Biology subjects

Cox, R.

Publications and source records attributed to Cox, R..

34 records · Page 2Linked to original sources

bioRxiv2021

4'-Fluorouridine is a broad-spectrum orally efficacious antiviral blocking respiratory syncytial virus and SARS-CoV-2 replication

The COVID-19 pandemic has underscored the critical need for broad-spectrum therapeutics against respiratory viruses. Respiratory syncytial virus (RSV) is a major threat to pediatric patients and the elderly. We describe 4-fluorouridine (4-FlU, EIDD-2749), a ribonucleoside analog that inhibits RSV, related RNA viruses, and SARS-CoV-2 with high selectivity index in cells and well-differentiated human airway epithelia. Polymerase inhibition in in vitro RdRP assays established for RSV and SARS-CoV-2 revealed transcriptional pauses at positions i or i+3/4 post-incorporation. Once-daily oral treatment was highly efficacious at 5 mg/kg in RSV-infected mice or 20 mg/kg in ferrets infected with SARS-CoV-2 WA1/2020 or variant-of-concern (VoC) isolate CA/2020, initiated 24 or 12 hours after infection, respectively. These properties define 4-FlU as a broad-spectrum candidate for the treatment of RSV, SARS-CoV-2 and related RNA virus infections. One-Sentence Summary4-Fluorouridine is an orally available ribonucleoside analog that efficiently treats RSV and SARS-CoV-2 infections in vivo.

microbiology↗

bioRxiv2021

Divergent epigenetic profiles from two differentially impacted wild populationsof estuarine cordgrass (Sporobolus alterniflorus)

The effects of urbanization on watershed ecosystems present critical challenges to modern survival. Organisms in urbanized areas experience high rates of evolutionary change, but genetic adaptation alone cannot mitigate the rapid and severe effects of urbanization on biodiversity. Highly resilient, foundation species are key to maintaining an ecosystems integrity in the face of urban stressors. However, the rapid collapse and disappearance of watershed ecosystems calls into question the extent to which we can rely on such species for their services. Our research investigates the molecular mechanisms by which the foundation ecosystems provider, Sporobolus alterniflorus, adapts to life in an urbanized environment. To elucidate these mechanisms, we quantified changes in global DNA methylation (% 5-mC) as a result of acute heat stress. Specimens from two differentially impacted populations across an urban to suburban geographical transect formed the basis of this study. These two populations of Sporobolus alterniflora exhibit inverse global DNA methylation patterns when exposed to the same acute heat stress. Our findings suggest that epigenetic mechanisms, such as DNA methylation, control rapid and transient adaptation, in the form of differential stress responses, to distinct environment challenges. Highlights for manuscript submissionO_LI{blacksquare} estuarine grasses native to the Bronx River, NY face stresses associated with low dissolved oxygen and urbanization C_LIO_LI{blacksquare} differentially impacted populations of estuarine grasses exhibit inverse global DNA methylation profiles in response to acute heat stress C_LIO_LI{blacksquare} DNA methylation may represent a mechanism by which plants transiently respond to environmental stressors, and this may represent a form of rapid adaptive evolution C_LIO_LI{blacksquare} stress priming by transgenerational epigenetic modification may enhance fitness in grasses native to the heavily impacted Bronx River estuary C_LI

plant biology↗

bioRxiv2020

Influences of time of day on generalization

Extracting shared structure across our experiences allows us to generalize our knowledge to novel contexts. How do different brain states influence this ability to generalize? Using a novel category learning paradigm, we assess the effect of both sleep and time of day on generalization that depends on the flexible integration of recent information. Counter to our expectations, we found no evidence that this form of generalization is better after a night of sleep relative to a day awake. Instead, we observed an effect of time of day, with better generalization in the morning than the evening. This effect also manifested as increased false memory for generalized information. In a nap experiment, we found that generalization did not benefit from having slept recently, suggesting a role for circadian rhythms apart from sleep. We found, however, that this time of day effect appears to be sensitive to category structure and to task engagement more generally. We propose that a state of lowered inhibition in the morning may facilitate spreading activation between otherwise separate memories, promoting this form of generalization.

neuroscience↗

bioRxiv2020

Therapeutic Targeting of Measles Virus Polymerase with ERDRP-0519Suppresses All RNA Synthesis Activity

Morbilliviruses, such as measles virus (MeV) and canine distemper virus (CDV), are highly infectious members of the paramyxovirus family. MeV is responsible for major morbidity and mortality in non-vaccinated populations. ERDRP-0519, a pan-morbillivirus small molecule inhibitor for the treatment of measles, targets the morbillivirus RNA-dependent RNA-polymerase (RdRP) complex and displayed unparalleled oral efficacy against lethal infection of ferrets with CDV, an established surrogate model for human measles. Resistance profiling identified the L subunit of the RdRP, which harbors all enzymatic activity of the polymerase complex, as the molecular target of inhibition. Here, we examined binding characteristics, physical docking site, and the molecular mechanism of action of ERDRP-0519 through label-free biolayer interferometry, photoaffinity cross-linking, and in vitro RdRP assays using purified MeV RdRP complexes and synthetic templates. Results demonstrate that unlike all other mononegavirus small molecule inhibitors identified to date, ERDRP-0519 inhibits all phosphodiester bond formation in both de novo initiation of RNA synthesis at the promoter and RNA elongation by a committed polymerase complex. Photocrosslinking and resistance profiling-informed ligand docking revealed that this unprecedented mechanism of action of ERDRP-0519 is due to simultaneous engagement of the L protein polyribonucleotidyl transferase (PRNTase)-like domain and the flexible intrusion loop by the compound, pharmacologically locking the polymerase in pre-initiation conformation. This study informs selection of ERDRP-0519 as clinical candidate for measles therapy and identifies a previously unrecognized druggable site in mononegavirus L polymerase proteins that can silence all synthesis of viral RNA. ImportanceThe mononegavirus order contains major established and recently emerged human pathogens. Despite the threat to human health, antiviral therapeutics directed against this order remain understudied. The mononegavirus polymerase complex represents a promising drug target due to its central importance for both virus replication and viral mitigation of the innate host antiviral response. In this study, we have mechanistically characterized a clinical candidate small-molecule MeV polymerase inhibitor. The compound blocked all phosphodiester bond formation activity, a unique mechanism of action unlike all other known mononegavirus polymerase inhibitors. Photocrosslinking-based target site mapping demonstrated that this class-defining prototype inhibitor stabilizes a pre-initiation conformation of the viral polymerase complex that sterically cannot accommodate template RNA. Function-equivalent druggable sites exist in all mononegavirus polymerases. In addition to its direct anti-MeV impact, the insight gained in this study can therefore serve as a blueprint for indication spectrum expansion through structure-informed scaffold engineering or targeted drug discovery.

microbiology↗

bioRxiv2020

Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation

The dynamic control of the actin cytoskeleton is a key aspect of essentially all animal cell movements. Experiments in single migrating cells and in vitro systems have provided an exceptionally deep understanding of actin dynamics. However, we still know relatively little of how these systems are tuned in cell-type specific ways, for example in the context of collective cell movements that sculpt the early embryo. Here, we provide an analysis of the actin severing and depolymerization machinery during vertebrate gastrulation, with a focus on Twinfilin1. We confirm previous results on the role of Twf1 in lamellipodia and extend those findings by linking Twf1, actin turnover, and cell polarization required for convergent extension during vertebrate gastrulation.

cell biology↗

bioRxiv2020

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins

Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles). Here, we use in vivo imaging to show that inner dynein arm (IDA) and outer dynein arm (ODA) subunits are partitioned into non-overlapping sub-regions within DynAPs. Using affinity purification mass-spectrometry of in vivo interaction partners, we also identify novel partners for inner and outer dynein arms. Among these, we identify C16orf71/Daap1 as a novel axonemal dynein regulator. Daap1 interacts with ODA subunits, localizes specifically to the cytoplasm, is enriched in DynAPs, and is required for the deployment of ODAs to axonemes. Our work reveals a new complexity in the structure and function of a cell-type specific liquid-like organelle that is directly relevant to human genetic disease.

cell biology↗

bioRxiv2020

Sharp-wave ripples in human amygdala and their coordination with hippocampus

Cooperative interactions between the amygdala and hippocampus are widely regarded as critical for overnight emotional processing of waking experiences, but direct support from the human brain for such a dialog is absent. Using intracranial recordings in four pre-surgical epilepsy patients (two male, two female), we discovered ripples within human amygdala during non-rapid eye movement (NREM) sleep. Like hippocampal ripples, amygdala ripples are strongly associated with sharp waves, are linked to sleep spindles, and tend to co-occur with their hippocampal counterparts. Moreover, sharp waves and ripples are temporally linked across the two brain structures, with amygdala ripples occurring during hippocampal sharp waves and vice versa. Combined with further evidence of interregional sharp wave and spindle synchronization, these findings offer a potential physiological substrate for the NREM-sleep-dependent consolidation and regulation of emotional experiences.

neuroscience↗

bioRxiv2019

Phase-based coordination of hippocampal and neocortical oscillations during human sleep

During sleep, new memories undergo a gradual transfer from the hippocampus (HPC) to the neocortex (NC). Precisely timed neural oscillations interacting within and between these brain structures are thought to mediate this sleep-dependent memory consolidation, but exactly which sleep oscillations instantiate the HPC-NC dialog, and via what mechanisms, remains elusive. Employing invasive electroencephalography in ten neurosurgical patients across a full night of sleep, we identified three broad classes of phase-based HPC-NC communication. First, we observed interregional phase synchrony for non-rapid eye movement (NREM) spindles, N2 and rapid eye movement (REM) theta, and N3 beta activity. Second, and most intriguingly, we found asymmetrical N3 cross-frequency phase-amplitude coupling between HPC SOs and NC activity spanning the delta to high-gamma/ripple bands, but not in the opposite direction. Lastly, N2 theta and NREM spindle synchrony were themselves modulated by HPC SOs. These novel forms of phase-based interregional communication emphasize the role of HPC SOs in the HPC-NC dialog, and may offer a physiological basis for the sleep-dependent reorganization of mnemonic content.

neuroscience↗

bioRxiv2019

Retromer repletion with AAV9-VPS35 restores endosomal function in the mouse hippocampus

Retromer has emerged as a master conductor of endosomal trafficking, and VPS35 and other retromer-related proteins are found to be deficient in late-onset Alzheimers disease (AD). Depleting VPS35 in neurons impairs retromer function, affecting for example the trafficking of the amyloid-precursor protein (APP) and the glutamate receptor GluA1. Whether VPS35 repletion, after chronic in vivo depletion, can rescue these impairments remains unknown. Here we set out to address this question by using a viral vector approach for VPS35 repletion. First, we completed a series of studies using neuronal cultures in order to optimize AAV9-VPS35 delivery, and to understand how exogenous VPS35 expression affects its endogenous levels as well as its binding to other retromer proteins. Next, we completed a series of studies in wildtype mice to determine the optimum protocol for in vivo delivery of AAV9-VPS35 to the hippocampus. We relied on this information to deliver AAV9-VPS35 to the hippocampus of mice genetically engineered to have chronic, neuronal-selective, VPS35 depletion. VPS35 repletion in the hippocampus was found to normalize APP cleavage and to restore glutamate receptor levels. Unexpectedly, chronic VPS35 depletion in neurons caused glial activation, similar to the pattern observed in AD, which was also partially normalized by VPS35 repletion. Taken together, these studies strengthen the mechanistic link between retromer and AD, and have therapeutic implications.

neuroscience↗

bioRxiv2019

Heterogeneous profiles of coupled sleep oscillations in human hippocampus

Cross-frequency coupling of sleep oscillations is thought to mediate memory consolidation. While the hippocampus is deemed central to this process, detailed knowledge of which oscillatory rhythms interact in the sleeping human hippocampus is lacking. Combining intracranial hippocampal and non-invasive electroencephalography from twelve neurosurgical patients, we characterized spectral power and coupling during non-rapid eye movement (NREM) and rapid eye movement (REM) sleep. Hippocampal coupling was extensive, with the majority of channels expressing spectral interactions. NREM consistently showed delta-ripple coupling, but ripples were also modulated by slow oscillations (SOs) and sleep spindles. SO-delta and SO-theta coupling, as well as interactions between delta/theta and spindle/beta frequencies also occurred. During REM, limited interactions between delta/theta and beta frequencies emerged. Moreover, oscillatory organization differed substantially between i) hippocampus and scalp, ii) sites along the anterior-posterior hippocampal axis, and iii) individuals. Overall, these results extend and refine our understanding of hippocampal sleep oscillations.

neuroscience↗

bioRxiv2019

Clueless forms dynamic, insulin-responsive bliss particles sensitive to stress

Mitochondria perform a myriad of biochemical functions in the cell that integrate ATP production and metabolism. While mitochondria contain their own genome, mtDNA, it only encodes thirteen proteins required for oxidative phosphorylation, thus well over one thousand proteins required for all mitochondrial functions are encoded in the nucleus. One such protein is Drosophila Clueless (Clu), whose vertebrate homolog is Clustered mitochondria homolog (Cluh). Clu/Cluh is a ribonucleoprotein that regulates mRNAs destined for import into mitochondria and is an essential protein that regulates cellular metabolism. Clu forms large particles in the cytoplasm, although how these particles relate to nutrition and metabolic stress is unknown. Using live-imaging, we show Clu particles are highly dynamic. Clu particles appear to be unique as they do not colocalize with many known cytoplasmic bodies. In addition, Clu particle formation is highly dependent on diet as ovaries from starved females no longer contain Clu particles although Clu protein levels remain the same and insulin is necessary and sufficient for Clu particle formation. Oxidative stress also disperses particle. Since Clu particles are only present under optimal conditions we are naming them bliss particles. These observations identify Clu particles as unique, stress-sensitive cytoplasmic ribonucleoprotein particles whose absence corresponds with altered mitochondrial function and localization.

cell biology↗

bioRxiv2018

Sleep selectively stabilizes contextual aspects of negative memories

Sleep and emotion are both powerful modulators of the long-term stability of episodic memories, but precisely how these factors interact remains unresolved. We assessed changes in item recognition, contextual memory, and affective tone for negative and neutral memories across a 12 h interval containing sleep or wakefulness in 71 human volunteers. Our data indicate a sleep-dependent stabilization of negative contextual memories, in a way not seen for neutral memories, item recognition, or across wakefulness. Furthermore, retention of contextual memories was positively associated with time spent in non-rapid eye movement sleep. Finally, our results offer partial support for the hypothesis that sleep attenuates emotional responses to previously memorized material.

neuroscience↗

bioRxiv2018

Large-Scale Structure and Individual Fingerprints of Locally Coupled Sleep Oscillations

The temporal coordination of slow oscillations and sleep spindles is believed to underlie processes of sleep-dependent memory consolidation and reorganization. Accumulating evidence of the predominantly local expression of these individual oscillatory rhythms suggests that their interaction may have a similar local component. However, it is unclear whether local coupling holds uniformly across the cortex, and whether and how these dynamics differ between fast and slow spindles, and sleep stages. Moreover, substantial individual variability in the expression of both spindles and slow oscillations raise the possibility that their cross-frequency interactions show similar individual differences. Using two nights of multi-channel electroencephalography recordings from 24 healthy individuals, we characterized the topography of slow oscillation-spindle coupling. We found that locally coupled oscillations occur over widespread cortical areas, but that their dynamics vary with spindle class, sleep stage, and location. Moreover, the phase of the slow oscillation cycle at which spindles were expressed differed markedly across individuals but was stable across nights. However, individual variability of coupling phase was not correlated with overnight memory change. These findings both add an important spatial aspect to our understanding of the temporal coupling of sleep oscillations and demonstrate the heterogeneity of coupling dynamics, which must be taken into account when formulating mechanistic accounts of sleep-related memory processing.

neuroscience↗

bioRxiv2017

Individual differences in frequency and topography of slow and fast sleep spindles

Sleep spindles are transient oscillatory waveforms occurring during non-rapid eye movement (NREM) sleep and are implicated in plasticity and memory processes. In humans, spindles can be classified as either slow or fast, but large individual differences in spindle frequency as well as methodological difficulties have hindered progress towards understanding their function. Using two nights of high-density electroencephalography recordings from healthy individuals, we first characterize the individual variability of NREM spectra and demonstrate the difficulty of determining subject-specific spindle frequencies. We then introduce a novel spatial filtering approach that can reliably separate subject-specific spindle activity into slow and fast components that are stable across nights and across N2 and N3 sleep. We then proceed to provide detailed analyses of the topographical expression of individualized slow and fast spindle activity. Group-level analyses conform to known spatial properties of spindles, but also uncover novel differences between sleep stages and spindle classes. Moreover, subject-specific examinations reveal that individual topographies show considerable variability that is stable across nights. Finally, we demonstrate that topographical maps depend nontrivially on the spindle metric employed. In sum, our findings indicate that group-level approaches mask substantial individual variability of spindle dynamics, in both the spectral and spatial domains. We suggest that leveraging, rather than ignoring, such differences may prove useful to further our understanding of the physiology and functional role of sleep spindles.

neuroscience↗

bioRxiv2016

Distributed alpha networks underlie individual differences in memory performance

Episodic memory, our ability to remember specific events, varies considerably across individuals. However, little is known about the neural basis of this variability. To address this issue, we investigated the role of distributed networks of oscillatory activity, as measured through electroencephalography (EEG). We observed that individual differences in alpha network structure reliably predict individual memory capacity. Specifically, individuals whose network profiles during encoding were most different from their resting state networks exhibited greatest subsequent memory performance, suggesting that optimal information processing requires substantial shifts in large-scale oscillatory organization. Furthermore, these results were not observed in circumscribed topographical regions or individual connections, indicating that distributed network approaches were more sensitive to functional processes than more conventional methods. These findings uncover a physiological correlate of individual differences in episodic memory and demonstrate the utility of multivariate EEG techniques to uncover brain-behavior correlates.

neuroscience↗

bioRxiv2016

Variability and stability of large-scale cortical oscillation patterns

Individual differences in brain organization exist at many spatial and temporal scales, contributing to the substantial heterogeneity underlying human thought and behavior. Oscillatory neural activity is crucial for these behaviors, but how such rhythms are expressed across the cortex within and across individuals has not been thoroughly characterized. Combining electroencephalography (EEG) with representational similarity and multivariate classification techniques, we provide a systematic characterization of brain-wide activity across frequency bands and oscillatory features during rest and task performance. Results indicate that oscillatory profiles exhibit sizable group-level correspondences, indicating the presence of common templates of oscillatory organization. At the same time, we observed well-defined subject-specific network profiles that were discernible above and beyond the structure shared across individuals. These individualized patterns were sufficiently stable over time to allow successful classification of individuals several months later. Finally, our findings indicate that the network structure of rhythmic activity varies considerably across distinct oscillatory frequencies and features, suggesting the existence of multiple, parallel information processing streams embedded in distributed electrophysiological activity. Together, these findings affirm the richness of spatiotemporal EEG signals and emphasize the utility of multivariate network analyses for understanding the role of brain oscillations in physiology and behavior.

neuroscience↗