Biology subjects

Hill, A.

Publications and source records attributed to Hill, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2022

Development of a high-throughput barrier function assay using primary human gut organoids

Disruptions in the gut epithelial barrier can lead to the development of chronic indications such as inflammatory bowel disease (IBD). Historically, barrier function has been assessed in cancer cell lines, which do not contain all human intestinal cell types, leading to poor translatability. To bridge this gap, we adapted human primary gut organoids grown as monolayers to assess barrier function. In this work we describe and characterize a novel 96-well human gut organoid-derived monolayer system that enables medium/high-throughput quantitative assessment of candidate therapeutics. Normal human intestine differentiation patterns and barrier function were characterized and confirmed to recapitulate key aspects of in vivo biology. Next, cellular response to TNF- (a central driver of IBD) was determined using a diverse cadre of readouts.These outputs included transcription factor phosphorylation, target gene expression, cytokine/chemokine production, and barrier function. Additionally, we showed that TNF- pathway antagonists rescued damage caused by TNF- in a dose-dependent manner, indicating that this system is suitable for quantitative assessment of barrier modulating factors. Taken together, we have established a robust primary cell-based 96-well system capable of interrogating questions around mucosal response. This system is well suited to provide pivotal functional data to support translational target and drug discovery efforts.

immunology↗

bioRxiv2022

Huntingtin Over-Expression Does Not Alter Overall Survival in Murine Cancer Models

A reduced incidence of various forms of cancer has been reported in Huntingtons disease (HD) patients and may be due to pro-apoptotic effects of mutant huntingtin. We tested this hypothesis by assessing the effects of huntingtin protein over-expression on survival in two murine cancer models. We generated yeast artificial chromosome (YAC) HD mice containing human huntingtin transgenes with various CAG tract lengths (YAC18, YAC72, YAC128) on either an Msh2 or p53 null background, which have increased cancer incidence. In both mouse models of cancer, the over-expression of either mutant or wild-type huntingtin had no significant effect on overall survival. These results do not support the hypothesis that mutant huntingtin expression is protective against cancer.

cancer biology↗

bioRxiv2022

Interlimb coordination in Parkinson's disease is affected by a visuospatial dual task

Parkinsons disease (PD) leads to reduced spatial and temporal interlimb coordination during gait as well as reduced coordination in the upper or lower limbs. Multi-tasking when walking is common during real-world activities, and affects some gait characteristics, like gait speed and variability. However, the impact of a dual task (DT) on intra and interlimb coordination of both lower and upper limbs when walking in people with PD remains unknown. Seventeen volunteers with mild to moderate PD (11 males, 65 {+/-} 8 years, 173 {+/-} 8 cm, 74 {+/-} 20 kg, Unified Parkinsons Disease Rating Scale motor section 10 {+/-} 5) participated in gait trials in an Extended-CAREN system, which includes a treadmill, 12-camera Vicon motion capture system, and a 180{degrees} field-of-view virtual reality projection screen. Participants completed a 3 min walking trial and a 2 min visuospatial word recognition DT trial at their preferred walking pace. Single and DT were compared with a paired t-test, and the less and more affected (LA, MA) sides were tested for equivalence in sensitivity to the DT. During the DT, we found the LA shoulder ROM decreased by 1.5{degrees}, and the LA shoulder peak flexion decreased by 1.1{degrees} (p<.028, gav>.12). The LA and MA hip ROM were differently affected by the dual task (p=.023), and intralimb coordination was affected by dual tasking equivalently between sides (p=.004). These results suggest that during normal single-task gait, people with PD use attentional resources to compensate for reduced arm swing. Furthermore, our results indicate that any effect of DT on lower intralimb coordination is not meaningfully different between the LA and MA sides. Statements and DeclarationsThe authors have no relevant financial or non-financial interests to disclose.

pathology↗

bioRxiv2022

Mechanisms regulating the frequency of inhibition-based gamma oscillations in primate prefrontal and parietal cortices

In primates, the dorsolateral prefrontal (DLPFC) and posterior parietal (PPC) cortices are critical nodes in the network mediating cognitive functions including attention and working memory. Notably, during working memory tasks, gamma oscillations, usually prominent in layer 3 (L3), are induced in both DLPFC and PPC but exhibit higher frequency in DLPFC. These oscillation frequency differences might be crucial for working memory function, but the mechanisms producing different oscillation frequencies in monkey DLPFC and PPC remain poorly understood. To investigate the basis of the DLPFC-PPC differences in oscillation frequency we studied GABAAR-mediated inhibition, which plays a crucial role in gamma oscillation production, in L3 pyramidal neurons (L3 PNs) from the rhesus monkey DLPFC or PPC. Recordings of GABAAR-mediated synaptic currents from L3 PNs, while suggesting a contribution to network synchronization in both areas, revealed no DLPFC-PPC differences in the strength or kinetics of GABAAR-mediated inhibition. Likewise, the expression of GABAAR genes in L3 PNs did not differ between regions. In the absence of differences in inhibition, DLPFC L3 PNs showed greater dendritic spine density and higher expression of AMPAR and NMDAR subunit genes relative to PPC L3 PNs, suggesting that the excitatory synaptic drive onto L3 PNs could be stronger in the DLPFC. Simulations in computational models of the cortical microcircuit showed that, with constant synaptic inhibition, increasing the strength of recurrent excitatory synaptic drive increased the network oscillation frequency. Hence, the DLPFC-PPC differences in gamma oscillation frequency could depend on stronger recurrent excitation in the DLPFC relative to PPC. Significance statementGamma oscillations may contribute to the neural substrate of working memory and exhibit a higher frequency in the prefrontal (DLPFC) than parietal (PPC) areas of primate cortex. To investigate the basis of these oscillation frequency differences which may be crucial for working memory encoding, we studied GABAAR-mediated inhibition on L3 pyramidal neurons (L3 PNs) from rhesus monkey DLPFC or PPC. Our data revealed no DLPFC-PPC differences in GABAAR-mediated inhibition but showed greater dendritic spine density in DLPFC L3 PNs, suggesting stronger excitatory synaptic drive. Simulations in computational network models showed that stronger recurrent excitatory synaptic drive increased the network oscillation frequency, suggesting that the higher oscillation frequency could depend on stronger recurrent excitation in the DLPFC relative to PPC.

neuroscience↗

bioRxiv2022

Dual spatially resolved transcriptomics for SARS-CoV-2 host-pathogen colocalization studies in humans

To advance our understanding of cellular host-pathogen interactions, technologies that facilitate the co-capture of both host and pathogen spatial transcriptome information are needed. Here, we present an approach to simultaneously capture host and pathogen spatial gene expression information from the same formalin-fixed paraffin embedded (FFPE) tissue section using the spatial transcriptomics technology. We applied the method to COVID-19 patient lung samples and enabled the dual detection of human and SARS-CoV-2 transcriptomes at 55 m resolution. We validated our spatial detection of SARS-CoV-2 and identified an average specificity of 94.92% in comparison to RNAScope and 82.20% in comparison to in situ sequencing (ISS). COVID-19 tissues showed an upregulation of host immune response, such as increased expression of inflammatory cytokines, lymphocyte and fibroblast markers. Our colocalization analysis revealed that SARS-CoV-2+ spots presented shifts in host RNA metabolism, autophagy, NF{kappa}B, and interferon response pathways. Future applications of our approach will enable new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes.

genomics↗

bioRxiv2021

Effects of arm swing amplitude and lower limb asymmetry on motor variability patterns during treadmill gait

Motor variability is a fundamental feature of gait. Altered arm swing and lower limb asymmetry (LLA) may be contributing factors having been shown to affect the magnitude and dynamics of variability in spatiotemporal and trunk motion. However, the effects on lower limb joints remain unclear. Full-body kinematics of 15 healthy young adults were recorded during treadmill walking using the Computer-Assisted Rehabilitation Environment system. Participants completed six trials, combining three arm swing (AS) amplitude (normal, active, held) and two LLA (symmetrical, asymmetrical) conditions. The mean standard deviation (meanSD), maximum Lyapunov exponent ({lambda}max), detrended fluctuation analysis scaling exponent of range of motion (DFA), and sample entropy (SaEn) were computed for tridimensional trunk, pelvis, and lower limb joint angles, and compared using repeated-measures ANOVAs. Relative to normal AS, active AS increased meanSD of all joint angles, {lambda}max of frontal plane hip and ankle angles, and SaEn of sagittal plane ankle angles. Active AS, however, did not affect {lambda}max or SaEn of trunk or pelvis angles. LLA increased meanSD of sagittal plane joint angles, {lambda}max of Euclidean norm trunk angle and of lower limb joint angles, and SaEn of ankle dorsiflexion/ plantarflexion, but decreased SaEn of tridimensional trunk angles and hip rotation in the slower moving leg. Alterations in lower limb variability with active AS and LLA suggest that young adults actively exploit their lower limb redundancies to maintain gait. This appears to preserve trunk stability and regularity during active AS but not during LLA.

bioengineering↗

bioRxiv2021

Exosomal transmission of α-synuclein initiates Parkinson's disease-like pathology

The intercellular transmission of -synuclein is proposed to be involved in the pathogenesis of Parkinsons disease (PD)1. Supporting this transmission hypothesis, -synuclein has been identified to act as a prion2 and has been found in cerebrospinal fluid (CSF), blood, and saliva3. However, the mechanism required to initiate the pathogenic spread of -synuclein in the body that results in PD remains unclear. Here we identify a mechanism for the loading of -synuclein into exosomes, resulting in prion-like transmission that is mediated by the ubiquitin ligase activator, Ndfip1. Risk factors associated with PD, including metal toxicity, lysosome dysfunction and pesticide exposure,4 stimulate the upregulation of Ndfip1 and increase the loading of -synuclein into exosomes. We used this pathway to promote the loading of endogenous -synuclein into exosomes, that when intranasally delivered to either wild type or M83 transgenic mice, resulted in Parkinsons-like pathology including motor impairments and brain amyloids. Recipient cells require -synuclein for pathogenesis, as delivery of exosomes containing -synuclein to Snca knockout mice did not generate brain amyloids or Parkinsons-like motor impairments. Our results demonstrate a novel mechanism to initiate the prion-like spread of -synuclein in exosomes, following exposure to risk factors for PD.

neuroscience↗

bioRxiv2021

Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a global pandemic. Safe and effective COVID-19 vaccines are now available, including mRNA-1273, which has shown 94% efficacy in prevention of symptomatic COVID-19 disease. However, the emergence of SARS-CoV-2 variants has led to concerns of viral escape from vaccine-induced immunity. Several variants have shown decreased susceptibility to neutralization by vaccine-induced immunity, most notably B.1.351 (Beta), although the overall impact on vaccine efficacy remains to be determined. Here, we present the initial evaluation in mice of 2 updated mRNA vaccines designed to target SARS-CoV-2 variants: (1) monovalent mRNA-1273.351 encodes for the spike protein found in B.1.351 and (2) mRNA-1273.211 comprising a 1:1 mix of mRNA-1273 and mRNA-1273.351. Both vaccines were evaluated as a 2-dose primary series in mice; mRNA-1273.351 was also evaluated as a booster dose in animals previously vaccinated with mRNA-1273. The results demonstrated that a primary vaccination series of mRNA-1273.351 was effective at increasing neutralizing antibody titers against B.1.351, while mRNA-1273.211 was effective at providing broad cross-variant neutralization. A third (booster) dose of mRNA-1273.351 significantly increased both wild-type and B.1.351-specific neutralization titers. Both mRNA-1273.351 and mRNA-1273.211 are being evaluated in pre-clinical challenge and clinical studies.

microbiology↗

bioRxiv2020

Tasmanian devil facial tumour-derived extracellular vesicles reveal mesenchymal transition markers and adhesion molecules related to metastasis.

Tasmanian devils are threatened with extinction by Devil Facial Tumor Disease (DFTD), which consists of two genetically independent transmissible cancers (DFT1 and DFT2). Both cancers typically cause death due to metastases. However, the mechanisms underpinning DFTD metastasis are not well understood. The nano-sized, membrane-enclosed extracellular vesicles (EVs) released by cancer cells have been implicated in metastasis, thus EVs may yield insights into DFTD metastasis. Here, we characterized EVs derived from cultured DFT1, DFT2, and devil fibroblast cells. The proteome of EVs was determined using data independent acquisition mass spectrometry and an in-house spectral library of >1,500 proteins. Relative to EVs from fibroblast cells, EVs from both DFT1 and DFT2 cell lines expressed higher levels of proteins associated with cell adhesion and focal adhesion functions. Furthermore, hallmark proteins of epithelial mesenchymal transition, which are associated with increased metastatic features in some cancers, were enriched in DFT2 EVs relative to DFT1 EVs, suggesting differential aggressiveness between the cancers and a target for novel differential diagnosis biomarkers. This first EV-based investigation of DFTD increases our understanding of the cancers EVs and their possible involvement in the metastatic process. As EVs are found in body fluids, these results offer potential for non-invasive biomarkers for DFTD.

cancer biology↗

bioRxiv2020

Low immunogenicity of malaria pre-erythrocytic stages can be overcome by vaccination

Vaccine discovery and development critically depends on predictive assays, which prioritise protective antigens. Immunogenicity is considered one important criterion for progression of candidate vaccines to further clinical evaluation, including phase I/II trials. Here, we tested this assumption in an infection and vaccination model for malaria pre-erythrocytic stages. We engineered Plasmodium berghei parasites that harbour a well-characterised epitope for stimulation of CD8+ T cells either as an antigen in the circumsporozoite protein (CSP), the surface coat protein of extracellular sporozoites or in the upregulated in sporozoites 4 (UIS4), a major protein associated with the parasitophorous vacuole membrane (PVM) that surrounds the intracellular exo-erythrocytic forms (EEF). We show that the antigen origin results in profound differences in immunogenicity with a sporozoite antigen eliciting robust and superior antigen-specific CD8+ T cell responses, whilst an EEF antigen evokes poor responses. However, despite their contrasting immunogenic properties, both sporozoite and EEF antigens gain access to antigen presentation pathways in hepatocytes, as recognition and targeting by vaccine-induced, antigen-specific effector CD8+ T cells results in high levels of protection when targeting both antigens. Our study is the first demonstration that poor immunogenicity of EEF antigens does not preclude their susceptibility to antigen-specific CD8+ T cell killing. Our findings that antigen immunogenicity is an inadequate predictor of vaccine susceptibility have wide-ranging implications on antigen prioritisation for the design and testing of next-generation pre-erythrocytic malaria vaccines.

immunology↗

bioRxiv2020

Characterization of Brain-Derived Extracellular Vesicle Lipids in Alzheimer's Disease

Lipid dyshomeostasis is associated with the most common form of dementia, Alzheimers disease (AD). Substantial progress has been made in identifying positron emission tomography (PET) and cerebrospinal fluid (CSF) biomarkers for AD, but they have limited use as front-line, non-invasive diagnostic tools. Small extracellular vesicles (EVs) are released by all cell types and contain an enriched subset of their parental cell molecular composition, including lipids. EVs are released from the brain into the periphery, providing a potential source of tissue and disease specific lipid biomarkers. However, the EV lipidome of the central nervous system (CNS) is currently unknown and the potential of brain-derived EVs (BDEVs) to inform on lipid dyshomeostasis in AD remains unclear. The aim of this study was to reveal the lipid composition of BDEVs in human frontal cortex tissue, and to determine whether BDEVs in AD have altered lipid profiles compared to age-matched neurological controls (NC). Here, using semi-quantitative mass spectrometry, we describe the BDEV lipidome, covering 4 lipid categories, 17 lipid classes and 692 lipid molecules. Frontal cortex-derived BDEVs were enriched in glycerophosphoserine (PS) lipids, a characteristic of small EVs. Here we report that BDEVs are enriched in ether-containing PS lipids. A novel finding that further establishes ether lipids as a feature of EVs. While no significant changes were detected in the frontal cortex in AD, the lipid profile of the BDEVs from this tissue exhibited disease related differences. AD BDEVs had altered glycerophospholipid (GP) and sphingolipid (SP) levels, specifically increased plasmalogen glycerophosphoethanolamine (PE-P) and decreased polyunsaturated fatty acyl containing lipids (PUFAs), and altered amide-linked acyl chain content in sphingomyelin (SM) and ceramide (Cer) lipids relative to vesicles from neurological control subjects. The most prominent alteration being a two-fold decrease in lipid species containing docosahexaenoic acid (DHA). The in-depth lipidome analysis provided in this study highlights the advantage of EVs over more complex tissues for improved detection of dysregulated lipids that may serve as potential biomarkers in the periphery.

molecular biology↗

bioRxiv2020

Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis

In many freshwater habitats, green algae form intracellular symbioses with a variety of heterotrophic host taxa including several species of freshwater sponge. These sponges perform important ecological roles in their habitats, and the poriferan:green algae partnerships offers unique opportunities to study the evolutionary origins and ecological persistence of endosymbioses. We examined the association between Ephydatia muelleri and its chlorophyte partner to identify features of host cellular and genetic responses to the presence of intracellular algal partners. Chlorella-like green algal symbionts were isolated from field-collected adult E. muelleri tissue harboring algae. The sponge-derived algae were successfully cultured and subsequently used to reinfect aposymbiotic E. muelleri tissue. We used confocal microscopy to follow the fate of the sponge-derived algae after inoculating algae-free E. muelleri grown from gemmules to show temporal patterns of symbiont location within host tissue. We also infected aposymbiotic E. muelleri with sponge-derived algae, and performed RNASeq to study differential expression patterns in the host relative to symbiotic states. We compare and contrast our findings with work in other systems (e.g., endosymbiotic Hydra) to explore possible conserved evolutionary pathways that may lead to stable mutualistic endosymbioses. Our work demonstrates that freshwater sponges offer many tractable qualities to study features of intracellular occupancy and thus meet criteria desired for a model system.

evolutionary biology↗

bioRxiv2020

Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells

Sickle cell disease (SCD), a group of inherited blood disorders with significant morbidity and early mortality, affects a sizeable global demographic largely of African and Indian descent. It is manifested in a mutated form of hemoglobin that distorts the red blood cells into a characteristic sickle shape with altered biophysical properties. Sickle red blood cells (sRBCs) show heightened adhesive interactions with inflamed endothelium, triggering obstruction of blood vessels and painful vaso-occlusive crisis events. Numerous studies have reported microfluidic-assay-based disease monitoring tools which rely on quantifying adhesion characteristics of adhered sRBCs from high resolution channel images. The current workflow for analyzing images from these assays relies on manual cell counting and detailed morphological characterization by a specially trained worker, which is time and labor intensive. Moreover manual counts by different individuals are prone to artifacts due to user bias. We present here a standardized and reproducible image analysis workflow designed to tackle these issues, using a two part deep neural network architecture that works in tandem for automatic, fast and reliable segmentation and classification into subtypes of adhered cell images. Our training utilized an exhaustive data set of images generated by the SCD BioChip, a microfluidic assay which injects clinical whole blood samples into protein-functionalized microchannels, mimicking physiological conditions in the microvasculature. The automated image analysis performs robustly in comparison to human classification: accuracies were similar to or better than those of the trained personnel, while the overall analysis time was improved by two orders of magnitude.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2020

Arrhythmogenesis as the failure of repolarization

Contemporary theories of cardiac fibrillation typically rely on the emergence of rotors to explain the transition from regular sinus rhythm to disordered electrophysiological activity. How those rotors spontaneously arise in the absence of re-entrant anatomical circuits is not fully understood. Here we propose a novel mechanism where arrhythmias are initiated by cardiac cells that fail to repolarize following a normal heartbeat. Those cells subsequently act as a focal ectopic source that drive the ensuing fibrillation. We used a simple computational model to investigate the impact of such cells in both homogeneous and heterogeneous excitable media. We found that heterogeneous media can tolerate a surprisingly large number of abnormal cells and still support normal rhythmic activity. At a critical limit the medium becomes chronically arrhythmogenic. Numerical analysis revealed that the critical threshold for arrhythmogenesis depends on both the strength of the coupling between cells and the extent to which the abnormal cells resist repolarization. Arrhythmogenesis was also found to emerge first at tissue boundaries where cells naturally have fewer neighbors to influence their behavior. These findings may explain why atrial fibrillation typically originates from the cuff of the pulmonary vein.Author summary Cardiac fibrillation is a medical condition where normal heart function is compromised as electrical activity becomes disordered. How fibrillation arises spontaneously is not fully understood. It is generally thought to be triggered by premature depolarization of the cardiac action potential in one or more cells. Those premature beats, known as early-afterdepolarizations, subsequently initiate a self-sustaining rotor in the otherwise normal heart tissue. In this study, we propose an alternative mechanism whereby arrhythmias are initiated by cardiac cells that fail to repolarize of their own accord but still operate normally when embedded in functional heart tissue. We find that such cells can act as focal ectopic sources under appropriate conditions of inter-cellular coupling. Moreover, cells on natural tissue boundaries are more susceptible to arrhythmia because they are coupled to fewer cells. This may explain why the pulmonary vein is often implicated as a source of atrial fibrillation.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2020

Influence of species and processing parameters on recovery and content of brain tissue-derived extracellular vesicles

Extracellular vesicles (EVs) are involved in a wide range of physiological and pathological processes by shuttling material out of and between cells. Tissue EVs may thus lend insights into disease mechanisms and also betray disease when released into easily accessed biological fluids. Since brain-derived EVs (bdEVs) and their cargo may serve as biomarkers of neurodegenerative diseases, we evaluated modifications to a published, rigorous protocol for separation of EVs from brain tissue and studied effects of processing variables on quantitative and qualitative outcomes. To this end, size exclusion chromatography (SEC) and sucrose density gradient ultracentrifugation were compared as final separation steps in protocols involving stepped ultracentrifugation. bdEVs were separated from brain tissues of human, macaque, and mouse. Effects of tissue perfusion and a model of post-mortem interval (PMI) before final bdEV separation were probed. MISEV2018-compliant EV characterization was performed, and both small RNA and protein profiling were done. We conclude that the modified, SEC-employing protocol achieves EV separation efficiency roughly similar to a protocol using gradient density ultracentrifugation, while decreasing operator time and, potentially, variability. The protocol appears to yield bdEVs of higher purity for human tissues compared with those of macaque and, especially, mouse, suggesting opportunities for optimization. Where possible, perfusion should be performed in animal models. The interval between death/tissue storage/processing and final bdEV separation can also affect bdEV populations and composition and should thus be recorded for rigorous reporting. Finally, different populations of EVs obtained through the modified method reported herein display characteristic RNA and protein content that hint at biomarker potential. To conclude, this study finds that the automatable and increasingly employed technique of SEC can be applied to tissue EV separation, and also reveals more about the importance of species-specific and technical considerations when working with tissue EVs. These results are expected to enhance the use of bdEVs in revealing and understanding brain disease.

neuroscience↗

bioRxiv2019

Misfolded α-synuclein causes hyperactive respiration without functional deficit in live neuronal cells

The misfolding and aggregation of the largely disordered protein, -synuclein, is a central pathogenic event that occurs in the synucleinopathies; a group of neurodegenerative disorders that includes Parkinsons disease. While there is a clear link between protein misfolding and neuronal vulnerability, the precise pathogenic mechanisms employed by disease-associated -synuclein are unresolved. Here, we studied the pathogenicity of misfolded -synuclein produced using the Protein Misfolding Cyclic Amplification (PMCA) assay. To do this, previous published methods were adapted to allow PMCA-induced protein fibrillization to occur under non-toxic conditions. Insight into potential intracellular targets of misfolded -synuclein was obtained using an unbiased lipid screen of 15 biologically relevant lipids that identified cardiolipin (CA) as a potential binding partner for PMCA-generated misfolded -synuclein. To investigate if such an interaction can impact the properties of -synuclein misfolding, protein fibrillization was carried out in the presence of the lipid. We show CA both accelerates the rate of -synuclein fibrillization and produces species that harbour enhanced resistance to proteolysis. Because CA is virtually exclusively expressed in the inner mitochondrial membrane, we then assessed the ability of these misfolded species to alter mitochondrial respiration in live non-transgenic SH-SY5Y neuroblastoma cells. Extensive analysis revealed misfolded -synuclein causes hyperactive mitochondrial respiration without causing any functional deficit. These data give strong support for the mitochondrion as a target for misfolded -synuclein and reveals persistent, hyperactive respiration as a potential up-stream pathogenic event associated with the synucleinopathies. Summary statementMisfolded -synuclein that was produced using the Protein Misfolding Cyclic Amplification (PMCA) assay was found to associate with cardiolipin and cause hyperactive respiration in neuronal cells.

neuroscience↗

bioRxiv2019

The effects of arm swing amplitude and lower-limb asymmetry on gait stability

Changes to arm swing and gait symmetry are symptomatic of several pathological gaits associated with reduced stability. The purpose of this study was to examine the relative contributions of arm swing and gait symmetry towards gait stability. We theorized that actively increasing arm swing would increase gait stability, while asymmetric walking would decrease gait stability. Fifteen healthy, young adults (23.4 {+/-} 2.8 yrs) walked on a split-belt treadmill under symmetric (1.2 m/s) and asymmetric walking (left/right, 5:4 speed ratio) with three different arm swings: held, normal, and active. Trunk local dynamic stability, inter-limb coordination, and spatiotemporal gait variability and symmetry were measured. Active arm swing resulted in improved local trunk stability, increased gait variability, and decreased inter-limb coordination (p < .013). The changes in local trunk stability and gait variability during active arm swing suggests that these metrics quantify fundamentally different aspects of stability and are not always comparable. Split-belt walking caused reduced local trunk stability, increased gait variability, and increased lower limb asymmetry (p < .003). However, the arm swing symmetry was unaffected by gait asymmetry, this suggests that deficits in gait stability in pathological gaits may be linked to increases in gait asymmetry rather than increases in arm swing asymmetry.

neuroscience↗

bioRxiv2019

The functional landscape of the human phosphoproteome

Protein phosphorylation is a key post-translational modification regulating protein function in almost all cellular processes. While tens of thousands of phosphorylation sites have been identified in human cells to date, the extent and functional importance of the phosphoproteome remains largely unknown. Here, we have analyzed 6,801 publicly available phospho-enriched mass spectrometry proteomics experiments, creating a state-of-the-art phosphoproteome containing 119,809 human phosphosites. To prioritize functional sites, 59 features indicative of proteomic, structural, regulatory or evolutionary relevance were integrated into a single functional score using machine learning. We demonstrate how this prioritization identifies regulatory phosphosites across different molecular mechanisms and pinpoint genetic susceptibilities at a genomic scale. Several novel regulatory phosphosites were experimentally validated including a role in neuronal differentiation for phosphosites present in the SWI/SNF SMARCC2 complex member. The scored reference phosphoproteome and its annotations identify the most relevant phosphorylations for a given process or disease addressing a major bottleneck in cell signaling studies.

genomics↗