Biology subjects

Ouyang, Z.

Publications and source records attributed to Ouyang, Z..

29 records · Page 2Linked to original sources

bioRxiv2021

Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases

Gaining insight into the downstream consequences of non-coding variants is an essential step towards the identification of therapeutic targets from genome-wide association study (GWAS) findings. Here we have harmonized and integrated 8,727 RNA-seq samples with accompanying genotype data from multiple brain-regions from 14 datasets. This sample size enabled us to perform both cis- and trans-expression quantitative locus (eQTL) mapping. Upon comparing the brain cortex cis-eQTLs (for 12,307 unique genes at FDR<0.05) with a large blood cis-eQTL analysis (n=31,684 samples), we observed that brain eQTLs are more tissue specific than previously assumed. We inferred the brain cell type for 1,515 cis-eQTLs by using cell type proportion information. We conducted Mendelian Randomization on 31 brain-related traits using cis-eQTLs as instruments and found 159 significant findings that also passed colocalization. Furthermore, two multiple sclerosis (MS) findings had cell type specific signals, a neuron-specific cis-eQTL for CYP24A1 and a macrophage specific cis-eQTL for CLECL1. To further interpret GWAS hits, we performed trans-eQTL analysis. We identified 2,589 trans-eQTLs (at FDR<0.05) for 373 unique SNPs, affecting 1,263 unique genes, and 21 replicated significantly using single-nucleus RNA-seq data from excitatory neurons. We also generated a brain-specific gene-coregulation network that we used to predict which genes have brain-specific functions, and to perform a novel network analysis of Alzheimers disease (AD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS) and Parkinsons disease (PD) GWAS data. This resulted in the identification of distinct sets of genes that show significantly enriched co-regulation with genes inside the associated GWAS loci, and which might reflect drivers of these diseases.

genomics↗

bioRxiv2021

The possible fidelity-speed-proofreading cost trade-offs in DNA replication due to the exonuclease proofreading

DNA replication is a high-fidelity information-copying processes which is realized by DNA polymerase (DNAP). The high fidelity was explained on the basis of the well-known kinetic-proofreading mechanism (KPR), under which the so-called fidelity-speed trade-off was studied theoretically. However, numerous biochemical experiments have shown that the high fidelity of DNA replication is achieved due to the initial discrimination of polymerase domain of DNAP, as well as the proofreading of the exonuclease domain of DNAP. This exonuclease-proofreading mechanism (EPR) is totally different from KPR. So the trade-off issues are worth being re-examined under EPR. In this paper, we use the first-passage method recently proposed by us to discuss the possible trade-offs in DNA replication under EPR. We show that there could be no fidelity-speed trade-off under EPR, i.e., the fidelity and the speed can be simultaneously enhanced by EPR in a large range of kinetic parameters. This provides a new perspective to understand the experimental data of the exonuclease activity of T7 DNAP and T4 DNAP. We also show that there exists the fidelity-proofreading cost trade-off, i.e., the fidelity is enhanced at the cost of increasing the futile hydrolysis of dNTP. A possible way to avoid this trade-off is to regulate the rate of DNAP translocation: slowing down the forward translocation (in the presence of the terminal mismatch) can enhance the fidelity without changing the speed and the proofreading cost. Our theoretical analysis offers deeper insights on the kinetics-function relation of DNAP. PACS numbers: 82.39.-k, 87.15.Rn, 87.16.A-

biophysics↗

bioRxiv2021

Sharpened and mechanically robust carbon fiber electrode arrays for neural interfacing

Bioelectric medicine treatments target disorders of the nervous system unresponsive to pharmacological methods. While current stimulation paradigms effectively treat many disorders, the underlying mechanisms are relatively unknown, and current neuroscience recording electrodes are often limited in their specificity to gross averages across many neurons or axons. Here, we develop a novel, durable carbon fiber electrode array adaptable to many neural structures for precise neural recording. Carbon fibers were sharpened using a reproducible blowtorch method that uses the reflection of fibers against the surface of a water bath. The arrays were developed by partially embedding carbon fibers in medical-grade silicone to improve durability. We recorded acute spontaneous electrophysiology from the rat cervical vagus nerve (CVN), feline dorsal root ganglia (DRG), and rat brain. Blowtorching resulted in fibers of 72.3 {+/-} 33.5 degree tip angle with 146.8 {+/-} 17.7 m exposed carbon. Silicone-embedded carbon fiber arrays were durable with 87.5% of fibers remaining after 50,000 passes. Observable neural clusters were recorded using sharpened carbon fiber electrodes from rat CVN (41.8 Vpp), feline DRG (101.1 Vpp), and rat brain (80.7 Vpp). Recordings from the feline DRG included physiologically-relevant signals from increased bladder pressure and cutaneous brushing. These results suggest that this carbon fiber array is a uniquely durable and adaptable neural recording device. In the future, this device may be useful as a bioelectric medicine tool for diagnosis and closed-loop neural control of therapeutic treatments and monitoring systems.

bioengineering↗

bioRxiv2020

cellxgene VIP unleashes full power of interactive visualization, plotting and analysis of scRNA-seq data in the scale of millions of cells

To meet the growing demands from scientists to effectively extract deep insights from single cell RNA sequencing, spatial transcriptomics, and emerging multiome datasets, we developed cellxgene VIP (Visualization In Plugin), a frontend interactive visualization plugin of cellxgene framework, which greatly expanded capabilities of the base tool in the following aspects. First, it generates a comprehensive set of over eighteen commonly used quality control and analytical plots in high resolution with highly customizable settings in real time. Second, it provides more advanced analytical functions to gain insights on cellular compositions and deep biology, such as marker gene identification, differential gene expression analysis, and gene set enrichment analysis. Third, it empowers advanced users to perform analysis in a Jupyter Notebook like environment, dubbed Command Line Interface (CLI) by programming in Python and/or R directly without limiting themselves to functional modules available via graphical user interface (GUI). Finally, it pioneers methods to visualize multi-modal data, such as spatial transcriptomics embedding aligned with histological image on one slice or multiple slices in a grid format, and the latest 10x Genomic Multiome dataset where both DNA accessibility and gene expression in the same cells are measured, under the same framework in an integrative way to fully leverage the functionalities mentioned above. Taken together, the open-source tool makes large scale single cell data visualization and analysis more accessible to biologists in a user-friendly manner and fosters computational reproducibility by simplifying data and code reuse through the CLI. Going forward, it has the potential to become a crowdsourcing ecosystem for the scientific community to contribute even more modules to the Swiss Army knife of single cell data exploration tools.

bioinformatics↗

bioRxiv2020

Closed-loop sacral neuromodulation for bladder function using dorsal root ganglia sensory feedback in an acute feline model

Overactive bladder patients suffer from a frequent, uncontrollable urge to urinate, which can lead to a poor quality of life. We aim to improve open-loop sacral neuromodulation therapy by developing a conditional stimulation paradigm using neural recordings from dorsal root ganglia (DRG) as sensory feedback. Experiments were performed in 5 anesthetized felines. We implemented a Kalman filter-based algorithm to estimate the bladder pressure in real-time using sacral-level DRG neural recordings and initiated sacral root electrical stimulation when the algorithm detected an increase in bladder pressure. Closed-loop neuromodulation was performed during continuous cystometry and compared to bladder fills with continuous and no stimulation. Overall, closed-loop stimulation increased bladder capacity by 13.8% over no stimulation (p < 0.001) and reduced stimulation time versus continuous stimulation by 57.7%. High-confidence bladder single units had a reduced sensitivity during stimulation, with lower linear trendline fits and higher pressure thresholds for firing observed during stimulation trials. This study demonstrates the utility of decoding bladder pressure from neural activity for closed-loop control of sacral neuromodulation. An underlying mechanism for sacral neuromodulation may be a reduction in bladder sensory neuron activity during stimulation. Real-time validation during behavioral studies is necessary prior to clinical translation of closed-loop sacral neuromodulation.

bioengineering↗

bioRxiv2020

MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function

Genetic variation in regulatory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity of the regulatory elements. However, it is unclear which TFs are prone to be affected by a given variant. Current motif analysis tools either prioritize TFs based on motif enrichment without linking to a function or are limited in their applications due to the assumption of linearity between motifs and their functional effects. Here, we present MAGGIE, a novel method for identifying motifs mediating TF binding and function. By leveraging measurements from diverse genotypes, MAGGIE uses a statistical approach to link mutation of a motif to changes of an epigenomic feature without assuming a linear relationship. We benchmark MAGGIE across various applications using both simulated and biological datasets and demonstrate its improvement in sensitivity and specificity compared to the state-of-the-art motif analysis approaches. We use MAGGIE to reveal insights into the divergent functions of distinct NF-{kappa}B factors in the pro-inflammatory macrophages, showing its promise in discovering novel functions of TFs. The Python package for MAGGIE is freely available at https://github.com/zeyang-shen/maggie.

bioinformatics↗

bioRxiv2019

Urodynamic parameters and anesthetic depth vary depending on anesthetic agent (alfaxalone, dexmedetomidine, propofol) at doses necessary to facilitate preclinical testing

Urodynamic studies, used to understand bladder function, diagnose bladder disease, and develop treatments for dysfunctions, are ideally performed with awake subjects. However, in animal models, especially cats (a common model of spinal cord injury and associated bladder pathology), anesthesia is often required for these procedures and can be a research confounder. This study compared the effects of select agents (dexmedetomidine, alfaxalone, propofol, isoflurane, and -chloralose) on urodynamic ({Delta}pressure, bladder capacity, bladder compliance, non-voiding contractions, bladder pressure slopes) and anesthetic (change in heart rate [{Delta}HR], average heart rate [HR], reflexes, induction/recovery times) parameters in repeated cystometrograms across five adult male cats. {Delta}pressure was greatest with propofol, bladder capacity was highest with -chloralose, non-voiding contractions were greatest with -chloralose. Propofol and dexmedetomidine had the highest bladder pressure slopes during the initial and final portions of the cystometrograms respectively. Cats progressed to a deeper plane of anesthesia (lower HR, smaller {Delta}HR, decreased reflexes) under dexmedetomidine, compared to propofol and alfaxalone. Time to induction was shortest with propofol, and time to recovery was shortest with dexmedetomidine. These agent-specific differences in urodynamic and anesthetic parameters in cats will facilitate appropriate study-specific anesthetic choices.

physiology↗

bioRxiv2019

Bladder pressure encoding by near-independent fibre subpopulations - implications for decoding

ObjectiveWe aim at characterising the encoding of bladder pressure (intravesical pressure) by a population of sensory fibres. This research is motivated by the possibility to restore bladder function in elderly patients or after spinal cord injury using implanted devices, so called bioelectronic medicines. For these devices, nerve-based estimation of intravesical pressure can enable a personalized and on-demand stimulation paradigm, which will be more effective and efficient. In this context, a better understanding of the encoding strategies employed by the body might in the future be exploited by informed decoding algorithms that enable a precise and robust bladderpressure estimation. ApproachTo this end, we apply information theory to microelectrode-array recordings from the cat sacral dorsal root ganglion while filling the bladder, conduct surrogate data studies to augment the data we have, and finally decode pressure in a simple informed approach. Main resultsWe find an encoding scheme by different main bladder neuron types that we divide into three response types (slow tonic, phasic, and derivative fibres). We show that an encoding by different bladder neuron types, each represented by multiple cells, offers reliability through within-type redundancy and high information rates through near-independence of different types. Our subsequent decoding study shows a potentially more robust decoding from mean responses of homogeneous cell pools. SignificanceWe have here, for the first time, analysed the encoding of intravesical pressure by a population of sensory neurons in a principled way using information theory. We show that even a simple adapted decoder can exploit the redundancy in the population to be more robust against cell loss. This work thus paves the way towards principled encoding studies in the periphery and towards a new generation of informed peripheral nerve decoders for bioelectronic medicines.

bioengineering↗

bioRxiv2019

Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data

Single-cell RNA-seq technologies are rapidly evolving but while very informative, in standard scRNAseq experiments the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to keep the localization of the cells have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To bridge the gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as gold standard genes with in situ hybridization data from the Berkeley Drosophila Transcription Network Project reference atlas. The 34 participating teams used diverse algorithms for gene selection and location prediction, while being able to correctly localize rare subpopulations of cells. Selection of predictor genes was essential for this task and such genes showed a relatively high expression entropy, high spatial clustering and the presence of prominent developmental genes such as gap and pair-ruled genes and tissue defining markers.

systems biology↗

bioRxiv2018

Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay

Rapid technological progress in the recent years has allowed the high-throughput interrogation of different types of biomolecules from single cells. Combining several of these readouts into integrated multi-omic assays is essential to comprehensively understand and model cellular processes. Here, we report the development of Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell: transcriptome, immune receptor clonotypes, surface markers, sample identity and sgRNAs. We demonstrate the use of ECCITE-seq to directly and efficiently capture sgRNA molecules and measure their effects on gene expression and protein levels, opening the possibility of performing high throughput single cell CRISPR screens with multimodal readout using existing libraries and commonly used vectors. Finally, by utilizing the combined phenotyping of clonotype and cell surface markers in immune cells, we apply ECCITE to study a lymphoma sample to discriminate cells and define molecular signatures of malignant cells within a heterogeneous population.

genomics↗

bioRxiv2018

Verified the effectiveness of AsCpf1 system in a variety of vertebrate species

CRISPR/Cpf1 system is a novel genomic editing tool. Because of its more sophisticated components, and lower off-target rate, it has the potential to become a better gene-editing tool. Previous reports showed that CRISPR/Cpf1 could work effectively in multiple species. But our data show that AsCpf1 activity has a big difference in different vertebrates. Using in vitro experiments, we finally learned that the difference between species is due to temperature.

developmental biology↗