Biology subjects

Bishop, C.

Publications and source records attributed to Bishop, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Levodopa induced dyskinesia severity is linked to distinct microstructural alterations in nigrostriatal and brainwide neural circuits

Dopaminergic replacement therapy via L-DOPA is the major medical therapy for Parkinsons Disease. Long-term L-DOPA administration is known to cause dyskinetic movements, L-DOPA Induced Dyskinesia (LID). It remains unclear if the LID related, maladaptive changes in brain structure/function are localized to neural circuits within the nigrostriatal DA system or have brainwide impact. We employed multi-shell diffusion magnetic resonance imaging and correlational tractography to investigate structural brain networks associated with daily administration of L-DOPA and the development of LID in the unilateral 6-hydroxydopamine rat model. 53% of rats receiving L-DOPA therapy developed severe LID. Tractography found brainwide statistical maps positively and negatively associated with LID severity highlighted by bilateral neural circuits contained in the lesioned nigrostriatal system as well as others including the cerebellum and prefrontal cortex. These results suggest that systemic dysfuntion in brainwide neural circuits forms the mechanistic basis the maladaptive changes underlying LID.

neuroscience↗

bioRxiv2026

Temporal stasis in three facets of biodiversity reveals mechanisms of community assembly across elevation gradients

Understanding spatial and temporal variation in community composition is central to protecting and monitoring biodiversity. Similarity in the composition of two communities decreases along spatial and temporal gradients, a relationship known as distance decay. Comparing distance-decay relationships across taxonomic, functional, and bioclimatic facets of diversity provides a means of interrogating niche-based versus neutral influences on community assembly. Furthermore, the context in which these facets yield overlapping or complementary information about global change impacts remains poorly understood. In this study, we examined spatiotemporal distance-decay relationships for taxonomic, functional, and bioclimatic facets of alpine plant diversity leveraging elevation gradients on five peaks in the White Mountains, California, USA, sampled at 3-4 time points between 2007 and 2024. Using multivariate Bayesian beta regression models, we estimated the slopes of elevation distance decay over multiple surveys and across taxonomic, functional and bioclimatic diversity to understand how spatial distance-decay relationships are changing through time and across different facets of diversity. We found strong spatial distance decay of taxonomic similarity across all peaks, with the highest elevation peak showing the strongest decay. Functional and bioclimatic similarities decayed more weakly than taxonomic similarity, suggesting environmental filtering shapes trait and niche distributions. Critically, spatial decay patterns showed no temporal signal across facets of diversity, indicating community stasis rather than biotic homogenization or differentiation. This study adds further evidence that xeric alpine plant communities are resisting climate change impacts through time.

ecology↗

bioRxiv2026

Physical contact reveals a hidden layer of cortical architecture

Neurons interact at synapses, but they also communicate through physical contact and proximity, including diffusion, glia-mediated interactions, and ephaptic coupling. Standard connectomes map synapses, but cannot capture the full set of cell-cell contacts that can support these pathways. Here we extract contactomes from two large mouse visual cortex volumes at nanoscale resolution and quantify every cell-cell contact, the shared surface area of each contact, and the relationship between contact and synaptic connectivity. We find that contactomes are 5 - 10x denser than synaptic graphs, revealing that neurons physically contact a much larger set of potential neighbors than they synaptically connect to. We further find that most nearby potential neighbors are already in physical contact, indicating that local structural change would add few new candidate synaptic partners. Finally, we find that astrocytes form a single large syncytium-like network that spans the tissue and directly contacts nearly all neurons, and that glial processes lie within a micron or two of almost every synapse, indicating that synapses reside within a pervasive glia-shaped microenvironment. Together, these results show that physical contact forms a distinct layer of brain architecture that extends far beyond the synaptic connectome.

neuroscience↗

bioRxiv2026

Hunting for Helminths: short- and long-read shotgun metagenomics for parasite detection in faecal samples

Soil-transmitted helminths (STHs) pose significant challenges to public health in endemic areas, necessitating reliable methods for their detection. Shotgun metagenomics enables simultaneous detection of STHs and microbes in a sample without prior knowledge of what is present. However, validation of shotgun metagenomics with known infection intensity or across different sequencing platforms has not been carried out for eukaryote parasites including STHs, and false positives remain a pervasive issue. We validated shotgun metagenomics as a method of STH detection in faecal samples. Using the Strongyloides ratti laboratory model of a STH infection we investigated how analytical methods (nucleotide-nucleotide matching, nucleotide-protein matching, marker gene detection, mitochondrial mapping), infection intensity and sequencing technology (short-read vs. long-read) affects sensitivity and specificity of detection. S. ratti was accurately detected at a standard laboratory dose, but low intensity infections were more difficult to detect. Only mitochondrial sequence mapping was 100% accurate at identifying S. ratti with no false positives. Overall, short-read outperformed long-read sequencing methods. We applied the same analytical methods to human faecal samples with confirmed infections for at least one of four STHs. Mitochondrial sequence mapping was also the most effective method for detecting STHs in human faecal samples, detecting 100% of Necator americanus and 92% of Ascaris spp. infections, but could not reliably detect STHs where DNA levels are expected to be low or variable. In conclusion, mitochondrial mapping was the most effective method of detection for sensitivity and specificity in both the laboratory system and human faecal samples. Our findings indicate that shotgun metagenomics should be approached cautiously using validated methods, particularly when infection intensity or DNA levels are expected to be low. Author SummarySoil-transmitted helminths (STH) such as the parasite Strongyloides, are important gastrointestinal parasites of humans and livestock. Accurate methods of detection for diagnostics and monitoring are important to implement suitable control and treatment strategies. Here we validate a shotgun metagenomics approach, where all DNA in a sample is sequenced, for detecting STH in faecal samples using a Strongyloides laboratory model for infection. Strongyloides was reliability detected in faecal samples at higher infection levels, but mitochondrial genome mapping of the sequences was the only analytical method that reliably detected Strongyloides at lower infections levels. These results were reflected in stool samples from humans infected with STH, where mitochondrial mapping was also the most reliable method. However, species that were associated with low levels of parasite material or DNA in the faeces including Strongyloides stercoralis, were more difficult to detect. We compared two sequencing methods: short-read Illumina and long-read Oxford Nanopore Technologies, but short-read outperformed long-read shotgun metagenomics. Contamination of bacteria sequences in parasite genome assemblies was problematic for analysis and contributed to false positive results. Future work should focus on specific targeting of eukaryote DNA either at the laboratory or bioinformatic stage to improve STH detection further.

molecular biology↗

bioRxiv2025

Preservation of dopamine neurotransmission during nigrostriatal neuron loss in rat Parkinson model: evidence for increased dopamine signaling in substantia nigra

During progressive nigrostriatal neuron loss in Parkinsons disease (PD), compensatory mechanisms are thought to maintain dopamine (DA) signaling at levels sufficient to mitigate locomotor impairment prior to substantial neuron loss. Whereas increased DA turnover in striatum has been considered a keystone compensatory mechanism indicative of augmented DA signaling, recent work indicates that increased DA biosynthesis in substantia nigra (SN), not striatum, compensates for tyrosine hydroxylase (TH) protein and neuronal loss. To extend interrogation of compensatory mechanisms that augment DA signaling during nigrostriatal neuron loss, we contemporaneously evaluated extracellular DA against tissue DA levels and quantified TH protein in the striatum and SN. Our unilateral 6-hydroxydopamine (6-OHDA) lesion approach produces progressive neuronal loss between 7 and 28 days, enabling evaluation of multiple DA signaling components in striatum vs SN. Loss of TH was [~]90% in striatum and [~]70% in the SN by 7 days after lesion induction. However, whereas loss of tissue DA matched TH loss in striatum (>90%) on both days after lesion, tissue DA loss in SN occurred only at day 28 (36%), despite major TH loss by day 7. This preservation of nigral DA tissue levels during lesion progression was associated with increased extracellular DA in SN after K+-dependent depolarization in striatum, which was not evident in a sham-operation group at the same time, early after lesion induction, signifying a DA lesion-specific adaptation in SN. In contrast in the striatum, lesion abolished the robust increase in extracellular DA, as seen in the sham-operation group. Together, these results indicate compensatory mechanisms that augment nigrostriatal DA signaling are engaged in the SN, not striatum, during progressive nigrostriatal neuron loss.

neuroscience↗

bioRxiv2025

The efficacy and accuracy of ribosomal RNA depletion methods

The depletion of ribosomal RNA (rRNA) is a critical step in RNA-sequence analyses, used to enhance the detection of non-rRNA molecules, such as messenger RNAs and non-coding RNAs. However, the efficiency and potential biases introduced by different rRNA depletion methods remain poorly characterized. Here, we evaluated three commercially available rRNA depletion kits - QIAseq FastSelect, riboPOOL, Zymo-Seq RiboFree - for their performance with the parasitic nematode Strongyloides ratti. We assessed the kits efficiency in rRNA removal, the recovery of expressed genes and transposable elements, and the detection of spliced leader sequences and genes operonic organization. Zymo-Seq demonstrated the highest sensitivity and minimal bias in a measure of gene expression, while QIAseq showed the least rRNA depletion and significant differential expression biases. Our findings underscore the importance of empirical validation of rRNA depletion methods, particularly for parasites and non-model organisms, and we suggest that Zymo-Seq as the optimal choice for S. ratti and related nematodes.

genomics↗

bioRxiv2025

Local graph-motif features improve gene interaction network prediction

Gene interaction networks specify how genes interact to produce an organisms phenotype. These networks are often incomplete due to absent or unobserved information. Predicting these missing links is critical for many applications, including genome-wide association studies and phenotype prediction. Efforts have previously applied graph neural networks (GNNs) to this missing-link prediction problem, but these techniques too have limitations when the sparsity of the networks is very high. Here, we apply a novel feature engineering technique that uses local graph motif incidence to enhance the feature set for variational graph autoencoders (VGAE). We compare the performance of our technique against state-of-the-art approaches, and then progressively hide more and more of the original graph edges. Our results show that VGAEs with our local-area motif prevalence (LAMP) features outperform state-of-the-art node embeddings for a wide range of missing edges on both a benchmark and a biological dataset. We also observe that this combined VGAE and LAMP technique has the potential to facilitate the search for novel genetic interactions in an experimental adaptive sampling context with far fewer samples. Improvements to gene interaction imputation can lower the barrier to new pharmaceutical and epidemiological discoveries by revealing hidden gene interactions that steer the development of potential drug targets.

bioinformatics↗

bioRxiv2024

Passage of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication

N-linked glycosylation of flavivirus envelope proteins is widely viewed as a requirement for optimal folding, processing and/or transit of envelope proteins, and the assembling virons, through the endoplasmic reticulum (ER) and Golgi. Herein we show that serial passage of ZIKVNatal in Rag1-/- mice generated two unique envelope glycan-deficient mutants, ZIKV-V153D and ZIKV-N154D, that, surprisingly, produced titers [~]1 to 2.6 logs higher than the glycosylated parental ZIKVNatal in Vero E6 cells and human brain organoids. RNA-Seq of infected organoids suggested that this increased replication fitness was associated with upregulation of the unfolded protein response (UPR). Cell death, cellular viral RNA and viral protein levels were not significantly affected, arguing that these glycan mutants enjoyed faster ER/Golgi folding, processing, assembly, transit, and virion egress, assisted by an upregulated UPR. Thus, ZIKV envelope N-linked glycosylation is not essential for promoting envelope folding, assembly and transit through the ER/Golgi, as aspartic acid (D) substitutions in the glycosylation motif achieve this with significantly greater efficiency. V153D and N154D mutants have not been employed in flavivirus envelope glycosylation studies. Instead, mutants such as N154A have been used, which may impart unfavorable properties that have a greater impact than the loss of the glycan. ZIKV-V153D and -N154D may avoid this by preserving the surface negative charge provided by the glycan moiety in the parental ZIKVNatal. In Ifnar-/- mice ZIKV-V153D and -N154D showed faster viremia onsets, but reduced viremic periods, than the parental ZIKVNatal, consistent with the contention that these glycans have evolved to delay neutralizing antibody activity. IMPORTANCEStudies seeking to understand the role(s) of N-linked glycosylation of flavivirus envelope proteins often introduce amino acid substitutions that disrupt the glycosylation motif, which in ZIKV has the sequence 153VNDT156. Unfortunately, such substitutions, for instance N154A, may themselves impart unfavorable properties on envelope that have a greater impact than the loss of the glycan moiety. Herein we describe two unique glycosylation motif mutants, ZIKV-V153D and -N154D that were positively selected during passage of ZIKVNatal in Rag1-/- mice. These N154 glycan-deficient viruses produced viral titers up to [~]400 fold higher than the parental ZIKVNatal in Vero cells and in human brain organoids. Such glycans are thus clearly not a requirement for optimal folding and trafficking of ZIKV envelope through the endoplasmic reticulum/Golgi. These results provide new insights into the molecular mechanisms underpinning viral fitness in vitro and in vivo, and also have implications for virus-like-particle vaccine design and production.

microbiology↗

bioRxiv2024

Oral cannabidiol administration in mice during pregnancy and lactation affects early postnatal body weight, fasting glucose, ingestive behavior, anxiety- and obsessive compulsive-like behaviors, and long-term object-memory in adult offspring in a sex-dependent manner

RationaleThe consequences of perinatal cannabidiol (CBD) exposure are severely understudied, but are important, given its widespread use and believed safety as a natural supplement. ObjectiveThe objective of this study was to test the health, metabolic, and behavioral consequences of perinatal CBD exposure on dams and their offspring raised to adult. MethodsPrimiparous female C57BL/6J mice were orally administered 100 mg/kg CBD in strawberry jam to expose offspring during gestation, lactation, or both using a cross-fostering design. Adult offspring were metabolically profiled using indirect calorimetry and intraperitoneal glucose tolerance testing. Adults were behaviorally phenotyped, video recorded, and mouse position tracked using DeepLabCut. ResultsCBD was detected in maternal plasma using LC-MS 10-min post consumption (34.2 {+/-} 1.7 ng/ul) and peaked within 30 min (371.0 {+/-} 34.0 ng/ul). Fetal exposure to CBD significantly decreased survival of the pups, and decreased male postnatal development, but did not alter litter size, maternal body weight or pup birth weight. We observed many sex-dependent effects of perinatal CBD exposure. Exposure to CBD during gestation and lactation increased meal size, caloric intake, and respiratory exchange ratio for adult male offspring, while exposure during lactation decreased fasting glucose, but had no effect on clearance. Adult female offspring exposed to CBD during lactation showed increased drink size. Perinatal CBD exposure increased obsessive compulsive- and decreased anxiety-like behaviors (marble burying, light-dark box, elevated-plus maze) in female mice, decreased long-term object memory in male mice, and had no effect on attention tasks for either sex. ConclusionsWe conclude that orally-administered CBD during pregnancy affects behavior and metabolism in a sex-dependent manner, and mice are differentially sensitive to exposure during gestation vs. lactation, or both. Because long-term changes are observed following perinatal exposure to the drug, and exposure significantly decreases survival to weaning, more research during development is warranted. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/602955v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1a9341dorg.highwire.dtl.DTLVardef@19c7356org.highwire.dtl.DTLVardef@5833baorg.highwire.dtl.DTLVardef@ac153c_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIMice can be trained to orally consume CBD using strawberry jam as the vehicle. C_LIO_LICBD administration to pregnant dams decreases pup survival to weaning age without significantly affecting maternal behavior. C_LIO_LIPerinatal CBD exposure decreases developmental body weight in males. C_LIO_LIGestational or lactational CBD increases the respiratory exchange ratio (RER), increases mean meal and drink size, and reduces fasting glucose in a sex-dependent manner. C_LIO_LICBD increases obsessive-compulsive like behavior in adult offspring, which could be eliminated in females by cross-fostering to a drug-free dam. C_LIO_LIPerinatal CBD selectively decreases anxiety-like behavior in females and decreases long-term object memory in males. C_LI

neuroscience↗

bioRxiv2024

EM-Compressor: Electron Microscopy Image Compression in Connectomics with Variational Autoencoders

The ongoing pursuit to map detailed brain structures at high resolution using electron microscopy (EM) has led to advancements in imaging that enable the generation of connectomic volumes that have reached the petabyte scale and are soon expected to reach the exascale for whole mouse brain collections. To tackle the high costs of managing these large-scale datasets, we have developed a data compression approach employing Variational Autoencoders (VAEs) to significantly reduce data storage requirements. Due to their ability to capture the complex patterns of EM images, our VAE models notably decrease data size while carefully preserving important image features pertinent to connectomics-based image analysis. Through a comprehensive study using human EM volumes (H01 dataset), we demonstrate how our approach can reduce data to as little as 1/128th of the original size without significantly compromising the ability to subsequently segment the data, outperforming standard data size reduction methods. This performance suggests that this method can greatly alleviate requirements for data management for connectomics applications, and enable more efficient data access and sharing. Additionally, we developed a cloud-based application named EM-Compressor on top of this work to enable on-thefly interactive visualization: https://em-compressor-demonstration.s3.amazonaws.com/EM-Compressor+App.mp4.

neuroscience↗

bioRxiv2024

PTEN Regulates Myofibroblast Activation in Valvular Interstitials Cells based on Subcellular Localization

Aortic valve stenosis (AVS) is characterized by altered mechanics of the valve leaflets, which disrupts blood flow through the aorta and can cause left ventricle hypotrophy. These changes in the valve tissue result in activation of resident valvular interstitial cells (VICs) into myofibroblasts, which have increased levels of SMA in their stress fibers. The persistence of VIC myofibroblast activation is a hallmark of AVS. In recent years, the tumor suppressor gene phosphatase and tensin homolog (PTEN) has emerged as an important player in the regulation of fibrosis in various tissues (e.g., lung, skin), which motivated us to investigate PTEN as a potential protective factor against matrix-induced myofibroblast activation in VICs. In aortic valve samples from humans, we found high levels of PTEN in healthy tissue and low levels of PTEN in diseased tissue. Then, using pharmacological inducers to treat VIC cultures, we observed PTEN overexpression prevented stiffness-induced myofibroblast activation, whereas genetic and pharmacological inhibition of PTEN further activated myofibroblasts. We also observed increased nuclear PTEN localization in VICs cultured on stiff matrices, and nuclear PTEN also correlated with smaller nuclei, altered expression of histones and a quiescent fibroblast phenotype. Together, these results suggest that PTEN not only suppresses VIC activation, but functions to promote quiescence, and could serve as a potential pharmacological target for the treatment of AVS.

cell biology↗

bioRxiv2024

Harnessing defective interfering particles and lipid nanoparticles for effective delivery of an anti-dengue virus RNA therapy

Presently, no approved antiviral drug targets dengue virus (DENV) infection. Treatment mainly relies on supportive measures, while DENV vaccines efficacy varies based on factors like vaccine type, circulating DENV serotypes and vaccinated population. This study explores using defective interfering particles (DIPs) and lipid nanoparticles (LNPs) to deliver an anti-DENV defective interfering RNA, known as DI290. Results showed that both DIPs and DI290 loaded LNPs (LNP-290) effectively suppressed DENV infection in human primary monocyte-derived macrophages (MDMs), THP-1 macrophages and human fibroblasts, representing cell types naturally targeted by DENV. Furthermore, LNP-290 demonstrated >log10 inhibition of DENV viral loads in IFNAR-deficient mice, which lack functional type I interferon (IFN) receptors. DI290-mediated inhibition was also effective in IFN regulatory factor 3 and 7 double knockout mice. RNA-Seq data from LNP-treated C57BL/6J mice, IFNAR-deficient mice and human MDMs treated with LNPs or DENV DIPs illustrated DI290 treatment heightened IFN responses, particularly IFN{gamma}, as well as IFN/{beta} and IFN{lambda}. DI290 thus induces a broad range of IFN responses, with IFN{gamma} and IFN{lambda} providing anti-viral activity when IFN/{beta} responses are absent. Mice administered LNP-290 also did not manifest acute overt clinical signs. In summary, these experiments suggest DI290s potential as a therapeutic approach for combating DENV infection.

microbiology↗

bioRxiv2024

Rostral Pedunculopontine Nucleus Infusion of M4 Positive Allosteric Modulator VU0467154 Augments L-DOPA Effects in Hemiparkinsonian Rats

Standard treatment for Parkinsons disease (PD) is dopamine replacement therapy with L-DOPA. However, chronic treatment often results in abnormal involuntary movements called L-DOPA-induced dyskinesia (LID). Prior evidence indicates that heightened striatal cholinergic tone may contribute to LID. Restoring cholinergic inhibition by targeting the inhibitory M4 muscarinic acetylcholine (ACh) receptor (M4) reduces LID in preclinical models. Although intrinsic striatal sources of ACh have been considered for their role in LID, extrinsic sources of ACh such as the pedunculopontine nucleus (PPN) have not been well investigated for their role in LID. Therefore, the current study employed hemiparkinsonian Long-Evans rats with a PPN-targeted cannula ipsilateral to 6-OHDA lesion. Following chronic treatment with L-DOPA, we examined the effect of local unilateral PPN infusion of M4 PAM VU0467154 on LID, motor performance, and c-fos expression within the PPN. It was expected that PPN infusion of VU0467154 would reduce LID, reduce L-DOPAs motor benefit, and globally reduce c-fos expression in the PPN. Contrary to our expectations, PPN infusion of M4 PAM did not significantly affect LID severity. Furthermore, the group receiving M4 PAM showed slightly elevated motor improvement compared to L-DOPA, and decreased c-fos expression specifically in PPN cholinergic neurons. These results suggest that local PPN ACh dynamics differ from those of the striatum. Specifically, our results suggest that PPN cholinergic neurons may be a promising therapeutic target for augmenting L-DOPA-mediated motor benefit without increasing LID.

neuroscience↗

bioRxiv2023

A Novel Semi-automated Proofreading and Mesh Error Detection Pipeline for Neuron Extension

AO_SCPLOWBSTRACTC_SCPLOWThe immense scale and complexity of neuronal electron microscopy (EM) datasets pose significant challenges in data processing, validation, and interpretation, necessitating the development of efficient, automated, and scalable error-detection methodologies. This paper proposes a novel approach that employs mesh processing techniques to identify potential error locations near neuronal tips. Error detection at tips is a particularly important challenge since these errors usually indicate that many synapses are falsely split from their parent neuron, injuring the integrity of the connectomic reconstruction. Additionally, we draw implications and results from an implementation of this error detection in a semi-automated proofreading pipeline. Manual proofreading is a laborious, costly, and currently necessary method for identifying the errors in the machine learning based segmentation of neural tissue. This approach streamlines the process of proofreading by systematically highlighting areas likely to contain inaccuracies and guiding proofreaders towards potential continuations, accelerating the rate at which errors are corrected.

neuroscience↗

bioRxiv2023

Unanticipated interacting features of human gut-associated lymphoid tissues link microbiota, intestinal immunity and autoimmunity

Gut-associated lymphoid tissue (GALT) is organised lymphoid tissue that is chronically activated by the intestinal microbiota. It generates the IgA response that is critical for intestinal homeostasis. By iterative application of multiplexed technologies, we identify enrichment of double-negative 2 (DN2:CD27-IgD-CD21loCD11chi) B cells in GALT, where they comprise the majority of intraepithelial and subepithelial B cells. We show that DN2 B cells in GALT interact with DC in the sub-epithelial dome that express DNASE1L3 and microbicides. Unlike in mice, DNASE1L3 in humans does not associate with apoptotic debris, but is located between sampled bacteria and host tissue where it is co-expressed with C1Q, consistent with management of bacterial debris. Thus we demonstrate that DN2 B cells that are otherwise associated with lupus nephritis, and DNASE1L3 and C1q that are lupus autoantigens, are microbiota-associated, interacting components of normal intestinal immunity.

immunology↗

bioRxiv2023

Moderate intensity aerobic exercise in 6-OHDA-lesioned rats alleviates established motor deficits and reduces neurofilament light and glial fibrillary acidic protein serum levels without increased striatal dopamine or tyrosine hydroxylase protein

BackgroundAlleviation of motor impairment by aerobic exercise (AE) in Parkinsons disease (PD) points to a CNS response that could be targeted by therapeutic approaches, but recovery of striatal dopamine (DA) or tyrosine hydroxylase (TH) has been inconsistent in rodent studies. ObjectiveTo increase translation of AE, 3 components were implemented into AE design to determine if recovery of established motor impairment, concomitant with >80% striatal DA and TH loss, was possible. We also evaluated if serum levels of neurofilament light (NfL) and glial fibrillary acidic protein (GFAP), blood-based biomarkers of disease severity in human PD, were affected. MethodsWe used a 6-OHDA hemiparkinson rat model featuring progressive nigrostriatal neuron loss over 28 days, with impaired forelimb use 7 days post-lesion, and hypokinesia onset 21 days post-lesion. After establishing forelimb use deficits, moderate intensity AE began 1-3 days later, 3x per week, for 40 min/session. Motor assessments were conducted weekly for 3 wks, followed by determination of striatal DA, TH protein and mRNA, and NfL and GFAP serum levels. ResultsSeven days after 6-OHDA lesion, recovery of depolarization-stimulated extracellular DA and DA tissue content was <10%, representing severity of DA loss in human PD, concomitant with 50% reduction in forelimb use. Despite severe DA loss, recovery of forelimb use deficits and alleviation of hypokinesia progression began after 2 weeks of AE and was maintained. Increased NfLand GFAP levels from lesion were reduced by AE. Despite these AE-driven changes, striatal DA tissue and TH protein levels were unaffected. ConclusionsThis proof-of-concept study shows AE, using exercise parameters within the capabilities most PD patients, promotes recovery of established motor deficits in a rodent PD model, concomitant with reduced levels of blood-based biomarkers associated with PD severity, without commensurate increase in striatal DA or TH protein.

neuroscience↗

bioRxiv2022

Trem2 Promotes Foamy Macrophage Lipid Uptake and Survival in Atherosclerosis

Atherosclerotic plaque formation is driven by the continued expansion of cholesterol loaded foamy macrophages within the arterial intima. Foamy macrophages are primarily derived from newly recruited monocytes, but factors regulating monocyte specification toward foamy macrophage differentiation and prolonged survival in plaque remain poorly understood. We used trajectory analysis of integrated single cell RNA-seq data, along with a genome-wide CRISPR screening approach to identify Triggering Receptor Expressed on Myeloid Cells 2 (Trem2) as a candidate regulator for foamy macrophage specification. Loss of Trem2 led to a reduced ability of foamy macrophages to take up additional oxidized low density lipoprotein (LDL) cholesterol in vitro. Competitive chimera experiments showed that Trem2-deficient macrophages were less competent to form foamy macrophages when competed against Trem2-sufficient macrophages in vivo. In addition, myeloid specific conditional deletion of Trem2 resulted in a dramatic attenuation of plaque progression, even when targeted in established atherosclerotic lesions. This was independent of changes in circulating inflammatory cytokines, monocyte recruitment, or serum cholesterol levels, but due to a reduction in plaque macrophage proliferation and enhanced cell death. Mechanistically, we link Trem2-deficient macrophages with an inability for cells to sense cholesterol loading and failure to upregulate efflux molecules. Accumulation of cholesterol in the endoplasmic reticulum enhanced activation of the ER-stress response that increased susceptibility for cholesterol-toxicity and cell death in foamy Trem2-deficient macrophages. Overall, this study identifies Trem2 as a regulator of foamy macrophage differentiation, atherosclerotic plaque growth, and as a putative therapeutic target for future intervention studies.

immunology↗

bioRxiv2021

Passage of SARS-CoV-2 in cells expressing human and mouse ACE2 selects for mouse-adapted and ACE2-independent viruses

Human ACE2 (hACE2) is the key cell attachment and entry receptor for SARS-CoV-2, with the original SARS-CoV-2 isolates unable to use mouse ACE2 (mACE2). Herein we describe a new system for generating mouse-adapted SARS-CoV-2 in vitro by serial passaging virus in co-cultures of cell lines expressing hACE2 and mACE2. Mouse-adapted viruses emerged with up to five amino acid changes in the spike protein, all of which have been seen in human isolates. Mouse-adapted viruses replicated to high titers in C57BL/6J mouse lungs and nasal turbinates, and caused severe lung histopathology. One mouse-adapted virus was also able to replicate efficiently in ACE2-negative cell lines, with ACE2-independent entry by SARS-CoV-2 representing a new biology for SARS-CoV-2 that has potential widespread implications for disease and intervention development.

microbiology↗