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Yang, A.

Publications and source records attributed to Yang, A..

108 records · Page 6Linked to original sources
bioRxiv2020

Epigenetic clock and DNA methylation analysis of porcine models of aging and obesity

DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age, epigenetic clocks, for many species. Using a custom methylation array, we generated DNA methylation data from n=238 porcine tissues including blood, bladder, frontal cortex, kidney, liver and lung, from domestic pigs (Sus scrofa domesticus) and minipigs (Wisconsin Miniature Swine). We present 4 epigenetic clocks for pigs that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (pig and human). Two dual-species human-pig pan-tissue clocks accurately measure chronological age and relative age, respectively. We also characterized CpGs that differ between minipigs and domestic pigs. Strikingly, several genes implicated by our epigenetic studies of minipig status overlap with genes (ADCY3, TFAP2B, SKOR1, and GPR61) implicated by genetic studies of body mass index in humans. In addition, CpGs with different levels of methylation between the two pig breeds were identified proximal to genes involved in blood LDL levels and cholesterol synthesis, of particular interest given the minipigs increased susceptibility to cardiovascular disease compared to domestic pigs. Thus, inbred differences of domestic and minipigs may potentially help to identify biological mechanisms underlying weight gain and aging-associated diseases. Our porcine clocks are expected to be useful for elucidating the role of epigenetics in aging and obesity, and the testing of anti-aging interventions.

developmental biology↗
bioRxiv2020

starmapVR: immersive visualisation of single cell spatial omic data

MotivationAdvances in high throughput single-cell and spatial omic technologies have enabled the profiling of molecular expression and phenotypic properties of hundreds of thousands of individual cells in the context of their two dimensional (2D) or three dimensional (3D) spatial endogenous arrangement. However, current visualisation techniques do not allow for effective display and exploration of the single cell data in their spatial context. With the widespread availability of low-cost virtual reality (VR) gadgets, such as Google Cardboard, we propose that an immersive visualisation strategy is useful. ResultsWe present starmapVR, a light-weight, cross-platform, web-based tool for visualising single-cell and spatial omic data. starmapVR supports a number of interaction methods, such as keyboard, mouse, wireless controller and voice control. The tool visualises single cells in a 3D space and each cell can be represented by a star plot (for molecular expression, phenotypic properties) or image (for single cell imaging). For spatial transcriptomic data, the 2D single cell expression data can be visualised alongside the histological image in a 2.5D format. The application of starmapVR is demonstrated through a series of case studies. Its scalability has been carefully evaluated across different platforms. Availability and implementationstarmapVR is freely accessible at https://holab-hku.github.io/starmapVR, with the corresponding source code available at https://github.com/holab-hku/starmapVR under the open source MIT license. Supplementary InformationSupplementary data are available at Bioinformatics online.

bioinformatics↗
bioRxiv2020

nMAGMA: a network enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia

MotivationAnnotating genetic variants from summary statistics of genome-wide association studies (GWAS) is crucial for predicting risk genes of various disorders. The multi-marker analysis of genomic annotation (MAGMA) is one of the most popular tools for this purpose, where MAGMA aggregates signals of single nucleotide polymorphisms (SNPs) to their nearby genes. However, SNPs may also affect genes in a distance, thus missed by MAGMA. Although different upgrades of MAGMA have been proposed to extend gene-wise variant annotations with more information (e.g. Hi-C or eQTL), the regulatory relationships among genes and the tissue-specificity of signals have not been taken into account. ResultsWe propose a new approach, namely network-enhanced MAGMA (nMAGMA), for gene-wise annotation of variants from GWAS summary statistics. Compared with MAGMA and H-MAGMA, nMAGMA significantly extends the lists of genes that can be annotated to SNPs by integrating local signals, long-range regulation signals, and tissue-specific gene networks. When applied to schizophrenia, nMAGMA is able to detect more risk genes (217% more than MAGMA and 57% more than H-MAGMA) that are reasonably involved in schizophrenia compared to MAGMA and H-MAGMA. Some disease-related functions (e.g. the ATPase pathway in Cortex) tissues are also uncovered in nMAGMA but not in MAGMA or H-MAGMA. Moreover, nMAGMA provides tissue-specific risk signals, which are useful for understanding disorders with multi-tissue origins.

bioinformatics↗
bioRxiv2020

Dynamics of Prion Proliferation Under CombinedTreatment of Pharmacological Chaperones andInterferons via a Mathematical Model

Prion diseases are lethal neurodegenerative disorders such as mad cow disease in bovines, chronic wasting disease in cervids, and Creutzfeldt-Jakob disease in humans. They are caused when the prion protein PrPC misfolds into PrPSc, which is capable of inducing further misfolding in healthy PrPC proteins. Recent in vivo experiments show that pharmacological chaperones can temporarily prevent this conversion by binding to PrPC molecules, and thus constitute a possible treatment. A second strategic approach uses interferons to decrease the concentration of PrPSc. In order to study the quantitative effects of these treatments on prion proliferation, we develop a model using a non-linear system of ordinary differential equations. By evaluating their efficacy and potency, we find that interferons act at lower doses and achieve greater prion decay rates. However, there are benefits in combining them with pharmacological chaperones in a two-fold therapy. This research is crucial to guide future prion experiments and inform potential treatment protocols.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗
bioRxiv2020

Sulfopin, a selective covalent inhibitor of Pin1, blocks Myc-driven tumor initiation and growth in vivo

The peptidyl-prolyl cis-trans isomerase, Pin1, acts as a unified signaling hub that is exploited in cancer to activate oncogenes and inactivate tumor suppressors, in particular through up-regulation of c-Myc target genes. However, despite considerable efforts, Pin1 has remained an elusive drug target. Here, we screened an electrophilic fragment library to discover covalent inhibitors targeting Pin1s active site nucleophile - Cys113, leading to the development of Sulfopin, a double-digit nanomolar Pin1 inhibitor. Sulfopin is highly selective for Pin1, as validated by two independent chemoproteomics methods, achieves potent cellular and in vivo target engagement, and phenocopies genetic knockout of Pin1. Although Pin1 inhibition had a modest effect on viability in cancer cell cultures, Sulfopin induced downregulation of c-Myc target genes and reduced tumor initiation and tumor progression in murine and zebrafish models of MYCN-driven neuroblastoma. Our results suggest that Sulfopin is a suitable chemical probe for assessing Pin1-dependent pharmacology in cells and in vivo. Moreover, these studies indicate that Pin1 should be further investigated as a potential cancer target.

cancer biology↗
bioRxiv2020

A gut sensor for sugar preference

Summary Paragraph/AbstractAnimals innately prefer caloric sugars over non-caloric sweeteners. Such preference depends on the sugar entering the intestine.1-4 Although the brain is aware of the stimulus within seconds,5-8 how the gut discerns the caloric sugar to guide choice is unknown. Recently, we discovered an intestinal transducer, known as the neuropod cell.9,10 This cell synapses with the vagus to inform the brain about glucose in the gut in milliseconds.10 Here, we demonstrate that neuropod cells distinguish a caloric sugar from a non-caloric sweetener using the electrogenic sodium glucose co-transporter 1 (SGLT1) or sweet taste receptors. Activation of neuropod cells by non-caloric sucralose leads to ATP release, whereas the entry of caloric sucrose via SGLT1 stimulates glutamate release. To interrogate the contribution of the neuropod cell to sugar preference, we developed a method to record animal preferences in real time while using optogenetics to silence or excite neuropod cells. We discovered that silencing these cells, or blocking their glutamatergic signaling, renders the animals unable to recognize the caloric sugar. And, exciting neuropod cells leads the animal to consume the non-caloric sweetener as if it were caloric. By transducing the precise identity of the stimuli entering the gut, neuropod cells guide an animals internal preference toward the caloric sugar.

neuroscience↗
bioRxiv2019

The interaction between p53 and Mdm2 is independent of MEG3-p53 association

The functions of long noncoding (lnc)RNAs such as MEG3 are defined by their interactions with other RNAs and proteins. These interactions, in turn, are shaped by their subcellular localization and temporal context. Therefore, it is important to be able to analyze the relationships of lncRNAs while preserving cellular architecture. The ability of MEG3 to suppress cell proliferation led to its recognition as a tumor suppressor. MEG3 has been proposed to activate p53 by disrupting the interaction of p53 with Mdm2. To test this mechanism in the native cellular context, we employed two-color direct stochastic optical reconstruction microscopy (dSTORM), a single-molecule localization microscopy (SMLM) technique to detect and quantify the localizations of p53, Mdm2, and MEG3 in U2OS cells. We developed a new cross-nearest neighbor/Monte Carlo algorithm to quantify the association of these molecules. Proof of concept for our method was obtained by examining the association between FKBP1A and mTOR, MEG3 and p53, and Mdm2 and p53. In contrast to previous models, our data support a model in which MEG3 modulates p53 independently of the interaction with Mdm2.

cell biology↗
bioRxiv2019

A cell-free biosynthesis platform for modular construction of protein glycosylation pathways

Glycosylation plays important roles in cellular function and endows protein therapeutics with beneficial properties. However, constructing biosynthetic pathways to study and engineer protein glycosylation remains a bottleneck. To address this limitation, we describe a modular, versatile cell-free platform for glycosylation pathway assembly by rapid in vitro mixing and expression (GlycoPRIME). In GlycoPRIME, crude cell lysates are enriched with glycosyltransferases by cell-free protein synthesis and then glycosylation pathways are assembled in a mix-and-match fashion to elaborate a single glucose priming handle installed by an N-linked glycosyltransferase. We demonstrate GlycoPRIME by constructing 37 putative protein glycosylation pathways, creating 23 unique glycan motifs. We then use selected pathways to design a one-pot cell-free system to synthesize a vaccine protein with an -galactose motif and engineered Escherichia coli strains to produce human antibody constant regions with minimal sialic acid motifs. We anticipate that our work will facilitate glycoscience and make possible new glycoengineering applications.

synthetic biology↗
bioRxiv2019

Exploring Environmental Coverages of Species: A New Variable Selection Methodology for Rulesets from the Genetic Algorithm for Ruleset Prediction

Variable selection for, and determination of variable importance within, species distribution models (SDMs) remain an important area of research with continuing challenges. Most SDM algorithms provide normally exhaustive searches through variable space, however, selecting variables to include in models is a first challenge. The estimation of the explanatory power of variables and the selection of the most appropriate variable set within models can be a second challenge. Although some SDMs incorporate the variable selection rubric inside the algorithms, there is no integrated rubric to evaluate the variable importance in the Genetic Algorithm for Ruleset Production (GARP). Here, we designed a novel variable selection methodology based on the rulesets generated from a GARP experiment. The importance of the variables in a GARP experiment can be estimated based on the consideration of the prevalence of each environmental variable in the dominant presence rules of the best subset of models and its coverage. We tested the performance of this variable selection method based on simulated species with both weak and strong responses to simulated environmental covariates. The variable selection method generally performed well during the simulations with over 2/3 of the trials correctly identifying most covariates. We then predict the distribution of Bacillus anthracis (the bacterium that causes anthrax) in the continental United States (US) and apply our variable selection procedure as a real-world example. We found that the distribution of B. anthracis was primarily determined by organic content, soil pH, calcic vertisols, vegetation, sand fraction, elevation, and seasonality in temperature and moisture.

ecology↗
bioRxiv2018

Comparison of antibody titres between intradermal and intramuscular rabies vaccination using inactivated vaccine in cattle in Bhutan.

In developing countries, the cost of vaccination limits the use of prophylactic rabies vaccination, especially in cattle. Intradermal vaccination delivers antigen directly to an area with higher number of antigen-presenting cells. Therefore, it could produce equivalent or higher antibody titres than conventional intramuscular vaccination even when a lower dose is given.\n\nThis study aimed to compare the antibody response in cattle vaccinated intramuscularly with 1mL of inactivated rabies vaccine (Raksharab, Indian Immunologicals) against intradermally vaccinated cattle with 0.2mL of the same vaccine. The study was conducted in Haa province of Bhutan where rabies is not endemic. One hundred cattle from 27 farms were selected for the study. Virus neutralising antibody (VNA) response was measured using the fluorescent antibody virus neutralisation test on the day of vaccination (day 0) and 14, 30, 60 and 90 days later.\n\nOverall, 71% of intradermally vaccinated cattle and 89% of the intramuscularly vaccinated cattle produced a protective response ([&ge;]0.5IU/mL). This difference was significant (P<0.02) on days 14 and 30 post vaccination with 36 and 58% in the intradermal group having titres [&ge;]0.5 IU/mL respectively compared to the equivalent figures of 78 and 77% in the intramuscular group. The mean VNA titres were lower for intradermal group than intramuscular group (p<0.001) with the mean difference being greater than 0.6 IU/mL. Although low dose intradermal vaccination did produce a detectable antibody response, it was inferior to intramuscular vaccination. Thus, although intradermal vaccination has the potential to reduce the cost of vaccination by reducing the dose required, this study showed that a single dose of 0.2mL intradermally was inferior to an intramuscular dose of 1mL. Further research evaluating dose and dose regimen is needed before intradermal vaccination using the Raksharab rabies vaccine can be recommended in cattle.

immunology↗
bioRxiv2018

Ecological niche modeling the potential geographic distribution of four Culicoides species of veterinary significance in Florida

Epizootic hemorrhagic disease (EHD) is a viral arthropod-borne disease affecting wild and domestic ruminants. EHD virus (EHDV) is transmitted to vertebrate animal hosts by biting midges in the genus Culicoides. Culicoides sonorensis Latreille is the only confirmed vector of EHDV in the United States but is considered rare in Florida and not sufficiently abundant to support EHDV transmission. This study used ecological niche modeling to map the potential geographical distributions and associated ecological variable space of four Culicoides species suspected of transmitting EHDV in Florida, including Culicoides insignis, Culicoides stellifer, Culicoides debilipalpis and Culicoides venustus. Models were developed with the Genetic Algorithm for Rule Set Production in DesktopGARP v1.1.3 using species occurrence data from field sampling along with environmental variables from WorldClim and Trypanosomiasis and Land use in Africa. For three Culicoides species (C. insignis, C. stellifer and C. debilipalpis) 96 - 98% of the presence points were predicted across the Florida landscape (63.77% - 72.53%). For C. venustus, models predicted 98.00% of presence points across 27.42% of Florida. Geographic variations were detected between species. Culicoides insignis was predicted to be restricted to peninsular Florida, and in contrast, C. venustus was predicted to be primarily in north Florida and the panhandle region. Culicoides stellifer and C. debilipalpis were predicted nearly statewide. Environmental conditions also differed by species, with some species ranges predicted by more narrow ranges of variables than others. The Normalized Difference Vegetation Index (NDVI) was a major predictor of C. venustus and C. insignis presence. For C. stellifer, Land Surface Temperature, Middle Infrared were the most limiting predictors of presence. The limiting variables for C. debilipalpis were NDVI Bi-Annual Amplitude and NDVI Annual Amplitude at 22.45% and 28.09%, respectively. The model outputs, including maps and environmental variable range predictions generated from these experiments provide an important first pass at predicting species of veterinary importance in Florida. Because EHDV cannot exist in the environment without the vector, model outputs can be used to estimate the potential risk of disease for animal hosts across Florida. Results also provide distribution and habitat information useful for integrated pest management practices.

ecology↗
bioRxiv2018

HPCI: A Perl module for writing cluster-portable bioinformatics pipelines

BackgroundMost biocomputing pipelines are run on clusters of computers. Each type of cluster has its own API (application programming interface). That API defines how a program that is to run on the cluster must request the submission, content and monitoring of jobs to be run on the cluster. Sometimes, it is desirable to run the same pipeline on different types of cluster. This can happen in situations including when:\n\nO_LIdifferent labs are collaborating, but they do not use the same type of cluster\nC_LIO_LIa pipeline is released to other labs as open source or commercial software\nC_LIO_LIa lab has access to multiple types of cluster, and wants to choose between them for scaling, cost or other purposes\nC_LIO_LIa lab is migrating their infrastructure from one cluster type to another\nC_LIO_LIduring testing or travelling, it is often desired to run on a single computer\nC_LI\n\nHowever, since each type of cluster has its own API, code that runs jobs on one type of cluster needs to be re-written if it is desired to run that application on a different type of cluster. To resolve this problem, we created a software module to generalize the submission of pipelines across computing environments, including local compute, clouds and clusters.\n\nResultsHPCI (High Performance Computing Interface) is a Perl module that provides the interface to a standardized generic cluster.\n\nWhen the HPCI module is used, it accepts a parameter to specify the cluster type. The HPCI module uses this to load a driver HPCD:: . This is used to translate the abstract HPCI interface to the specific software interface.\n\nSimply by changing the cluster parameter, the same pipeline can be run on a different type of cluster with no other changes.\n\nConclusionThe HPCI module assists in writing Perl programs that can be run in different lab environments, with different site configuration requirements and different types of hardware clusters. Rather than having to re-write portions of the program, it is only necessary to change a configuration file.\n\nUsing HPCI, an application can manage collections of jobs to be runs, specify ordering dependencies, detect success or failure of jobs run and allow automatic retry of failed jobs (allowing for the possibility of a changed configuration such as when the original attempt specified an inadequate memory allotment).

bioinformatics↗
bioRxiv2018

Herd Immunity Alters the Conditions for Performing Dose Schedule Comparisons: An Individual-based Model of Pneumococcal Carriage

BACKGROUND BACKGROUND METHODS RESULTS DISCUSSION CONCLUSIONS LIST OF ABBREVIATIONS Ethics approval and consent... Consent for publication Availability of data and... Competing interests Funding Authors' contributions DECLARATIONS REFERENCES Mass vaccination of infants and toddlers with pneumococcal conjugate vaccines (PCVs) has led to large declines in pneumococcal disease in countries around the world [1]. These vaccines currently contain 10 or 13 different capsular polysaccharides from Streptococcus pneumoniae, each conjugated to a protein carrier. In S. pneumoniae, the chemical structure of the capsular polys ...

epidemiology↗
bioRxiv2018

Structural differences between pri-miRNA paralogs promotes alternative Drosha cleavage and expands target repertoires

MicroRNA (miRNA) processing begins with Drosha cleavage, the fidelity of which is critical for downstream processing and mature miRNA target specificity. To understand how pri-miRNA sequence and structure influence Drosha cleavage, we studied the maturation of three pri-miR-9 paralogs, which encode the same mature miRNA but differ in the surrounding scaffold. We show that pri-miR-9-1 has a unique Drosha cleavage profile due to its distorted and flexible stem structure. Cleavage of pri-miR-9-1, but not pri-miR-9-2 or pri-miR-9-3, generates an alternative-miR-9 with a shifted seed sequence that expands the scope of its target RNAs. Analyses of low grade glioma patient samples indicate that the alternative-miR-9 plays a distinct role in preventing tumor progression. To generalize our model, we provide evidence that distortion of pri-miRNA stems correlates with Drosha cleavage at non-canonical sites. Our studies reveal that pri-miRNA paralogs can have distinct functions via differential Drosha processing.

molecular biology↗
bioRxiv2018

Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads

MotivationRead alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for further downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align reads which should have been aligned, a problem we termed as the false-negative non-alignment problem.\n\nResultsWe have developed Scavenger, a pipeline for recovering unaligned reads using a novel mechanism which utilises information from aligned reads. Scavenger performs recovery of unaligned reads by re-aligning unaligned reads against a putative location derived from aligned reads with sequence similarity against unaligned reads. We show that Scavenger can successfully recover unaligned reads in both simulated and real RNA-seq datasets, including single-cell RNA-seq data. The reads recovered contain more genetic variants compared to previously aligned reads, indicating that divergence between personal and reference genomes plays a role in the false-negative non-alignment problem. We also explored the impact of read recovery on downstream analyses, in particular gene expression analysis, and showed that Scavenger is able to both recover genes which were previously non-expressed and also increase gene expression, with lowly expressed genes having the most impact from the addition of recovered reads. We also found that the majority of genes with >1 fold change in expression after recovery are categorised as pseudogenes, indicating that pseudogene expression can be affected by the false-negative non-alignment problem. Scavenger helps to solve the false-negative non-alignment problem through recovery of unaligned reads using information from previously aligned reads.\n\nAvailabilityScavenger is available via an open source license in https://github.com/VCCRI/Scavenger/\n\nContactj.ho@victorchang.edu.au

bioinformatics↗
bioRxiv2017

Comparing neurotransmitter metabolism in the brain of patients with symptomatic and aysmptomatic Alzheimer’s disease and healthy individuals

INTRODUCTIONThree of the four treatments for Alzheimers disease are cholinesterase inhibitors targeting the pathological reduction of acetylcholine levels. Here we aimed to determine the role of other neurotransmitter pathways in AD pathology.\n\nMETHODSTissue samples were obtained from three groups, controls, AD and asymptomatic AD i.e. cognitively normal individuals that had significant AD neuropathology. Three brain areas were studied, the middle frontal gyrus (MFG) the inferior temporal gyrus (ITG) and the cerebellum.\n\nRESULTS11 of 15 measured metabolites were shown to be associated with disease. Decreases in dopamine were seen in the ASYMAD group in the MFG when compared to control and AD patients (FC=0.78, p=4.1x10-3). In AD patients changes were mainly seen in the ITGs inhibitory GABAergic system.\n\nDISCUSSIONThese results indicate that dopamine could be depleted in brains with Alzheimers pathology but intact cognition, while and imbalance of several neurotransmitters is evident in the brain of AD patients.

neuroscience↗
bioRxiv2017

Adaptive Evolution Of Transcription Factor Binding Affinities

Understanding the molecular basis of gene expression evolution is a central problem in evolutionary biology. However, connecting changes in gene expression to increased fitness, and identifying the functional basis of those changes, remains challenging. To study adaptive evolution of gene expression in real time, we performed long term experimental evolution (LTEE) of Saccharomyces cerevisiae (budding yeast) in ammonium-limited chemostats. Following several hundred generations of continuous selection we found significant divergence of nitrogen-responsive gene expression in lineages with increased fitness. In multiple independent lineages we found repeated selection for non-synonymous mutations in the zinc finger DNA binding domain of the activating transcription factor (TF), GAT1, that operates within incoherent feedforward loops to control expression of the nitrogen catabolite repression (NCR) regulon. Missense mutations in the DNA binding domain of GAT1 reduce its binding affinity for the GATAA consensus sequence in a promoter-specific manner, resulting in increased expression of ammonium permease genes via both direct and indirect effects, thereby conferring increased fitness. We find that altered transcriptional output of the NCR regulon results in antagonistic pleiotropy in alternate environments and that the DNA binding domain of GAT1 is subject to purifying selection in natural populations. Our study shows that adaptive evolution of gene expression can entail tuning expression output by quantitative changes in TF binding affinities while maintaining the overall topology of a gene regulatory network.

evolutionary biology↗