Biology subjects

Jackson, N.

Publications and source records attributed to Jackson, N..

36 records · Page 2Linked to original sources

bioRxiv2024

Formulation, Characterization, and in vivo Immunogenicity of Heat-Stabilized Dissolvable Microneedles Containing a Novel VLP Vaccine

Since its introduction, vaccination has heavily improved health outcomes. However, implementing vaccination efforts can be challenging, particularly in low and middle-income countries with warmer climates. Microneedle technology has been developed for its simple and relatively painless applications of vaccines. However, no microneedle vaccine has yet been approved by the FDA. A few hurdles must be overcome, including the need to evaluate the safety and biocompatibility of the polymer used to fabricate these microneedles. Additionally, it is important to demonstrate reliable immune responses comparable to or better than those achieved through traditional administration routes. Scalability in manufacturing and the ability to maintain vaccine potency during storage and transportation are also critical factors. In this study, we developed vaccine-loaded dissolvable microneedles that showed preclinical immunogenicity after storage in extreme conditions. We developed our microneedles using the conventional micromolding technique with polyacrylic acid (PAA) polymer, incorporating a novel virus-like particle (VLP) vaccine targeting arboviruses. We performed characterization studies on these microneedles to assess needle sharpness, skin insertion force, and VLP integrity. We also investigated the thermostability of the vaccine after storing the microneedles at elevated temperatures for approximately 140 days. Finally, we evaluated the immunogenicity of this vaccine in mice, comparing transdermal (microneedle) with intramuscular (hypodermic needle) administration. We successfully fabricated and characterized VLP-loaded microneedles that could penetrate the skin and maintain vaccine integrity even after exposure to extreme storage conditions. These microneedles also elicited robust and long-lasting antibody responses similar to those achieved with intramuscular administration.

bioengineering↗

bioRxiv2024

Structural Insights into the Assembly and Regulation of 2'-O RNA Methylation by SARS-CoV-2 nsp16/nsp10

2-O-ribose methylation of the first transcribed base (adenine or A1 in SARS-CoV-2) of viral RNA mimics the host RNAs and subverts the innate immune response. How nsp16, with its obligate partner nsp10, assembles on the 5-end of SARS-CoV-2 mRNA to methylate the A1 has not been fully understood. We present a [~] 2.4 [A] crystal structure of the heterotetrameric complex formed by the cooperative assembly of two nsp16/nsp10 heterodimers with one 10-mer Cap-1 RNA (product) bound to each. An aromatic zipper-like motif in nsp16 and the N-terminal regions of nsp10 and nsp16 orchestrate an oligomeric assembly for efficient methylation. The front catalytic pocket of nsp16 stabilizes the upstream portion of the RNA while the downstream RNA remains unresolved, likely due to its flexibility. An inverted nsp16 dimer extends the positively charged surface area for longer RNA to influence the catalysis. Additionally, a non-specific nucleotide-binding pocket on the backside of nsp16 plays a critical role in catalysis, further contributing to its enzymatic activity.

microbiology↗

bioRxiv2024

Replication Kinetics, Pathogenicity and Virus-induced Cellular Responses of Cattle-origin Influenza A(H5N1) Isolates from Texas, United States

The host range of HPAIV H5N1 was recently expanded to include ruminants, particularly dairy cattle in the United States. Shortly after, human H5N1 infection was reported in a dairy worker in Texas following exposure to infected cattle. Herein, we rescued the cattle-origin influenza A/bovine/Texas/24-029328-02/2024(H5N1, rHPbTX) and A/Texas/37/2024(H5N1, rHPhTX) viruses, identified in dairy cattle and human, respectively, and their low pathogenic forms, rLPbTX and rLPhTX, with monobasic HA cleavage sites. Intriguingly, rHPhTX replicated more efficiently than rHPbTX in mammalian and avian cells. Still, variations in the PA and NA proteins didnt affect their antiviral susceptibility to PA and NA inhibitors. Compared to rHPbTX and rLPbTX, the rHPhTX and rLPhTX exhibited higher pathogenicity and efficient replication in infected C57BL/6J mice. The lungs of rHPhTX-infected mice produced higher inflammatory cytokines/chemokines than rHPbTX-infected mice. Our results highlight potential risk of HPAIV H5N1 virus adaptation in human and/or dairy cattle during the current multistate/multispecies outbreak.

microbiology↗

bioRxiv2024

Cellular N-myristoyl transferases Are Required for Mammarenavirus Multiplication

The mammarenavirus matrix Z protein plays critical roles in virus assembly and cell egress, whereas heterotrimer complexes of a stable signal peptide (SSP) together with glycoprotein subunits GP1 and GP2, generated via co-and post-translational processing of the surface glycoprotein precursor GPC, form the spikes that decorate the virion surface and mediate virus cell entry via receptor-mediated endocytosis. The Z protein and SSP undergo N-terminal myristoylation by host cell N-myristoyltransferases (NMT1 and NMT2), and G2A mutations that prevent myristoylation of Z or SSP have been shown to affect Z mediated virus budding and GP2 mediated fusion activity required to complete the virus cell entry process. In the present work, we present evidence that the validated on-target specific pan NMT inhibitor DDD85464 exerts a potent antiviral activity against the prototypic mammarenavirus lymphocytic choriomeningitis virus (LCMV) that correlated with reduced Z budding activity and GP2 mediated fusion activity, as well as proteasome mediated degradation of the Z protein. The potent anti-mammarenaviral activity of DDD85646 was also observed with the hemorrhagic fever causing mammarenaviruses Junin (JUNV) and Lassa (LASV) viruses. Our results support exploration of NMT inhibition as a broad-spectrum antiviral against human pathogenic mammarenaviruses.

microbiology↗

bioRxiv2024

Multiple layers of innate immune response antagonism of SARS-CoV-2

Several SARS-CoV-2 proteins have been shown to counteract the host innate immune response, mostly using in vitro protein expression, which may not fully reflect their role in the context of viral infection. In addition, while each viral protein was characterized in a different experimental system, their relative contribution in immunosuppression remains unclear. Here we used a SARS-CoV-2 bacterial artificial chromosome with en passant mutagenesis to recover a panel of twelve infectious recombinant SARS-CoV-2 viruses, each with mutations in either NSP1, NSP2, NSP3, NSP6, NSP12, NSP13, NSP14, NSP15, NSP16, ORF3a, ORF6 or ORF8. We used the interferon-stimulated response element (ISRE)-driven luciferase assay in 293T-ACE2/TMPRSS2 cells to test the panel, demonstrating that mutations in many proteins, especially in NSP1 and NSP15, increased the type I interferon response relative to the parental wild-type virus. RNA-seq analysis of mutant-virus infected Calu-3 cells showed that the mutations in NSP1 or NSP15 lead to higher expression of multiple genes involved in innate immune response, cytokine-mediated signaling and regulation of lymphocyte proliferation. Furthermore, mutations in either NSP1 or NSP15 resulted in a greater maturation of human monocyte-derived dendritic cells in vitro. Infection of K18 hACE2 transgenic mice with either NSP1 or NSP15 mutated viruses demonstrated attentuated respiratory tract replication. Analysis of lung immune cells from infected mice by single-cell RNA-seq identified 15 populations of major myeloid and lymphoid cells with changes in the pattern of their activation associated with viral infection. The effects of mutations in NSP1 or NSP15 on these responses are consistent with differences in the immunosuppressive mechanisms utilized by the two proteins. Overall, these data demonstrate different and redundant mechanisms of innate immune antagonism by SARS-CoV-2 and suppression of activation of antigen presenting cells and T and B lymphocytes mediated by multiple viral proteins. AUTHOR SUMMARYThe mechanisms by which SARS-CoV-2 and its proteins modulate host immunity, specifically the interferon response, are still not clear. We generated twelve infectious SARS-CoV-2 viruses with mutations in individual proteins and demonstrated that many of them have interferon-antagonizing activity and immunosuppressive effects in human cells and in the K18 hACE mouse model of infection. We idemtified distinct and redundant mechanisms of immunosuppression of SARS-CoV-2 mediated by multiple individual viral proteins, with 9 out of the 12 tested proteins showing some immunosuppressive effect in at least one experimental system. The demonstrated immunosuppressive effects extend from the innate response to immune cells to pathologic changes in vivo. Importantly, this work shows, for the first time, a comparison of the effects of multiple viral proteins in the context of authentic viral infection, rather than in a surrogate system, and shows the relative contribution of each viral protein under identical experimental conditions. Overall, our data indicates that SARS-CoV-2 antagonizes multiple immune mechanisms, particularly type I interferon signaling, activation of innate immune cells and T and B lymphocyte functions with the greatest effects due to NSP1 and NSP15.

microbiology↗

bioRxiv2023

Activation of Protein Kinase R (PKR) Plays a Pro-Viral Role in Mammarenavirus Infected Cells

Many viruses, including mammarenaviruses, have evolved mechanisms to counteract different components of the host cell innate immunity, which is required to facilitate robust virus multiplication. The double strand (ds)RNA sensor protein kinase receptor (PKR) pathway plays a critical role in the cell antiviral response. Whether PKR can restrict the multiplication of the Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) and the mechanisms by which LCMV may counteract the antiviral functions of PKR have not yet been investigated. Here we present evidence that LCMV infection results in very limited levels of PKR activation, but LCMV multiplication is enhanced in the absence of PKR. In contrast, infection with a recombinant LCMV with a mutation affecting the 3-5 exonuclease (ExoN) activity of the viral nucleoprotein (NP) resulted in robust PKR activation in the absence of detectable levels of dsRNA, which was associated with severely restricted virus multiplication that was alleviated in the absence of PKR. However, pharmacological inhibition of PKR activation resulted in reduced levels of LCMV multiplication. These findings uncovered a complex role of the PKR pathway in LCMV-infected cells involving both pro-and anti- viral activities. IMPORTANCEAs with many other viruses, the prototypic Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) can interfere with the host cell innate immune response to infection, which includes the double strand (ds)RNA sensor protein kinase receptor (PKR) pathway. A detailed understanding of LCMV-PKR interactions can provide novel insights about mammarenavirus-host cell interactions and facilitate the development of effective antiviral strategies against human pathogenic mammarenaviruses. In the present work, we present evidence that LCMV multiplication is enhanced in PKR- deficient cells, but pharmacological inhibition of PKR activation unexpectedly resulted in severely restricted propagation of LCMV. Likewise, we document a robust PKR activation in LCMV-infected cells in the absence of detectable levels of dsRNA. Our findings have revealed a complex role of the PKR pathway during LCMV infection and uncovered the activation of PKR as a druggable target for the development of antiviral drugs against human pathogenic mammarenaviruses.

microbiology↗

bioRxiv2023

SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused millions of deaths since emerging in 2019. Innate immune antagonism by lethal CoVs such as SARS-CoV-2 is crucial for optimal replication and pathogenesis. The conserved nonstructural protein 15 (nsp15) endoribonuclease (EndoU) limits activation of double-stranded (ds)RNA-induced pathways, including interferon (IFN) signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L) during diverse CoV infections including murine coronavirus and Middle East respiratory syndrome (MERS)-CoV. To determine how nsp15 functions during SARS-CoV-2 infection, we constructed a mutant recombinant SARS-CoV-2 (nsp15mut) expressing a catalytically inactive nsp15. Infection with SARS-CoV-2 nsp15 mut led to increased activation of the IFN signaling and PKR pathways in lung-derived epithelial cell lines and primary nasal epithelial air-liquid interface (ALI) cultures as well as significant attenuation of replication in ALI cultures compared to wild-type (WT) virus. This replication defect was rescued when IFN signaling was inhibited with the Janus activated kinase (JAK) inhibitor ruxolitinib. Finally, to assess nsp15 function in the context of minimal (MERS-CoV) or moderate (SARS-CoV-2) innate immune induction, we compared infections with SARS-CoV-2 nsp15mut and previously described MERS-CoV nsp15 mutants. Inactivation of nsp15 had a more dramatic impact on MERS-CoV replication than SARS-CoV-2 in both Calu3 cells and nasal ALI cultures suggesting that SARS-CoV-2 can better tolerate innate immune responses. Taken together, SARS-CoV-2 nsp15 is a potent inhibitor of dsRNA-induced innate immune response and its antagonism of IFN signaling is necessary for optimal viral replication in primary nasal ALI culture. SIGNIFICANCESevere acute respiratory syndrome coronavirus (SARS-CoV)-2 causes a spectrum of respiratory disease ranging from asymptomatic infections to severe pneumonia and death. Innate immune responses during SARS-CoV-2 infection have been associated with clinical disease severity, with robust early interferon responses in the nasal epithelium reported to be protective. Thus, elucidating mechanisms through which SARS-CoV-2 induces and antagonizes host innate immune responses is crucial to understanding viral pathogenesis. CoVs encode various innate immune antagonists, including the conserved nonstructural protein 15 (nsp15) which contains an endoribonuclease (EndoU) domain. We demonstrate that SARS-CoV-2 EndoU is a crucial interferon antagonist, by providing further evidence for the role of the conserved CoV nsp15 in antagonizing innate immune activation, thereby optimizing CoV replication.

microbiology↗

bioRxiv2023

The SARS-CoV-2 Spike is a virulence determinant and plays a major role on the attenuated phenotype of Omicron virus in a feline model of infection

To assess the role of the Omicron BA.1 Spike (S) protein in the pathogenesis of the severe acute respiratory coronavirus 2 (SARS-CoV-2), we generated recombinant viruses harboring the S D614G mutation (rWA1-D614G) and the Omicron BA.1 S gene (rWA1-Omi-S) in the backbone of the ancestral SARS-CoV-2 WA1 strain genome. The recombinant viruses were characterized in vitro and in vivo. Viral entry, cell-cell fusion, viral plaque size, and viral replication kinetics of the rWA1-Omi-S virus were markedly impaired when compared to the rWA1-D614G virus, demonstrating a lower fusogenicity and ability to spread cell-to-cell of rWA1-Omi-S. To assess the contribution of the Omicron BA.1 S protein to SARS-CoV-2 pathogenesis the pathogenicity of rWA1-D614G and rWA1-Omi-S viruses were compared using a feline model of infection. While the rWA1-D614G-inoculated cats became lethargic and showed increased body temperatures on days 2 and 3 post-infection (pi), rWA1-Omi-S-inoculated cats remained subclinical and gained weight throughout the 14-day experimental period. Animals inoculated with rWA1-D614G presented higher levels of infectious virus shedding in nasal secretions, when compared to rWA1-Omi-S-inoculated animals. In addition, tissue replication of the rWA1-Omi-S was markedly reduced compared to the rWA1-D614G, as evidenced by lower in situ viral RNA and lower viral load in tissues on days 3 and 5 pi. Histologic examination of the nasal turbinate and lungs revealed intense inflammatory infiltration in rWA1-D614G-inoculated animals, whereas rWA1-Omi-S-inoculated cats presented only mild to modest inflammation. Together, these results demonstrate that the S protein is a major virulence determinant for SARS-CoV-2 playing a major role for the attenuated phenotype of the Omicron virus. Author summaryThe SARS-CoV-2 Omicron sublineage BA.1 spread rapidly across the globe in late 2021/early 2022. Experimental studies have shown an overall lower pathogenicity of Omicron BA.1 when compared to the ancestral SARS-CoV-2 lineage B.1 (D614G). Recently, we have demonstrated that the Omicron BA.1.1 variant presents lower pathogenicity when compared to D614G (B.1) lineage in a feline model of SARS-CoV-2 infection. There are over 50 mutations in the Omicron genome, of which more than two thirds are present in the S gene. To assess the role of the Omicron BA.1 S on virus pathogenesis, recombinant viruses harboring the S D614G mutation (rWA1-D614G) and the Omicron BA.1 Spike gene (rWA1-Omi-S) in the backbone of the ancestral SARS-CoV-2 WA1 were characterized in vitro and in vivo. While the Omicron BA.1 S gene results in early entry into cells, the rWA1-Omi-S presents impaired cell-cell spread and fusogenic activity. Inoculation of cats with the recombinant viruses revealed an attenuated phenotype of rWA1-Omi-S, demonstrating a critical role for S protein on the pathogenicity of SARS-CoV-2 and indicating that the Omi-S is a major determinant of the attenuated disease phenotype of Omicron strains.

microbiology↗

bioRxiv2023

Century-old chromatin architecture preserved with formaldehyde

Co-ordinated regulation or dysregulation of chromatin architecture underpins fundamental biological processes, such as embryonic development, disease, cellular programming and response to environmental stress. The dynamic and plastic nature of chromatin accessibility is a major driver of phenotypic diversity, but we know shockingly little about the temporal dynamics of chromatin reorganisation and almost nothing prior to the existence of flash-frozen specimens. Linking two disparate fields by their common use and application of the preservative formaldehyde, we present an approach to characterise chromatin architecture in formaldehyde-preserved specimens up to 117 years old. We characterise how over-fixation modulates but does not eliminate genome-wide patterns of differential chromatin accessibility. Our novel analytical approach identifies promoter regions enriched for gene ontology terms matching the tissue of origin, resulting in sex-specific and environment-dependent genome-wide profiles. Contrary to prevailing dogma, we show that over-fixation is essential for the successful recovery of historical chromatin architecture. Our methodological and analytical advances open the door to the first detailed and comprehensive view of the epigenetic past and reveal a new role for museum collections in understanding chromatin architecture dynamics over the last century.

genomics↗

bioRxiv2023

A network medicine approach to elucidate mechanisms underlying menopause-induced knee osteoarthritis

Post-menopausal women present with the highest incidence and morbidity of knee osteoarthritis (KOA), but no disease-modifying therapies are available. This treatment gap may be driven by the absence of menopause in preclinical studies, as rodents do not naturally maintain a menopausal phenotype. Here, we employed a chemically-induced menopause model to map the trajectory of KOA at the tissue and proteome levels and test therapeutics in silico. Middle-aged female mice were randomized to sesame oil (non-menopause) or 4-vinycyclohexene diepoxide (menopause) injections. Following comprehensive validation of our model, knees were collected across perimenopause and menopause for histology, and cartilage samples were micro-dissected for mass spectrometry proteomics. Menopause mice displayed aggravated cartilage degeneration and synovitis relative to non-menopause mice. An unbiased pathway analysis revealed progesterone as a predominant driver of pathological signaling cascades within the cartilage proteome. Network medicine-based analyses suggested that menopause induction amplifies chondrocyte senescence, actin cytoskeleton-based stress, and extracellular matrix disassembly. We then used in silico drug testing to evaluate how restoration of sex hormones impacted the cartilage network. The greatest restoration was observed with combined estradiol/progesterone treatment (i.e., hormone therapy), although in silico treatment with a senolytic drug also partially recovered the cartilage proteome. Taken together, our findings using a translatable female aging model demonstrate that menopausal aging induces progressive cartilage degeneration and amplifies age-related synovitis. These changes may be driven by a previously unappreciated role of progesterone loss and menopause-induced cellular senescence. Lastly, in silico treatment suggests an estradiol/progesterone cocktail or senolytics may attenuate menopause-induced cartilage pathology. One Sentence SummaryMenopause induces cartilage degradation, senescence, and extracellular matrix disassembly, while hormone therapy restores the cartilage proteome.

pathology↗

bioRxiv2022

PAF1 and FACT cooperate with MLL-AF4 to drive enhancer activity in leukemia

Aberrant enhancer activation has been identified as a key mechanism driving oncogene expression in many cancers. Here we use TOPmentation (Transcription factor-OPtimized ChIPmentation) to probe enhancer usage in primary MLL-rearranged acute lymphoblastic leukemia. We find that MLL-AF4, commonly held to promote transcription by binding to gene promoters, is also present at many active enhancers, where it assembles a complex of transcriptional co-activators normally found in the gene body. This includes DOT1L, ENL, PAF1, and a newly identified interaction with the histone chaperone FACT. By chemical degradation, we demonstrate that PAF1 and FACT are required for enhancer activity, including maintaining histone H3K27 acetylation, enhancer RNA transcription and enhancer-promoter interactions. This work identifies novel roles for PAF1 and FACT in enhancer function, and reveals an enhancer-targeting mechanism by which MLL-AF4 upregulates transcription, recruiting transcription machinery through a network of multivalent interactions to control enhancer activity and gene expression in acute leukemias.

molecular biology↗

bioRxiv2022

Protection from Omicron and other VOCs by Bivalent S-Trimer COVID-19 Vaccine

The Omicron variant of SARS-COV-2 (GISAID GRA clade [B.1.1.529, BA.1 and BA.2]) is now the single dominant Variant of Concern (VOC). The high number of mutations in the Omicron Spike (S) protein promotes humoral immunological escape. Although a third homologous boost with S, derived from the ancestral strain, was able to increase neutralizing antibody titers and breadth including to Omicron, the magnitude of virus neutralization could benefit from further optimization. Moreover, combining SARS-COV-2 strains as additional valences may address the current antigenicity range occupied by VOCs. Using Trimer-Tag platform we have previously demonstrated phase 3 efficacy and safety of a prototypic vaccine SCB-2019 in the SPECTRA trial and have submitted applications for licensure. Here, we successfully generated a bivalent vaccine candidate including both Ancestor and Omicron variant S-proteins. Preclinical studies demonstrate this SARS-CoV-2 bivalent S-Trimer subunit vaccine elicits high titers of neutralizing antibodies against all VOCs, with markedly enhanced Omicron specific neutralizing antibody responses.

immunology↗

bioRxiv2022

Reduced sensorimotor beta dynamics could represent a "slowed movement state" in healthy individuals

Beta oscillations (~13-30 Hz) recorded from the sensorimotor cortex have canonical amplitude changes during movement. Specifically, a movement-related beta decrease (MRBD) occurs before movement, and a post-movement beta rebound (PMBR) follows. We investigated how the MRBD and PMBR vary with movement speed. Individuals performed a task with blocks that generated longer reaction times (RTs) and shorter RTs (Slow and Fast blocks, respectively) while scalp-electroencephalography (EEG) was recorded. The timing of task events before movement was also modulated to generate blocks with certain and uncertain timing (Fixed and Varied blocks, respectively). Beta modulation was reduced in Slow blocks compared to Fast blocks (i.e., a less negative MRBD and less positive PMBR). For the movement certainty manipulation, we saw mixed behavioral and EEG results. Our primary findings align with previous work which has shown reduced movement-related beta modulation in patients with Parkinsons disease. We propose that a "slowed movement state", whether it is experimentally induced or a manifestation of Parkinsons disease bradykinesia, is represented through reduced beta dynamics. Altogether, the MRBD and PMBR may represent motor speed on a continuum with Parkinsons disease as an extreme example of slowed movement.

neuroscience↗

bioRxiv2021

The nematode worm C. elegans chooses between bacterial foods exactly as if maximizing economic utility

In value-based decision making, options are selected according to subjective values assigned by the individual to available goods and actions. Despite the importance of this faculty of the mind, the neural mechanisms of value assignments, and how choices are directed by them, remain obscure. To investigate this problem, we used a classic measure of utility maximization, the Generalized Axiom of Revealed Preference, to quantify internal consistency of food preferences in Caenorhabditis elegans, a nematode worm with a nervous system of only 302 neurons. Using a novel combination of microfluidics and electrophysiology, we found that C. elegans food choices fulfill the necessary and sufficient conditions for utility maximization, indicating that nematodes behave as if they maintain, and attempt to maximize, an underlying representation of subjective value. Food choices are well-fit by a utility function widely used to model human consumers. Moreover, as in many other animals, subjective values in C. elegans are learned, a process we find requires intact dopamine signaling. Differential responses of identified chemosensory neurons to foods with distinct growth potentials are amplified by prior consumption of these foods, suggesting that these neurons may be part of a value-assignment system. The demonstration of utility maximization in an organism with a very small nervous system sets a new lower bound on the computational requirements for utility maximization and offers the prospect of an essentially complete explanation of value-based decision making at single neuron resolution in this organism.

neuroscience↗

bioRxiv2020

Heightened β-adrenergic receptor function in the TgF344-AD rat model drives synaptic potentiation and supports learning and memory

The central noradrenergic (NA) system is critical for maintenance of attention, behavioral flexibility, spatial navigation, and learning and memory, those cognitive functions lost first in early Alzheimers disease (AD). In fact, the locus coeruleus (LC), the sole source of norepinephrine (NE) for >90% of the brain, is the first site of pathological tau accumulation in human AD with axon loss throughout forebrain, including hippocampus. The dentate gyrus (DG) is heavily innervated by LC-NA axons, where released norepinephrine (NE) acts on {beta}-adrenergic receptors (ARs) at excitatory synapses from entorhinal cortex (EC) to facilitate long-term synaptic plasticity and memory formation. These synapses dysfunction in early AD prior to cognitive impairment. In the TgF344-AD rat model, degeneration of LC-NA axons in hippocampus recapitulates human AD, providing a preclinical model to investigate synaptic and behavioral consequences. Using immunohistochemistry, Western blot analysis, and brain slice electrophysiology in 6-9 month old wild type and TgF344-AD rats, we discovered that loss of LC-NA axons co-insides with heightened {beta}-AR function at medial perforant path-dentate granule cell synapses (MPP-DCG) that is responsible for the increase in LTP magnitude at these synapses. Furthermore, novel object recognition is facilitated in TgF344-AD rats that requires {beta}-ARs, and pharmacological blockade of {beta}-ARs unmasks a deficit in extinction learning only in TgF344-AD rats, indicating a greater reliance on {beta}-ARs in both behaviors. Thus, a compensatory increase in {beta}-AR function during prodromal AD in TgF344-AD rats heightens synaptic plasticity and preserves some forms of learning and memory. Significance StatementThe locus coeruleus (LC), a brain region located in the brainstem which is responsible for attention and arousal, is damaged first by Alzheimers disease pathology. The LC sends axons to hippocampus where released norepinephrine (NE) modulates synaptic function required for learning and memory. How degeneration of LC axons and loss of NE in hippocampus in early AD impacts synaptic function and learning and memory is not well understood despite the importance of LC in cognitive function. We used a transgenic AD rat model with LC axon degeneration mimicking human AD and found that heightened function of {beta} adrenergic receptors in the dentate gyrus increased synaptic plasticity and preserved learning and memory in early stages of the disease.

neuroscience↗

bioRxiv2019

VETA: a Matlab toolbox for the collection and analysis of electromyography combined with transcranial magnetic stimulation

The combination of electromyography (EMG) and transcranial magnetic stimulation (TMS) offers a powerful non-invasive approach for investigating corticospinal excitability in both humans and animals. Acquiring and analyzing the data produced with this combination of tools requires overcoming multiple technical hurdles. Due in part to these technical hurdles, the field lacks standard routines for EMG data collection and analysis. This poses a problem for study replication and direct comparisons. Although software toolboxes already exist that perform either online EMG data visualization or offline analysis, there currently are no openly available toolboxes that flexibly perform both and also interface directly with peripheral EMG and TMS equipment. Here, we introduce Visualize EMG TMS Analyze (VETA), a MATLAB-based toolbox that supports simultaneous EMG data collection and visualization as well as automated offline processing and is specially tailored for use with motor TMS. The VETA toolbox enables the simultaneous recording of EMG, timed administration of TMS, and presentation of behavioral stimuli from a single computer. These tools also provide a streamlined analysis pipeline with interactive data visualization. Finally, VETA offers a standard EMG data format to facilitate data sharing and open science.

physiology↗

bioRxiv2019

Characteristics of Beta Waveform Shape in Parkinson's Disease Detected with Scalp Electroencephalography

Neural activity in the beta frequency range (13-30 Hz) is excessively synchronized in Parkinsons Disease (PD). Previous work using invasive intracranial recordings and non-invasive scalp electroencephalography (EEG) has shown that correlations between beta phase and broadband gamma amplitude (i.e., phase-amplitude coupling) are elevated in PD, perhaps a reflection of this synchrony. Recently, it has also been shown, in invasive human recordings, that nonsinusoidal features of beta oscillation shape also characterize PD. Here we show that these features of beta waveform shape also distinguish PD patients on and off medication using non-invasive recordings in a dataset of 15 PD patients with resting scalp EEG. Specifically, beta oscillations over sensorimotor electrodes in PD patients off medication had greater sharpness asymmetry and steepness asymmetry than on medication (sign rank, p=0.006, p=0.003 respectively). We also showed that beta oscillations over sensorimotor cortex most often had a canonical shape and that using this prototypical shape as an inclusion criterion increased the effect size of our findings. Together our findings suggest that novel ways of measuring beta synchrony that incorporate waveform shape could improve detection of PD pathophysiology in non-invasive recordings.

neuroscience↗

bioRxiv2018

A combined in silico, in vitro and clinical approach to characterise novel pathogenic missense variants in PRPF31 in retinitis pigmentosa

At least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31 and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localise to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood.\n\nIn this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T>A, p.Ile114Asn.\n\nThis work demonstrates how in silico modelling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.

genetics↗