, new compounds were used to modify Gs and Us in the plant model system Oryza sativa and in the prokaryotic organisms Bacillus subtilis and Echerichia coli, as well as human cells. To complement the scope of RNA structural probing by chemical modifications in the model organism yeast, we analyzed the effectiveness of guanine modification by a family of aldehyde derivatives, the glyoxal family, in Saccharomyces cerevisiae and Candida albicans. We also explored the effectiveness of uracil modification by carbodiimide N-cyclohexyl-N-(2-morpholinoethyl) carbodiimide metho-p-toluenesulfonate (CMCT) in vivo. We show that among the glyoxal family, phenylglyoxal (PGO) is the best guanine probe for structural probing in S. cerevisiae and C. albicans. We also demonstrate uracil modification by CMCT in S. cerevisiae in vivo. Further, we show that PGO treatment does not affect the processing of different RNA species in the cell and is not toxic for the cells under the conditions we have established for RNA structural probing. Our results provide the conditions for in vivo probing the reactivity of guanine and uracil in RNA structures in yeast and offer a valuable tool for studying RNA structure and function in two widely used yeast model systems.

biochemistry↗

bioRxiv2022

SmartGate is a spatial metabolomics tool for resolving tissue structures

Imaging mass spectrometry (IMS) is one of the powerful tools in spatial metabolomics for obtaining metabolite data and probing the internal microenvironment of organisms. It has dramatically advanced the understanding of the structure of biological tissues and the drug treatment of diseases. However, the complexity of IMS data hinders the further acquisition of biomarkers and the study of certain specific activities of organisms. To this end, we introduce an artificial intelligence tool SmartGate to enable automatic peak picking and spatial structure identification in an iterative manner. SmartGate selects discriminative m/z features from the previous iteration by differential analysis and employs a graph attention auto-encoder model to perform spatial clustering for tissue segmentation using the selected features. We applied SmartGate to diverse IMS data at multicellular or subcellular spatial resolutions and compared it with four competing methods to demonstrate its effectiveness. SmartGate can significantly improve the accuracy of spatial segmentation and identify biomarker metabolites based on tissue structure-guided differential analysis. For multiple consecutive IMS data, SmartGate can effectively identify structures with spatial heterogeneity by introducing three-dimensional spatial neighbor information.

bioinformatics↗

bioRxiv2020

Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2

The Coronavirus Disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) quickly become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about G-quadruplexes on the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes both in the positive and negative-sense viral stands. The identified potential G-quadruplexes exhibits similar features to the G-quadruplexes detected in the human transcriptome. Within some bat and pangolin related beta coronaviruses, the G-quartets rather than the loops are under heightened selective constraints. We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. Further analysis revealed that the SARS-CoV-2 SUD-like sequence is almost conserved among 16,466 SARS-CoV-2 samples. And the SARS-CoV-2 SUDcore-like dimer displayed similar electrostatic potential pattern to the SUD dimer. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, we hope our fundamental research could provide new insights for the SARS-CoV-2 drug discovery.

bioinformatics↗

bioRxiv2020

A colorimetric comparison of sunless with natural skin tan

The main ingredient of sunless tanning products is dihydroxyacetone (DHA). DHA reacts with the protein and amino acid composition in the surface layers of the skin, producing melanoidins, which changes the skin colour, imitating natural skin tan caused by melanin. The purpose of this study was to characterise DHA-induced skin colour changes and to test whether we can predict the outcome of DHA application on skin tone changes. To assess the DHA-induced skin colour shift quantitatively, colorimetric and spectral measurements of the inner forearm were obtained before, four hours and 24 hours after application of a 7.5% concentration DHA gel in the experimental group (n = 100). In a control group (n = 60), the same measurements were obtained on both the inner forearm (infrequently sun-exposed) and the outer forearm (frequently sun-exposed); the difference between these two areas was defined as the naturally occurring tan. Skin colour shifts caused by DHA tanning and by natural tanning were compared in terms of lightness (L*), redness (a*) and yellowness (b*) in the standard CIELAB colour space. Naturalness of the DHA-induced skin tan was evaluated by comparing the trajectory of the chromaticity distribution in (L*, b*) space with that of naturally occurring tan. Twenty-four hours after DHA application, approximately 20% of the skin colour samples became excessively yellow, with chromaticities outside the natural range in (L*, b*) space. A principal component analysis was used to characterise the tanning pathway. Skin colour shifts induced by DHA were predicted by a multiple regression on the chromaticities and the skin properties. The model explained up to 49% of variance in colorimetric components with a median error of less than 2 {Delta}E. We conclude that the control of both the magnitude and the direction of the colour shift is a critical factor to achieve a natural appearance.

neuroscience↗

bioRxiv2020

Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins

The outbreak of 2019-nCoV in the central Chinese city of Wuhan at the end of 2019 poses unprecedent public health challenges to both China and the rest world1. The new coronavirus shares high sequence identity to SARS-CoV and a newly identified bat coronavirus2. While bats may be the reservoir host for various coronaviruses, whether 2019-nCoV has other hosts is still ambiguous. In this study, one coronavirus isolated from Malayan pangolins showed 100%, 98.2%, 96.7% and 90.4% amino acid identity with 2019-nCoV in the E, M, N and S genes, respectively. In particular, the receptor-binding domain of the S protein of the Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference. Comparison of available genomes suggests 2019-nCoV might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. Infected pangolins showed clinical signs and histopathological changes, and the circulating antibodies reacted with the S protein of 2019-nCoV. The isolation of a coronavirus that is highly related to 2019-nCoV in the pangolins suggests that these animals have the potential to act as the intermediate host of 2019-nCoV. The newly identified coronavirus in the most-trafficked mammal could represent a continuous threat to public health if wildlife trade is not effectively controlled.

microbiology↗

bioRxiv2019

Separation and detection of minimal length isomeric glycopeptide neoantigen epitopes centering GSTA region of MUC1 by LC-MS

MUC1 ranks No.2 on the list of targets for cancer immunotherapy. We previously reported monoclonal antibodies binding to glycopeptide neoantigen epitopes centering GSTA sequence of the highly glycosylated tandem repeat region of MUC1. Epitopes centering GSTA sequence are also predicted by NetMHC programs to bind to MHC molecules, although empirical data are lacking. Detecting isomeric MUC1 glycopeptide epitopes by mass spectrometry (MS) remains a technical challenge since antigenic epitopes are often shorter than 10 amino acids. MUC1 digests by Arg-C-specific endopeptidase clostripain could generate heterogenous icosapeptides, but isomeric 20-residue glycopetides could not be separated by liquid chromatography. In this study, we used pronase from Streptomyces griseus, which has no amino acid sequence preference for enzymatic cleavage sites, to digest a pair of synthetic glycopeptide isomers RPAPGST(Tn)APPAHG and RPAPGS(Tn)TAPPAHG, and analyzed the digests by LC-MS using electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) methods. The results showed that glycopeptide isomers containing 8 to 11 amino acids could be efficiently generated by pronase digestion. Such glycopeptide isomers of minimal epitope lengths were clearly distinguished by characteristic MS/MS ion patterns and elution profiles of liquid chromatography. A glycopeptide library was generated which may serve as standards for measuring neoantigen epitopes centering GSTA sequence.

immunology↗

bioRxiv2018

Weakly supervised classification of rare aortic valve malformations using unlabeled cardiac MRI sequences

Biomedical repositories such as the UK Biobank provide increasing access to prospectively collected cardiac imaging, however these data are unlabeled which creates barriers to their use in supervised machine learning. We develop a weakly supervised deep learning model for classification of aortic valve malformations using up to 4,000 unlabeled cardiac MRI sequences. Instead of requiring highly curated training data, weak supervision relies on noisy heuristics defined by domain experts to programmatically generate large-scale, imperfect training labels. For aortic valve classification, models trained with imperfect labels substantially outperform a supervised model trained on hand-labeled MRIs. In an orthogonal validation experiment using health outcomes data, our model identifies individuals with a 1.8-fold increase in risk of a major adverse cardiac event. This work formalizes a learning baseline for aortic valve classification and outlines a general strategy for using weak supervision to train machine learning models using unlabeled medical images at scale.

bioinformatics↗