Biology subjects

Wu, H.

Publications and source records attributed to Wu, H..

At least 325 records · Page 18Linked to original sources

bioRxiv2023

Impact of Peripheral Auditory Structure on the Development of Auditory-Language Network in Children with Profound Sensorineural Hearing Loss

Profound congenital sensorineural hearing loss (SNHL) prevents children from developing spoken language. Cochlear implantation and auditory brainstem implantation can provide hearing sensation, but language development outcomes can vary, particularly for patients with inner ear malformations and/or cochlear nerve deficiency (IEM&CND). Currently, the peripheral auditory structure is evaluated through visual inspection of clinical imaging, but this method is insufficient for surgical planning and prognosis. The central auditory pathway is also challenging to examine in vivo due to its delicate subcortical structures. Previous attempts to locate subcortical auditory nuclei using fMRI responses to sounds are not applicable to deaf patients. In this study, we developed a new pipeline for mapping the auditory pathway using structural and diffusional MRI. We used a fixel-based approach to investigate the structural development of the auditory-language network for profound SNHL children with normal peripheral structure and those with IEM&CND under six years old. Our findings indicate that the language pathway is more sensitive to peripheral auditory condition than the central auditory pathway, highlighting the importance of early intervention for profound SNHL children to provide timely speech inputs. We also propose a comprehensive pre-surgical evaluation extending from the cochlea to the auditory-language network, which has promising clinical potential.

neuroscience↗

bioRxiv2023

T492I mutation alters SARS-CoV-2 properties via modulating viral non-structural proteins

The historically dominant SARS-CoV-2 Delta variants and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on a combination of in silico analyses, we predicted that the T492I mutation increases the transmissibility and adaptability of the virus. We confirmed this hypothesis by performing competition experiments in hamsters and in human airway tissue culture models. Furthermore, we show that the T492I mutation also increases the replication capacity and infectiveness of the virus, and improves its ability to evade antibody neutralization induced by previous variants. Mechanistically, the T492I mutation increases cleavage efficiency of the viral main protease NSP5 by enhancing enzyme-substrate binding, resulting in increased production of nearly all non-structural proteins processed by NSP5. Importantly, T492I mutation suppresses the viral RNA associated chemokines in monocytic macrophages, which may contribute to the attenuated pathogenicity of Omicron variants. Our results highlight the importance of the NSP4 mutation in the evolutionary dynamics of SARS-CoV-2 and identify a novel target for the development of broad-spectrum antiviral agents.

microbiology↗

bioRxiv2022

Predicting regulators of epithelial cell state through regularized regression analysis of single cell multiomic sequencing

Chronic disease processes are marked by cell-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We developed a regularized regression approach, RENIN, (Regulatory Network Inference) to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generated a single nucleus multiomic dataset from seven adult human kidney biopsies and applied RENIN to study drivers of a failed injury response associated with kidney disease. We demonstrate that RENIN is highly effective tool at predicting key cis- and trans-regulatory elements.

genomics↗

bioRxiv2022

The deacetylase dependent and independent role of HDAC3 in cardiomyopathy

BackgroundCardiomyopathy is a common disease of cardiac muscle that negatively affects cardiac function. HDAC3 commonly functions as co-repressor by removing acetyl moieties from histone tails. However, a deacetylase-independent role of HDAC3 has also been described. Cardiac deletion of HDAC3 causes reduced cardiac contractility accompanied by lipid accumulation. The molecular function of HDAC3 in cardiomyopathy remains unknown. We have used the powerful genetic tools in Drosophila to investigate the enzymatic and non-enzymatic roles of HDAC3 in cardiomyopathy. Methods and ResultsUsing the Drosophila heart model, we showed that cardiac-specific HDAC3 knockdown leads to prolonged systoles and reduced cardiac contractility. Immunohistochemistry revealed structural abnormalities characterized by myofiber disruption in HDAC3 knock down hearts. Cardiac-specific HDAC3 knockdown showed increased levels of whole body triglycerides and increased fibrosis. The introduction of deacetylase-dead HDAC3 mutant in HDAC3 KD background showed comparable results with wild type HDAC3 in aspects of contractility and Pericardin deposition. However, deacetylase-dead HDAC3 mutants failed to improve triglyceride accumulation. ConclusionsOur data indicate that HDAC3 plays a deacetylase-independent role in maintaining cardiac contractility and preventing Pericardin deposition as well as a deacetylase-dependent role to maintain triglyceride homestasis.

physiology↗

bioRxiv2022

Oxytocin enhances the triangular association among behavioral performance, resting state, and task-state functional connectivity

The role of oxytocin (OT) in social behavior and social brain networks has been widely documented. However, the effect of OT on the association between social behavior and brain functional connectivity (FC) is yet to be comprehensively explored. In this study, using a face-perception task and multiple connectome-based predictive (CPM) models, we aimed to: 1) determine whether OT could enhance the association between task behavioral performance, resting-state functional connectivity (rsFC), and task-state functional connectivity (tsFC), and 2) if so, determine the role of OT in enhancing this triangular association. We found that both rsFC and tsFC could independently and significantly predict task performance in the OT group, but not in the placebo (PL) group. In addition, the correlation coefficient between rsFC and tsFC was substantially higher in the OT group than in the PL group. The strength of these associations could be partly explained by OT altering the brains FCs related to social cognition and face-perception in both resting and task states, mainly in brain regions such as the limbic system, prefrontal cortex (PFC), temporal poles (TP), and temporoparietal junction (TPJ). Together, these results suggest that neuropeptides can increase the consistency of individual differences in different modalities (e.g., behavioral and brain level data).

neuroscience↗

bioRxiv2022

The pan-genome and local adaptation of Arabidopsis thaliana

Arabidopsis thaliana has been used as a model species for research in a diverse collection of plant species. However, previous studies based on single reference genomes and short-read sequencing data are restricted to detecting variable genes and large structural variation (SV) underlying local adaptation. Here we de novo assemble high-quality chromosomal genomes of 38 A. thaliana ecotypes (with 6 relict ones) using PacBio-HiFi long-read sequencing. From these newly assembled genomes, we annotate several thousand new genes through pan-genomic analysis in comparison to the previous reference genome. The identified variable genes are mainly enriched in and associated with ecological adaptation and this species substantially expands its gene repertoire for local adaptation. We construct a graph-based pan-genome and identify 62,525 SVs which overlap with 14,243 genes. These genes are enriched in multiple ecological adaptation functions, including secondary metabolic processes, enzyme regulation, and biotic/abiotic stimulus. For example, a 566 bp insertion in the promoter of the light-adaptation KNAT3 gene was specific to the high-altitude relict Tibet-0 ecotype. This SV reduces the expression level of KNAT3 and promotes A. thaliana adaptation to habitats high in light radiation. In addition, compared with the SNPs, the SVs identified in this study captured the missing heritability and we detected novel SV associations with environmental variables in their native range, highlighting the value of SVs in environmental adaptation. The genome resources presented here will help pinpoint genetic changes that include both SVs and the ecotype-specific genes for local adaptation of A. thaliana and increase our understanding of the molecular mechanisms in this model species to respond to varied habitats.

genomics↗

bioRxiv2022

Full-length αIIbβ3 CryoEM structure reveals intact integrin initiate-activation intrinsic architecture

Integrin IIb{beta}3 is the key receptor regulating platelet retraction and accumulation, thus pivotal for hemostasis, and arterial thrombosis as well as a proven drug-target for antithrombotic therapies. Here we resolve the cryoEM structures of the intact full-length IIb{beta}3, which covers three distinct states along the activation pathway. Here, we resolve intact IIb{beta}3 structure at 3[A] resolution, revealing the overall topology of the heterodimer with the transmembrane (TM) helices and the head region ligand-binding domain tucked in a specific angle proximity to the TM region. In response to the addition of a Mn2+ agonist, we resolved two coexisting states, "intermediate" and "pre-active". Our structures show conformational changes of the intact IIb{beta}3 activating trajectory, as well as a unique twisting of the lower integrin legs representing an intermediate state (TM region at a twisting conformation) and a coexisting pre-active state (bent and opening in leg), which is required for inducing the transitioning platelets to accumulate. Our structure provides for the first time direct structural evidence for the lower legs involvement in full-length integrin activation mechanisms. Additionally, our structure offers a new strategy to target the IIb{beta}3 lower leg allosterically instead of modulating the affinity of the IIb{beta}3 head region.

biochemistry↗

bioRxiv2022

Circular single-stranded DNA is a superior homology-directed repair donor template for efficient genome engineering

The toolbox for genome editing in basic research and therapeutic applications is rapidly expanding. While efficient targeted gene ablation using nuclease editors has been demonstrated from bench to bedside, precise transgene integration remains a technical challenge. AAV6 has been a prevalent donor carrier for homology-directed repair (HDR) mediated genome engineering but has reported safety issues, manufacturing constraints, and restricted applications due to its 4.5 Kb packaging limit. Non-viral targeted genetic knock-ins rely primarily on double-stranded DNA (dsDNA) and linear single-stranded DNA (lssDNA) donors. Both dsDNA and lssDNA have been previously demonstrated to have low efficiency and cytotoxicity. Here, we developed a non-viral genome writing catalyst (GATALYST) system which allows production of ultrapure, minicircle single-stranded DNAs (cssDNAs) up to [~]20 Kb as donor templates for highly efficient precision transgene integration. cssDNA donors enable knock-in efficiency of up to 70% in induced pluripotent stem cells (iPSCs), superior efficiency in multiple clinically relevant primary cell types, and at multiple genomic loci implicated for clinical applications with various nuclease editor systems. When applied to immune cell engineering, cssDNA engineered CAR-T cells exhibit more potent and durable anti-tumor efficacy than those engineered from AAV6 viral vectors. The exceptional precision and efficiency, improved safety, payload flexibility, and scalable manufacturability of cssDNA unlocks the full potential of genome engineering with broad applications in therapeutic development, disease modeling and other research areas. HighlightsO_LIScalable production of minicircle ssDNA (cssDNA) with highly engineered phagemid system C_LIO_LIGenome writing catalyst (GATALYST) system with cssDNA donor template demonstrates superior efficiency and safety in various cell types and genomic loci C_LIO_LIGATALYST gene writing system enables ultra-large transgene integration C_LIO_LIcssDNA engineered CAR-T outperforms AAV engineered CAR-T with superior anti-tumor function C_LI

bioengineering↗

bioRxiv2022

The dynamic nature of neurotensin receptor 1 (NTS1) allostery and signaling bias

The neurotensin receptor 1 (NTS1) is a G protein-coupled receptor (GPCR) with promise as a drug target for the treatment of pain, schizophrenia, obesity, addiction, and various cancers. A detailed picture of the NTS1 structural landscape has been established by X-ray crystallography and cryo-EM and yet, the molecular determinants for why a receptor couples to G protein versus arrestin transducers remain poorly defined. We used 13C{varepsilon}H3-methionine NMR spectroscopy to show that phosphatidylinositol-4,5-bisphosphate (PIP2) promotes transducer complexation not by dramatically altering the receptor structure but by strengthening long-range allosteric connections, in the form of correlated conformational kinetics, between the orthosteric pocket and highly-conserved activation motifs. {beta}-arrestin-1 further remodels the receptor ensemble by reducing conformational exchange kinetics for a subset of resonances, whereas G protein coupling has little to no effect on the rate. A {beta}-arrestin biased allosteric modulator transforms the NTS1:G protein complex into a concatenation of substates, without triggering transducer dissociation, suggesting that it may function by stabilizing signaling incompetent G protein conformations such as the non-canonical state. Together, our work demonstrates the importance of kinetic information to a complete picture of the GPCR activation landscape.

biochemistry↗

bioRxiv2022

The Neural Correlates of Arousal: The Ventral Posterolateral Nucleus-Global Transient Co-Activation

Arousal and awareness are two components of consciousness whose the neural mechanisms remain unclear. Spontaneous increases of global (brain-wide) blood-oxygenation-level-dependent (BOLD) signal has been found to be sensitive to changes in arousal. By contrasting BOLD datasets with altered arousal levels, we found that the activation of ventral posterolateral nucleus (VPL) decreased during transient increase in the global signal (top 17% data) in low arousal and awareness states (non-rapid eye movement sleep and anesthesia) as compared to wakefulness, and even in eye-closed (compared with eyes-open) in healthy awake-states, while this activation remained unchanged in patients with unresponsive wakefulness syndrome characterized by high arousal without awareness. These results demonstrate that co-activation of the VPL and global activity is critical to arousal, but not to awareness. One-Sentence SummaryThe VPL nucleus-global brain transient co-activation is related to physiological arousal but not to perceptual awareness.

neuroscience↗

bioRxiv2022

Decoding protein binding landscape on circular RNAs with base-resolution Transformer models

Circular RNAs (circRNAs) interact with RNA-binding proteins (RBPs) to modulate gene expression. To date, most computational methods for predicting RBP binding sites on circRNAs focus on circRNA fragments instead of circRNAs. These methods detect whether a circRNA fragment contains binding sites, but cannot determine where are the binding sites and how many binding sites are on the circRNA transcript. We report a hybrid deep learning-based tool, CircSite, to predict RBP binding sites at single-nucleotide resolution and detect key contributed nucleotides on circRNA transcripts. CircSite takes advantage of convolutional neural networks (CNNs) and Transformer for learning local and global representations of circRNAs binding to RBPs, respectively. We construct 37 datasets of RBP-binding circRNAs for benchmarking and the experimental results show that CircSite offers accurate predictions of RBP binding nucleotides and detects key subsequences aligning well with known binding motifs.

bioinformatics↗

bioRxiv2022

Elevated alpha-synuclein attenuates phagocytosis in SNCA triplication human iPSC-derived neuron:microglia co-cultures

Synucleinopathies such as Parkinsons disease (PD) are characterized by pathologic production, aggregation, and cell-to-cell transmission of -synuclein (-syn) protein that results in impaired cellular function. While neurons of the substantia nigra pars compacta express high levels of -synuclein and are highly vulnerable to its aberrant expression or conformation, brain-resident macrophages (microglia) are also sensitive to abnormal -synuclein, with recent reports indicating that elevated levels impair phagocytic ability in vivo and in vitro. To explore the impact of elevated -syn on microglial function we employed a co-culture model containing iPSC-derived neurons and microglia-like cells. iPSCs from healthy control donors and a Parkinsons donor with an allelic triplication of the SNCA gene locus were differentiated into neurons and microglia-like cells. In monoculture, neurons and microglia generated from the SNCA triplication donor expressed higher levels of SNCA transcript and protein. Neurons were found to have significantly greater expression of SNCA compared to microglia, regardless of donor genotype. Co-cultures of neurons and microglia revealed that microglia cultured with SNCA triplication neurons displayed reduction in phagocytosis of fluorescent E. coli, irrespective of microglia donor genotype. SNCA mRNA and protein expression could be reduced with treatment with an antisense oligonucleotide (ASO) targeting SNCA. ASO treatment partially rescued microglia phagocytosis in SNCA triplication co-cultures and in co-cultures containing SNCA triplication neurons and healthy control microglia. Our results complement and extend previous findings of impaired microglial function in the presence of elevated -synuclein in a novel patient-derived co-culture model that utilizes more disease-relevant conditions rather than the relaying on the addition of exogenous -synuclein.

neuroscience↗

bioRxiv2022

Incorporating genome-wide association study results into genomic prediction enhances the predictive ability of growth and phenology traits in Norway spruce

Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) effects by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects, especially for an oligogenic trait. Using QTLs detected in the genome-wide association study (GWAS) could improve genomic prediction, including informative marker selection and adding a QTL with the largest effect size as a fixed effect. Here, we performed GWAS and genomic selection studies in a population with 904 clones from 32 full-sib families using a newly developed 50k SNP Norway spruce array. In total, GWAS identified 41 SNPs associated with budburst stage (BB) and the SNP with the largest effect size explained 5.1% of the phenotypic variation (PVE). For the other five traits like growth and wood quality traits, only 2 - 13 SNPs were detected and PVE of the strongest effects ranged from 1.2% to 2.0%. GP with approximately 100 preselected SNPs based on the smallest p-values from GWAS showed the largest predictive ability (PA) for the oligogenic trait BB. But for the other polygenic traits, approximate 2000-4000 preselected SNPs, indicated by the smallest Akaike information criterion to offer the best model fit, still resulted in PA being similar to that of GP models using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was [≥]2.5%.

genetics↗

bioRxiv2022

PdeMIXTA04 triggers epidermal cells of placenta to differentiate into poplar catkins through forming MBW complexes with PdeMYC and PdeWD40

Differentiation of plant epidermal cells is a keen research topic in plant biology. Our study on Populus deltoides revealed that epidermal cells of the female flower placenta protruded to form catkin fibers immediately after pollination. We discovered that PdeMIXTA04 was explicitly expressed in placenta of female poplar flowers. Heterologous expression of PdeMIXTA04 in Arabidopsis demonstrated that it significantly promoted the leaf epidermal cells to differentiate into trichomes. Compared with the wild type, significant increases in trichome density and trichome branches were observed on leaves of all 35S:PdeMIXTA04 transgenic lines. Furthermore, transformation of PdeMIXTA04 in the trichomeless Arabidopsis mutant (gl1) restored trichome development to that of the wild type. GUS expression in poplar, driven by the promoter of PdeMIXTA04, also confirmed trichome-specific expression. We then screened a yeast library with PdeMIXTA04 and captured two interacting genes, PdeMYC and PdeWD40. Interactions between these two proteins were verified by yeast two-hybrid (Y2H), biomolecular fluorescence complementation (BiFC), dual-luciferase (dual-LUC), and pull-down assays, indicating that PdeMIXTA04 functions through the MYB-BHLH-WD40 (MBW) ternary complex. Our work presents evidence of PdeMIXTA04 as a candidate gene for editing to resolve catkins associated pollution and provides distinctive understanding of the molecular mechanism triggering differentiation of plant epidermal cells.

molecular biology↗

bioRxiv2022

A Model of High-Speed Endovascular Sonothrombolysis with Vortex Ultrasound-Induced Shear Stress to Treat Cerebral Venous Sinus Thrombosis

This research aims to demonstrate a novel vortex ultrasound enabled endovascular thrombolysis method designed for treating cerebral venous sinus thrombosis (CVST). This is a topic of significant importance since current treatment modalities for CVST still fail in as many as 20-40% of the cases and the incidence of CVST has increased since the outbreak of the COVID-19 pandemic. Compared with conventional anticoagulant or thrombolytic drugs, sonothrombolysis has the potential to remarkably shorten the required treatment time owing to the direct clot targeting with acoustic waves. However, previously reported strategies for sonothrombolysis have not demonstrated clinically meaningful outcomes (e.g., recanalization within 30 minutes) in treating large, completely occluded veins or arteries. In this paper, we demonstrated a new vortex ultrasound technique for endovascular sonothrombolysis utilizing wave-matter interaction-induced shear stress to enhance the lytic rate substantially. Our in vitro experiment showed that the lytic rate was increased by at least 64.3 % compared with the nonvortex endovascular ultrasound treatment. A 3.1 g, 7.5 cm long, completely occluded in vitro 3D model of acute CVST was fully recanalized within 8 minutes with a record-high lytic rate of 237.5 mg/min for acute bovine clot in vitro. Furthermore, we confirmed that the vortex ultrasound causes no vessel wall damage over ex vivo bovine veins. This vortex ultrasound thrombolysis technique potentially presents a new life-saving tool for severe CVST cases that cannot be efficaciously treated using existing therapies.

bioengineering↗

bioRxiv2022

5-MeO-DMT modifies innate behaviors and promotes structural neural plasticity in mice

Serotonergic psychedelics are gaining increasing interest as potential therapeutics for a range of mental illnesses. Compounds with short-lived subjective effects may be clinically useful because dosing time would be reduced, which may improve patient access. One short-acting psychedelic is 5-MeO-DMT, which has been associated with improvement in depression and anxiety symptoms in early clinical studies. However relatively little is known about the behavioral effects and neural mechanisms of 5-MeO-DMT in animal models. Here we characterized the effects of 5-MeO-DMT on innate behaviors and dendritic architecture in mice. We showed that 5-MeO-DMT induces a dose-dependent increase in head-twitch response that is shorter in duration than that induced by psilocybin at all doses tested. 5-MeO-DMT also substantially suppresses social ultrasonic vocalizations produced during mating behavior. 5-MeO-DMT produces long-lasting increases in dendritic spine density in the mouse medial frontal cortex that are driven by an elevated rate of spine formation. However, unlike psilocybin, 5-MeO-DMT did not affect the size of dendritic spines. These data provide insights into the behavioral and neural consequences underlying the action of 5-MeO-DMT and highlight similarities and differences with those of psilocybin.

neuroscience↗

bioRxiv2022

Wnt signaling regulates passive cell competition in the retina by inducing differential cell adhesion

Self-assortation of progenitor cells during development is essential for establishment of distinct tissue identity. This is exemplified in the eye, where the early optic cup is divided into the neural retina (NR) in the center and the ciliary margin (CM) in the periphery. Previous studies have demonstrated that Wnt signaling is required for specification of the CM, but here we show that genetic ablation of Wnt signaling mediator {beta}-catenin in the peripheral optic cup failed to prevent the formation of the CM-derived ciliary body and iris in adult animals. Mosaic analysis revealed that this was only partially due to loss of adherens junctions among {beta}-catenin deficient cells, which were preferentially excluded from the CM. Even in {beta}-catenin mutant cells that can maintain adherens junctions, their inability to mediate Wnt signaling resulted in a change from P-cadherin to N-cadherin expression. We showed that this cadherin switch was sufficient to segregate otherwise identical cells into separate clusters. As a result, the ciliary body and iris were still formed after inactivation of Wnt signaling in the peripheral retina. These results showed that the dual functions of {beta}-catenin in adherens junction and Wnt signaling are required for the passive cell competition to constitute retinal compartments.

developmental biology↗

bioRxiv2022

Ultra-fast joint-genotyping with SparkGOR

MotivationOur aim was to simplify and speedup joint-genotyping, from sequence based variation data of individual samples, while maintaining as high sensitivity and specificity as possible. ResultsWe have leveraged versatile GOR data structures to store biallelic representations of variants and sequence read coverage in a very efficient way, allowing for very fast joint-genotyping that is an order of magnitude faster than any joint-genotyping method published to date. Furthermore, it can be easily extended and executed much faster in an incremental fashion. Concordance analysis based on the Genome In A Bottle (GIAB) samples shows favorable results when compared with the de-facto standard approach, using gVCF files and GATK joint-calling. Additionally, we have developed variant quality classification using XGBoost and variant training sets derived from the GIAB samples. The entire business logic is implemented efficiently and concisely in SparkGOR. AvailabilitySparkGOR is open-source and freely available at https://github.com/gorpipe. Contacthakon@genuitysci.com

bioinformatics↗