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Wong, D.

Publications and source records attributed to Wong, D..

33 records · Page 2Linked to original sources
bioRxiv2021

Carbapenem-Resistant Acinetobacter baumannii in US hospitals: diversification of circulating lineages and antimicrobial resistance

Carbapenem-resistant Acinetobacter baumannii (CRAb) are a major cause of healthcare-associated infections. CRAb are typically multidrug-resistant and infection is difficult to treat. Despite the urgent threat that CRAb pose, few systematic studies of CRAb clinical and molecular epidemiology have been conducted. The Study Network of Acinetobacter as a Carbapenem-Resistant Pathogen (SNAP) is designed to investigate the clinical characteristics and contemporary population structure of CRAb circulating in US hospital systems using whole genome sequencing (WGS). Analysis of the initial 120 SNAP patients from four US centers revealed that CRAb remain a significant threat to hospitalized patients, affecting the most vulnerable patients and resulting in 24% all-cause 30-day mortality. The majority of currently circulating isolates belonged to ST2Pas, a part of Clonal Complex 2 (CC2), which is the dominant drug-resistant lineage in the United States and Europe. We identified three distinct sub-lineages within CC2, which differed in their antibiotic resistance phenotypes and geographic distribution. Most concerning, colistin resistance (38%) and cefiderocol (10%) resistance were common within CC2 sub-lineage C (CC2C), where the majority of isolates belonged to ST2Pas/ST281Ox. Additionally, we identified a newly emergent lineage, ST499Pas that was the most common non-CC2 lineage in our study and had a more favorable drug susceptibility profile compared to CC2. Our findings suggest a shift within the CRAb population in the US during the past 10 years, and emphasize the importance of real-time surveillance and molecular epidemiology in studying CRAb dissemination and clinical impact. ImportanceCarbapenem-resistant Acinetobacter baumannii (CRAb) constitute a major threat to public health. To elucidate the molecular and clinical epidemiology of CRAb in the US, clinical CRAb isolates were collected along with data on patient characteristics and outcomes and bacterial isolates underwent whole genome sequencing and antibiotic susceptibility phenotyping. Key findings included emergence of new sub-lineages within the globally predominant clonal complex (CC) 2, increased colistin and cefiderocol resistance within one of the CC2 sub-lineages, and the emergence of ST499Pas as a previously unrecognized CRAb lineage in US hospitals.

microbiology↗
bioRxiv2021

Novel design of imputation-enabled SNP arrays for breeding and research applications supporting multi-species hybridisation

Array-based SNP genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Infinium Wheat Barley 40K SNP array. We show the approach delivers high-quality and high-resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimising ascertainment bias. Comprising mostly biallelic markers designed to be species-specific and single-copy, it permits highly accurate imputation in diverse germplasm to improve statistical power for GWAS and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Ae. tauschii (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheats, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley and that directly connect to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool Pretzel (https://plantinformatics.io/) which enables the arrays content to be visualised and interrogated interactively in the context of numerous genetic and genomic resources to more seamlessly connect research and breeding. The array is available for use by the international wheat and barley community. Short summaryDesigning SNP genotyping arrays for closely related species with broad applicability in both research and breeding is challenging. Here we describe a novel generic approach to select SNP content for such arrays and demonstrate its utility in wheat and barley to: O_LIcapture haplotypic diversity while minimising ascertainment bias; C_LIO_LIaccurately impute to high SNP density in diverse germplasm; C_LIO_LIgenerate high-quality high-resolution genotypic data; and C_LIO_LIjointly hybridise samples to the same bead chip array. C_LI

genetics↗
bioRxiv2021

Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk

Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across several cell types. Genome-wide association studies (GWAS) have identified over 170 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements (CREs). Here, we applied single-cell ATAC-seq to profile 28,316 cells across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants via quantitative trait locus and sequence-based predictive modeling. We identified a number of candidate mechanisms for smooth muscle cell transition states and identified putative binding sites for risk variants. We further employed CRE to gene linkage to nominate disease-associated key driver transcription factors such as PRDM16 and TBX2. This single cell atlas provides a critical step towards interpreting cis-regulatory mechanisms in the vessel wall across the continuum of CAD risk.

genomics↗
bioRxiv2020

Single-cell RNA-seq analysis of human coronary arteries using an enhanced workflow reveals SMC transitions and candidate drug targets

Background and AimsThe atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability or other plaque phenotypes are not yet available. We sought to investigate the human atherosclerotic cellular environment using scRNA-seq to uncover potential therapeutic approaches. We aimed to make our workflow user-friendly, reproducible, and applicable to other disease-specific scRNA-seq datasets. MethodsHere we incorporate automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into an enhanced and reproducible scRNA-seq analysis workflow. Notably, we also developed an R Shiny based interactive web application to enable further exploration and analysis of the scRNA dataset. ResultsWe applied this analysis workflow to a human coronary artery scRNA dataset and revealed distinct derivations of chondrocyte-like and fibroblast-like cells from smooth muscle cells (SMCs), and show the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several attractive avenues for future pharmacological repurposing in precision medicine. Further, our interactive web application, PlaqView (www.plaqview.com), allows other researchers to easily explore this dataset and benchmark applicable scRNA-seq analysis tools without prior coding knowledge. ConclusionsThese results suggest novel effects of chemotherapeutics on the atherosclerotic cellular environment and provide future avenues of studies in precision medicine. This publicly available workflow will also allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems. PlaqView allows for rapid visualization and analysis of atherosclerosis scRNA-seq datasets without the need of prior coding experience. Future releases of PlaqView will feature additional larger scRNA-seq and scATAC-seq atherosclerosis-related datasets, thus providing a critical resource for the field by promoting data harmonization and biological interpretation.

genomics↗
bioRxiv2020

CRYPTOCHROMES confer robustness, not rhythmicity, to circadian timekeeping

SummaryCircadian (approximately daily) rhythms are a pervasive property of mammalian cells, tissues, and behaviour, ensuring physiological and metabolic adaptation to solar time. Models of daily cellular timekeeping revolve around transcriptional feedback repression, whereby CLOCK and BMAL1 activate the expression of clock proteins PERIOD (PER) and CRYPTOCHROME (CRY), which in turn repress CLOCK/BMAL1 activity. CRY proteins are thus considered essential negative regulators of the oscillation; a function supported by behavioural arrhythmicity of CRY-deficient mice when kept under constant conditions. Challenging this interpretation, however, we find evidence for persistent circadian rhythms in mouse behaviour and cellular PER2 levels when CRY is absent. CRY-less oscillations are variable in their expression and have a shorter period than wild type controls. Importantly, we find classic circadian hallmarks such as temperature compensation and determination of period by casein kinase 1{delta}/{varepsilon} activity to be maintained. In the absence of CRY-mediated transcriptional feedback repression and rhythmic Per2 transcription, PER2 protein rhythms are sustained for several cycles, accompanied by circadian variation in protein stability. We suggest that, whereas circadian transcriptional feedback imparts robustness and functionality onto biological clocks, the core timekeeping mechanism is post-translational. Our findings suggest that PER proteins normally act as signalling hubs that transduce timing information to the nucleus, imparting daily rhythms upon the activity of transcriptional effectors. Highlights[tpltrtarr] PER/CRY-mediated negative feedback is dispensable for mammalian circadian timekeeping [tpltrtarr]Circadian variation in PER2 levels persists in the absence of rhythmic Per2 transcription [tpltrtarr]CK1 and GSK3 are plausible mechanistic components of a cytoscillator mechanism [tpltrtarr]CRY-mediated feedback repression imparts robustness to biological timekeeping In briefCircadian turnover of mammalian clock protein PERIOD2 persists in the absence of canonical transcriptional feedback repression and rhythmic clock gene activity, demanding a re-evaluation of cellular clock function and evolution.

cell biology↗
bioRxiv2020

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

Single cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3 mRNA capture of [~]50,000 single cells or individual nuclei in a single run. The precise pressure-based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efficiencies that compare favorably in the field. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of different buffers and barcoded bead configurations to facilitate diverse applications. Finally, by 3 mRNA profiling asynchronous human and mouse cells at different phases of the cell cycle, we demonstrate the systems ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this identified multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and flexible technology for future transcriptomic studies, and other related applications, at cell resolution.

genomics↗
bioRxiv2019

Glutamate and Dysconnection in the Salience Network: Neurochemical, Effective-connectivity, and Computational Evidence in Schizophrenia

In the dysconnection hypothesis, psychosis is caused by NMDA hypofunction resulting in aberrant network connectivity. Combining a cognitive-control task, functional magnetic resonance spectroscopy, and functional magnetic resonance imaging, we tested this hypothesis in the salience network of 20 first-episode psychosis (FEP) and 20 healthy control (HC) subjects. Across groups, glutamate concentration in the dorsal anterior cingulate cortex (dACC) was associated with higher and lower inhibitory connectivity in the dACC and in the anterior insula (AI) respectively. Crucially, glutamate concentration correlated negatively with the inhibitory influence on the excitatory neuronal population in the dACC of FEP subjects. Furthermore, aberrant computational parameters of the cognitive-control task performance were associated with aberrant inhibitory connections. Finally, the strength of connections from the dACC to the AI correlated negatively with severity of social withdrawal. These findings support a link between glutamate-mediated cortical disinhibition, deficits in effective connectivity, and computational performance in psychosis.

neuroscience↗
bioRxiv2019

Prevalence of RFC1-Mediated Spinocerebellar Ataxia in a United States Ataxia Cohort

ObjectiveRepeat expansions in RFC1 and DAB1 have recently been identified as causing cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) and spinocerebellar ataxia 37 (SCA37), respectively. We evaluated the prevalence of these repeat-expansions in an undiagnosed ataxia cohort from the United States.\n\nMethodsA cohort of 596 patients with undiagnosed familial or sporadic cerebellar ataxia were evaluated at a tertiary referral ataxia center and excluded for common genetic causes of cerebellar ataxia. Patients were then screened for the presence of pathogenic repeat expansions in RFC1 (AAGGG) and DAB1 (ATTTC) using fluorescent repeat primed polymerase chain reaction (RP-PCR). Two additional undiagnosed ataxia cohorts from different centers, totaling 96 and 13 patients respectively, were subsequently screened for RFC1 resulting in a combined 705 subjects tested.\n\nResultsIn the initial cohort, 42 samples were identified with one expanded allele in the RFC1 gene (7.0%), and 9 had two expanded alleles (1.5%). For the additional cohorts, we found 12 heterozygous samples (12.5%) and 7 biallelic samples (7.3%) in the larger cohort, and 1 heterozygous sample (7.7%) and 3 biallelic samples (23%) in the second. In total, 19 patients were identified with biallelic repeat expansions in RFC1 (2.7%). Of these 19 patients, 6 (32%) had a clinical diagnosis of CANVAS, 10 had cerebellar ataxia with neuropathy (53%), and 3 had spinocerebellar ataxia (16%). No patients were identified with expansions in the DAB1 gene.\n\nConclusionIn a large undiagnosed ataxia cohort from the United States, biallelic pathogenic repeat expansion in RFC1 was observed in 2.7%. Testing should be strongly considered in ataxia patients, especially those with CANVAS or neuropathy.

genetics↗
bioRxiv2019

Controlling swelling and release of hyaluronic acid during aqueous storage by in situ cross-linking during spray drying with alginate

The success of hyaluronic acid in over-the-counter cosmetics has been limited by its poor storage stability in aqueous environments due to premature swelling and hydrolysis. Here, hyaluronic acid was prepared in dry microparticles, encapsulated by spray-drying in patented in situ calcium cross-linked alginate microcapsules (CLAMs) to minimize swelling and release in aqueous formulations. CLAMs prepared with 61% (d.b.) hyaluronic acid (HA-CLAMs) demonstrated restricted plumping, limited water absorption capacity, and reduced leaching; retaining up to 49 % hyaluronic acid after 2 hrs in water. A new method using chelated soluble calcium resulted in particles with significantly improved hyaluronic acid retention in water. Chelate HA-CLAMs exhibited nearly full retention of hyaluronic acid over 2 hr incubation in water, and remained visibly insoluble after 1 year of storage in water at 4{degrees}C. Successful hyaluronic acid retention in CLAMs is likely due to the ability of hyaluronic acid to participate in calcium cross-linking.

bioengineering↗
bioRxiv2019

ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing

The zinc finger e-box binding homeobox 1 (ZEB1) transcription factor is a master regulator of the epithelial to mesenchymal transition (EMT), and of the reverse mesenchymal to epithelial transition (MET) processes. ZEB1 plays an integral role in mediating cell state transitions during cell lineage specification, wound healing and disease. EMT/MET are characterized by distinct changes in molecular and cellular phenotype that are generally context-independent. Posterior polymorphous corneal dystrophy (PPCD), associated with ZEB1 insufficiency, provides a new biological context in which to understand and evaluate the classic EMT/MET paradigm. PPCD is characterized by a cadherin-switch and transition to an epithelial-like transcriptomic and cellular phenotype, which we study in a cell-based model of PPCD generated using CRISPR-Cas9-mediated ZEB1 knockout in corneal endothelial cells (CEnCs). Transcriptomic and functional studies support the hypothesis that CEnC undergo a MET-like transition in PPCD, termed endothelial to epithelial transition (EnET), and lead to the conclusion that EnET may be considered a corollary to the classic EMT/MET paradigm.

cell biology↗
bioRxiv2018

Cortical responses to natural speech reflect probabilistic phonotactics

Humans comprehend speech despite the various challenges of real-world environments, such as loud noise and mispronunciation. Our auditory system is robust to these thanks to the integration of the upcoming sensory input with prior knowledge and expectations built on language-specific regularities. One such regularity regards the permissible phoneme sequences, which determine the likelihood that a word belongs to a given language (phonotactic probability; \"blick\" is more likely to be an English word than \"bnick\"). Previous research suggested that violations of these rules modulate brain evoked responses such as the N400 and the late positive complex. Yet several fundamental questions remain unresolved, especially regarding the neural encoding and integration strategy of phonotactic information. Here, we used linear modelling approaches to assess the influence of phonotactic probabilities on the brain responses to narrative speech measured with non-invasive EEG. We found that the relationship between continuous speech and EEG responses is best described when the speech descriptor includes phonotactic probabilities. This provides us with a methodology to isolate and measure the brain responses to phonotactics using natural speech at the individual subject-level. Furthermore, such low-frequency signals showed the strongest speech-EEG interactions at latencies of 100-400 ms, supporting a pre-lexical role of phonotactic information.\n\nSignificance StatementSpeech is composed of basic units, called phonemes, whose combinations comply with language-specific regularities determining whether a sequence \"sounds\" as a plausible word. Our ability to detect irregular combinations requires matching incoming sequences with our internal expectations, a process that supports speech segmentation and learning. However, the neural mechanisms underlying this phenomenon have not yet been established. Here, we examine this in the human brain using narrative speech. We identified a brain signal reflecting the likelihood that a word belongs to the language, which may offer new opportunities to investigate speech perception, learning, development, and impairment. Our data also suggest a pre-lexical role of this phenomenon, thus supporting and extending current mechanistic perspectives.

neuroscience↗
bioRxiv2018

Multiway Canonical Correlation Analysis of Brain Signals

Brain signals recorded with electroencephalography (EEG), magnetoencephalography (MEG) and related techniques often have poor signal-to-noise ratio due to the presence of multiple competing sources and artifacts. A common remedy is to average over repeats of the same stimulus, but this is not applicable for temporally extended stimuli that are presented only once (speech, music, movies, natural sound). An alternative is to average responses over multiple subjects that were presented with the same identical stimuli, but differences in geometry of brain sources and sensors reduce the effectiveness of this solution. Multiway canonical correlation analysis (MCCA) brings a solution to this problem by allowing data from multiple subjects to be fused in such a way as to extract components common to all. This paper reviews the method, offers application examples that illustrate its effectiveness, and outlines the caveats and risks entailed by the method.

neuroscience↗
bioRxiv2018

1H MR Spectroscopy of the Motor Cortex Immediately following Transcranial Direct Current Stimulation at 7 Tesla

Transcranial direct current stimulation (tDCS) is a form of non-invasive brain stimulation that may modulate cortical excitability, metabolite concentration, and human behaviour. The supplementary motor area (SMA) has been largely ignored as a potential target for tDCS neurorehabilitation but is an important region in motor compensation after brain injury with strong efferent connections to the primary motor cortex (M1). The objective of this work was to measure tissue metabolite changes in the human motor cortex immediately following tDCS. We hypothesized that bihemispheric tDCS would change levels of metabolites involved in neuromodulation including N-acetylaspartate, glutamate, and creatine. In this single-blind, randomized, cross-over study, fifteen healthy adults aged 21-60 participated in two 7T MRI sessions, to identify changes in metabolite concentrations by magnetic resonance spectroscopy. Immediately after 20 minutes of tDCS, there were no significant changes in metabolite levels or metabolite ratios comparing tDCS to sham. However there was a trend toward increased NAA/tCr concentration (p=0.08) in M1 under the stimulating cathode. There was a strong, positive correlation between the change in the absolute concentration of NAA and the change in the absolute concentration of tCr (p<0.001) suggesting an effect of tDCS. Both NAA and creatine are important markers of neurometabolism. Our findings provide novel insight into the modulation of neural metabolites in the motor cortex immediately following application of bihemispheric tDCS.

biophysics↗
bioRxiv2017

Decoding the auditory brain with canonical component analysis

The relation between a stimulus and the brain response that it evokes can shed light on perceptual processes within the brain. It can also be harnessed to control external devices for Brain Computer Interface (BCI) applications. While the classic event-related potential (ERP) is appropriate for isolated stimuli, more sophisticated \"decoding\" strategies are needed to address ongoing stimuli such as speech, music or environmental sounds. Here we describe an approach based on Canonical Correlation Analysis (CCA) that finds the optimal transform to apply to both stimulus and response to reveal correlations between the two. Compared to prior methods based on forward or backward models for stimulus-response mapping, CCA finds significantly higher correlation scores, thus providing increased sensitivity to relatively small effects, and supports classifier schemes that yield higher classification scores. CCA strips the brain response of variance unrelated to the stimulus, and the stimulus representation of variance that does not affect the response, and thus improves our observation of the relation between stimulus and response.

neuroscience↗