Biology subjects

Lewis, C. M.

Publications and source records attributed to Lewis, C. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Phage RyR-domain proteins degrade ADPR-based immune signals and fuel NAD synthesis

Bacterial, plant, and animal cells synthesize nucleotide immune signals as a conserved strategy to defend against viral infection1-4. In bacteria, Thoeris anti-phage defense systems convert nicotinamide adenine dinucleotide (NAD+) into the cyclic ADP-ribose signals 2'cADPR and 3'cADPR to activate downstream effectors and restrict viral replication5-8. Phage proteins can bind and sequester Thoeris signals6,9-13, but no mechanisms are known to degrade the exceptionally stable 2'cADPR and 3'cADPR molecules and terminate immune activation. Here we use a forward biochemical screen to discover the mycobacteriophage protein RyDEP as the founding member of an enzyme family that cleaves 2'cADPR and 3'cADPR to inactivate Thoeris defense. We show that RyDEP is a glycosidase that cleaves the ribose-ribose linkage in 2' and 3' cADPR immune signals to both inactivate host defense and enable direct restoration of NAD+. A crystal structure of the RyDEP-3'cADPR complex in the post-cleavage state explains the molecular basis of immune signal degradation and reveals surprising homology with the Repeat12 domain of animal ryanodine receptors (RyRs) that control calcium flux and muscle contraction14,15. We demonstrate that diverse phage RyDEP proteins tune RyR-domain activity to either degrade or sequester immune signals. Our results define RyR-domain proteins as regulators of nucleotide immune signaling and explain how viruses subvert host antiviral defense.

microbiology↗

bioRxiv2026

Layer-specific wide-field calcium imaging of neocortical activity

The mammalian neocortex is highly organized in local microcircuits and through long-range projection patterns between different regions. Since various features of local and long-range connectivity are determined by the cortical layer in which the respective neurons reside, understanding the flow of cortical information within and across layers is essential. Wide-field calcium imaging enables mesoscale functional mapping of genetically identified neurons across cortical areas. However, it has been applied primarily to superficial cortical layers, and systematic comparisons of wide-field signals across cortical layers are scarce. Here, we apply wide-field calcium imaging to different cortical layers using transgenic mouse lines with selective expression of GCaMP6f in layers 2/3, 5, and 6. We address several challenges of layer-specific wide-field imaging and provide possible solutions. First, to improve the registration of functional data to standard atlases, we demonstrate the benefit of layer-specific registration maps that are warped on the basis of the depth-dependent surface projections of the labeled cell populations. These maps help to assign the imaged calcium signals to the specific regions from which they originate. Second, we measure the depth-dependent blurring of wide-field fluorescence signals induced by light scattering and reveal stronger blurring in deep vs. superficial layers, in line with previous theoretical predictions from simulations. We used measured point spread functions to deconvolve single-whisker-evoked calcium signals in the barrel cortex and demonstrate improved signal confinement to individual barrel columns across layers. Finally, we investigate cross-regional functional connectivity during awake resting state periods for distinct layers. We find that mesoscopic functional connectivity is largely conserved between the cortical layers, with subtle differences for key regions of the default mode network (retrosplenial cortex and medial prefrontal cortex). Our approaches facilitate the comprehensive characterization of layer-specific cortico-cortical interactions, expanding wide-field calcium imaging as a powerful tool to investigate the layered organization of distributed brain dynamics.

neuroscience↗

bioRxiv2026

pamiR: INVESTIGATING PLANT CELLS ONE ORGANELLE AT A TIME

Functional genetic redundancy (FGR) within gene families limits the discovery of gene function in plants because single-gene perturbations often fail to produce informative phenotypes. Artificial microRNAs (amiRNAs) provide a strategy to silence multiple related genes simultaneously. However, the existing amiRNA-based libraries used for genetic gene function discovery in plants do not account for the subcellular localization of gene products, which can lead to pleiotropic or difficult-to-interpret phenotypes. Plastids are essential plant cell organelles that integrate central metabolic and signaling processes, including photosynthesis, hormone biosynthesis, and environmental responses. Here we introduce pamiR, a plastid-targeted amiRNA library designed to enable organelle-specific gene function discovery in Arabidopsis thaliana. Using plastid proteomic datasets, we identified high-confidence plastid-localized proteins and designed amiRNAs to target their gene(s) (families) minimizing FGR. This amiRNA library was introduced in a vector with fluorescence-accumulating seed technology enabling rapid, herbicide-free selection and screening in the first generation. Validation by next-generation sequencing, confirmed high representation and uniform distribution of amiRNAs within pamiR. Proof-of-concept screens recovered mutants affecting known and additional candidate genes involved in photosynthesis and abscisic acid biosynthesis. Therefore, the pamiR library provides a fast platform for plastid-focused genetic screens that is compatible with existing mutant collections. One-sentence summaryThe plastid amiRNA (pamiR) library enables organelle-specific forward genetics without functional genetic redundancy.

plant biology↗

bioRxiv2025

The oral microbiome of King Richard III of England

Metagenomic investigation of archaeological dental calculus has provided insights into the changing oral health, disease, and diet of past human societies, but little is known about the oral microbiota of exceptionally high-status individuals, whose diet and lifestyle sharply differed from the general population. Here we analyze the dental calculus metagenome of King Richard III of England (1452-1485) and compare it to new and previously published dental calculus metagenomes from predominantly non-elite contexts in England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Deep sequencing and de novo assembly enabled the investigation of metagenome-assembled genomes (MAGs) from periopathogens within the genus Tannerella. DNA preservation within the dental calculus of King Richard III was found to be exceptional, yielding an extraordinarily well-preserved oral microbiota. Oral microbiome species diversity fell within the range previously observed among other northern European populations over the past 7,000 years, suggesting that a royal lifestyle and a rich diet did not substantially shift his oral microbiome composition. Reconstructed Tannerella genomes contained many virulence factors found today among periopathogens, including Tannerella forsythia. Insufficient plant and animal DNA was recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA for dietary reconstruction, even when well-preserved. The dental calculus of King Richard III has produced one of the richest and best preserved ancient oral metagenomes studied to date and contributes to understanding the ecology and evolution of the human oral microbiome.

microbiology↗

bioRxiv2025

Biomechanical Phenotyping Reveals Unique Mechanobiological Signatures of Early-Onset Colorectal Cancer

While both incidence and mortality of sporadic average-onset colorectal cancer (AO CRC, above 50 years of age) are in constant decline, sporadic early-onset colorectal cancer (EO CRC, under 50 years of age) is rising rapidly. Yet, the causes behind this rise remain poorly understood. Epidemiological studies indicate that lifestyle and environmental exposures may result in chronic inflammation, which is known to trigger tissue fibrosis. This study tests the hypothesis that fibrotic remodeling and biomechanical stiffening of colorectal tissues represent measurable hallmarks and potential drivers of EO CRC. Using primary human tissues, this work shows that EO CRC is associated with changes in collagen microstructure, increased stiffness and elevated viscosity of primary tumors. Spatial transcriptional profiling and immunostaining reveal pro-fibrotic signatures in stromal cells, alongside enhanced Yes-associated protein (YAP) mechanotransduction and proliferation in epithelial cells of EO CRC tissues. Mechanistically, increasing matrix stiffness in vitro promotes proliferation of epithelial cells in 2D and 3D colorectal cancer models. Together, these findings establish EO CRC as a disease marked by early and widespread biomechanical remodeling, suggesting that a fibrotic and stiffened tissue microenvironment may orchestrate EO CRC tumor initiation.

bioengineering↗

bioRxiv2024

A hybrid micro-ECoG for functionally targeted multi-site and multi-scale investigation

Brain function relies on coordinated activity across a wide range of spatial and temporal scales. The activity of single neurons depends on their unique pattern of local and long-range connectivity and thus on large-scale patterns of distributed activity across brain-wide networks. Understanding integrated, whole brain function requires new tools capable of recording from anatomically connected populations in distributed brain areas to bridge local and global dynamics. Here, we present high-density, micro-electrocorticography arrays that facilitate multi-scale studies of brain activity. The hybrid arrays integrate the desirable features of silicone elastomers and polyimide films. The silicone elastomer superstructure provides optical transparency and permits repeated penetration with rigid intracortical arrays. The polyimide films enable fine feature definition through photolithography. This combination facilitates high-throughput functional mapping of brain areas to define functionally characterized targets and permits targeted insertion of depth electrodes through the same array for dense local sampling. We demonstrate their suitability for functional mapping of cortical regions in rats, cats and marmosets and the benefit of the resulting functional maps for targeting functionally defined populations for multi-area laminar recordings. Finally, we demonstrate the utility of the hybrid {micro}ECoG for local optogenetic stimulation and its use in investigating cortico-cortical interactions through feedforward optogenetic stimulation. Together, these capabilities make the hybrid {micro}ECoG a compelling tool for systems neuroscience.

neuroscience↗

bioRxiv2024

Top-down modulation of visual cortical stimulus encoding and gamma independent of firing rates

Neurons in primary visual cortex integrate sensory input with signals reflecting the animals internal state to support flexible behavior. Internal variables, such as expectation, attention, or current goals, are imposed in a top-down manner via extensive feedback projections from higher-order areas. We optogenetically activated a high-order visual area, area 21a, in the lightly anesthetized cat (OptoTD), while recording from neuronal populations in V1. OptoTD induced strong, up to several fold, changes in gamma-band synchronization together with much smaller changes in firing rate, and the two effects showed no correlation. OptoTD effects showed specificity for the features of the simultaneously presented visual stimuli. OptoTD-induced changes in gamma synchronization, but not firing rates, were predictive of simultaneous changes in the amount of encoded stimulus information. Our findings suggest that one important role of top-down signals is to modulate synchronization and the information encoded by populations of sensory neurons.

neuroscience↗

bioRxiv2022

Centripetal integration of past events by hippocampal astrocytes

An essential feature of neurons is their ability to centrally integrate information from their dendrites. The activity of astrocytes, in contrast, has been described as mostly uncoordinated across cellular compartments without clear central integration. Here, we describe conditional centripetal integration as a principle of how astrocytes integrate calcium signals from their distal processes to induce somatic activation. We found in mouse hippocampus that global astrocytic activity, as recorded with population calcium imaging, is well explained as a leaky integration of past neuronal and behavioral events on a timescale of seconds. Salient past events, indicated by pupil dilations, facilitated propagation of calcium signals from distal processes to the soma on this slow timescale. Centripetal propagation was reproduced by optogenetic activation of the locus coeruleus, a key regulator of arousal, and reduced by pharmacological inhibition of 1-adrenergic receptors. Together, our results establish astrocytes as computational units of the brain that slowly and conditionally integrate calcium signals to activate their somata upon behaviorally relevant events.

neuroscience↗

bioRxiv2022

Nav1.1 in mammalian sensory neurons is required for normal motor behaviors

AO_SCPLOWBSTRACTC_SCPLOWThe voltage-gated sodium channel (NaV), NaV1.1, is well-studied in the central nervous system; conversely, its contribution to peripheral sensory neuron function is more enigmatic. Here, we identify a new role for NaV1.1 in mammalian proprioception. RNAscope analysis and in vitro patch clamp recordings in genetically identified mouse proprioceptors show ubiquitously channel expression and significant contributions to intrinsic excitability. Notably, genetic deletion of NaV1.1 in sensory neurons caused profound and visible motor coordination deficits in conditional knockout mice of both sexes, similar to conditional Piezo2-knockout animals, suggesting this channel is a major contributor to sensory proprioceptive transmission. Ex vivo muscle afferent recordings conditional knockout mice found that loss of NaV1.1 leads to inconsistent and unreliable proprioceptor firing characterized by action potential failures during static muscle stretch; conversely, afferent responses to dynamic vibrations were unaffected. This suggests that while a combination of Piezo2 and other NaV isoforms are sufficient to elicit activity in response to transient stimuli, NaV1.1 is required for transmission of receptor potentials generated during sustained muscle stretch. Impressively, recordings from afferents of heterozygous conditional knockout animals were similarly impaired, and heterozygous conditional knockout mice also exhibited motor behavioral deficits. Thus, NaV1.1 haploinsufficiency in sensory neurons impairs both proprioceptor function and motor behaviors. Importantly, human patients harboring NaV1.1 loss-of-function mutations often present with motor delays and ataxia; therefore, our data suggest sensory neuron dysfunction contributes to the clinical manifestations of neurological disorders in which NaV1.1 function is compromised. Collectively, we present the first evidence that NaV1.1 is essential for mammalian proprioceptive signaling and behaviors.

neuroscience↗

bioRxiv2022

Using Local Genetic Correlation Improves Polygenic Score Prediction Across Traits

IntroductionThe predictive utility of polygenic scores (PGS) is steadily increasing as genome-wide association studies (GWAS) increase in sample size and diversity, and as PGS methodology is further developed. Multivariate PGS approaches incorporate GWAS results for secondary phenotypes which are genetically correlated with the target phenotype. These improve prediction over using PGS for only the target phenotype. However, previous methods have only considered the genome-wide estimates of SNP-based heritability (h2SNP) and genetic correlation (rg) between target and secondary phenotypes. In this study, we assess the impact of local h2SNP and rg within specific loci on cross-trait prediction. MethodsWe evaluate PGS using three target phenotypes (depression, intelligence, BMI) in the UK Biobank, with GWAS summary statistics matching the target phenotypes and 14 genetically correlated secondary phenotypes. PGS SNP-weights were derived using MegaPRS. Local h2SNP and rg were estimated using LAVA. We then evaluated PGS after reweighting SNP-weights according to local h2SNP and rg estimates between the target and secondary phenotypes. Elastic net models containing PGS for multiple phenotypes were evaluated using nested 10-fold cross validation. ResultsModelling target and secondary PGS significantly improved target phenotype prediction over the target PGS alone, with relative improvements ranging from 0.8-12.2%. Furthermore, we show reweighting PGS by local h2SNP and rg estimates can enhance the predictive utility of PGS across phenotypes, with additional relative improvements of 0.2%-2.8%. Reweighting PGS by local h2SNP and rg improved target phenotype prediction most when there was a mixture of positive and negative local rg estimates between target and secondary phenotypes. ConclusionModelling PGS for secondary phenotypes consistently improves prediction of target phenotypes, and this approach can be further enhanced by incorporating local h2SNP and rg estimates to highlight relevant genetic effects across phenotypes.

genomics↗

bioRxiv2021

Dendritic integration of sensory and reward information facilitates learning

Learning goal-directed behavior requires association of pertinent sensory stimuli with behaviorally relevant outcomes. In the mammalian neocortex, dendrites of pyramidal neurons are suitable association sites1-3 but how their activities adapt during learning remains elusive. Here, we track calcium signals in apical dendrites of layer 5 (L5) pyramidal neurons in mouse barrel cortex during texture discrimination learning4. We observe diverse task-related responses, either localized to branches or widespread throughout the apical tuft. However, even in expert mice, the tufts capability to discriminate go/no-go stimuli remains poor. Yet, we identify two prevailing response types in dendritic branches: 1) responses to unexpected outcome (reward) in naive mice that decrease with growing task proficiency, and 2) responses associated with salient sensory stimuli, especially the outcome-predicting texture touch, that strengthen upon learning. We demonstrate that these response types match distinct unsigned components of the temporal difference error5 by replicating our results with a reinforcement learning model. Moreover, optogenetic apical inhibition of L5 neurons during the outcome time window prevents naive animals from learning the task, consistent with the effect of equivalent model perturbation. Our findings suggest that salience signals in L5 apical dendrites facilitate the recruitment of task-relevant neurons via dendritic gain modulation.

neuroscience↗

bioRxiv2021

Striatum-projecting prefrontal cortex neurons support working memory maintenance

The medial prefrontal cortex (mPFC) and the dorsomedial striatum (dmStr) are linked to working memory (WM) but how striatum-projecting mPFC neurons contribute to WM encoding, maintenance, or retrieval remains unclear. Here, we probed mPFC[->]dmStr pathway function in freely-moving mice during a T-maze alternation test of spatial WM. Fiber photometry of GCaMP6m-labeled mPFC[->]dmStr projection neurons revealed strongest activity during the delay period that requires WM maintenance. Demonstrating causality, optogenetic inhibition of mPFC[->]dmStr neurons only during the delay period impaired performance. Conversely, enhancing mPFC[->]dmStr pathway activity--via pharmacological suppression of HCN1 or by optogenetic activation during the delay-- alleviated WM impairment induced by NMDA receptor blockade. Consistently, cellular-resolution miniscope imaging resolved preferred activation of >50% mPFC[->]dmStr neurons during WM maintenance. This subpopulation was distinct from neurons showing preference for encoding and retrieval. In all periods, including the delay, neuronal sequences were evident. Striatum-projecting mPFC neurons thus critically contribute to spatial WM maintenance.

neuroscience↗

bioRxiv2021

The Core Human Fecal Metabolome

Summary ParagraphAmong the biomolecules at the center of human health and molecular biology is a system of molecules that defines the human phenotype known as the metabolome. Through an untargeted metabolomic analysis of fecal samples from human individuals from Africa and the Americas--the birthplace and the last continental expansion of our species, respectively--we present the characterization of the core human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the core human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features like leucyl-leucine dipeptides and urobilin as major metabolic correlates of these behavioral shifts. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a core human fecal metabolome. This study represents the first characterization of the core human fecal metabolome through untargeted analyses of populations along an industrialization gradient.

biochemistry↗

bioRxiv2020

The role of anatomical connection strength for interareal communication in macaque cortex

What is the relationship between anatomical connection strength and rhythmic synchronization? Simultaneous recordings of 15 cortical areas in two macaque monkeys show that interareal networks are functionally organized in spatially distinct modules with specific synchronization frequencies, i.e. frequency-specific functional connectomes. We relate the functional interactions between 91 area pairs to their anatomical connection strength defined in a separate cohort of twenty six subjects. This reveals that anatomical connection strength predicts rhythmic synchronization and vice-versa, in a manner that is specific for frequency bands and for the feedforward versus feedback direction, even if interareal distances are taken into account. These results further our understanding of structure-function relationships in large-scale networks covering different modality-specific brain regions and provide strong constraints on mechanistic models of brain function. Because this approach can be adapted to non-invasive techniques, it promises to open new perspectives on the functional organization of the human brain.

neuroscience↗

bioRxiv2020

Cortical resonance selects coherent input

Synchronization has been implicated in neuronal communication, but causal evidence remains indirect. We used optogenetics to generate depolarizing currents in pyramidal neurons of cat visual cortex, emulating excitatory synaptic inputs under precise temporal control, while measuring spike output. Cortex transformed constant excitation into strong gamma-band synchronization, revealing the well-known cortical resonance. Increasing excitation with ramps increased the strength and frequency of synchronization. Slow, symmetric excitation profiles revealed hysteresis of power and frequency. Crucially, white-noise input sequences enabled causal analysis of network transmission, establishing that cortical resonance selectively transmits coherent input components. Models composed of recurrently coupled excitatory and inhibitory units uncovered a crucial role of feedback inhibition and suggest that hysteresis can arise through spike-frequency adaptation. The presented approach provides a powerful means to investigate the resonance properties of local circuits and probe how these properties transform input and shape transmission.

neuroscience↗

bioRxiv2020

Evaluation of Polygenic Prediction Methodology within a Reference-Standardized Framework

BackgroundThe predictive utility of polygenic scores is increasing, and many polygenic scoring methods are available, but it is unclear which method performs best. This study evaluates the predictive utility of polygenic scoring methods within a reference-standardized framework, which uses a common set of variants and reference-based estimates of linkage disequilibrium and allele frequencies to construct scores. MethodsEight polygenic score methods were tested: p-value thresholding and clumping (pT+clump), SBLUP, lassosum, LDPred1, LDPred2, PRScs, DBSLMM and SBayesR, evaluating their performance to predict outcomes in UK Biobank and the Twins Early Development Study (TEDS). Strategies to identify optimal p-value threshold and shrinkage parameters were compared, including 10-fold cross validation, pseudovalidation and infinitesimal models (with no validation sample), and multi-polygenic score elastic net models. ResultsLDPred2, lassosum and PRScs performed strongly using 10-fold cross-validation to identify the most predictive p-value threshold or shrinkage parameter, giving a relative improvement of 16-18% over pT+clump in the correlation between observed and predicted outcome values. Using pseudovalidation, the best methods were PRScs and DBSLMM, with a relative improvement of >10% over other pseudovalidation and infinitesimal methods (lassosum, SBLUP, SBayesR, LDPred1, LDPred2). PRScs pseudovalidation was only 3% worse than the best polygenic score identified by 10-fold cross validation. Elastic net models containing polygenic scores based on a range of parameters consistently improved prediction over any single polygenic score. ConclusionWithin a reference-standardized framework, the best polygenic prediction was achieved using LDPred2, lassosum and PRScs, modeling multiple polygenic scores derived using multiple parameters. This study will help researchers performing polygenic score studies to select the most powerful and predictive analysis methods.

genomics↗

bioRxiv2020

Opto-E-Dura: a Soft, Stretchable ECoG Array for Multimodal, Multi-scale Neuroscience

Soft, stretchable materials hold great promise for the fabrication of biomedical devices due to their capacity to integrate gracefully with and conform to biological tissues. Conformal devices are of particular interest in the development of brain interfaces where rigid structures can lead to tissue damage and loss of signal quality over the lifetime of the implant. Interfaces to study brain function and dysfunction increasingly require multimodal access in order to facilitate measurement of diverse physiological signals that span the disparate temporal and spatial scales of brain dynamics. Here we present the Opto-e-Dura, a soft, stretchable, 16-channel electrocorticography array that is optically transparent. We demonstrate its compatibility with diverse optical and electrical readouts enabling multimodal studies that bridge spatial and temporal scales. The device is chronically stable for weeks, compatible with wide-field and 2-photon calcium imaging and permits the repeated insertion of penetrating multi-electrode arrays. As the variety of sensors and effectors realizable on soft, stretchable substrates expands, similar devices that provide large-scale, multimodal access to the brain will continue to improve fundamental understanding of brain function.

neuroscience↗

bioRxiv2020

Strategy guides feature recall of a single object in working memory task

Over past couple of decades our understanding of visual working memory (VWM), and working memory in general, has been predominantly in line with the capacity debate. We recently opened a new line of inquiry regarding the recall of a single object to go beyond the capacity debate, and showed that a series of feature probe questions about a single object yields poorer recall later in the sequence (Sengupta et al, 2020). In the current work we focused on another aspect of sequential feature recall - mainly regarding whether recall can be improved by asking the same question twice. To that end, we chose to focus on two features - color and location, and we contrasted repeat and non-repeat (from the standpoint of feature questions) trials in a series of two experiments. In repeat trials either color or location would be probed twice consecutively. In non-repeat trials color and location probes were presented one after the other in random order. In all trials the stimulus was a small colored oriented line presented for 1 sec in a location within 4o of visual angle. The recall of color and location were mapped onto continuous variable like Sengupta et al, 2020 - for instance, color recall was mapped onto a color wheel. In the first experiment, we used an unaltered color wheel when the color question was repeated. For the second experiment, we used a rotated color wheels for two consecutive color recall trials. We observed an increase in recall error for both repeat and non-repeat condition for location when the probe was at the second question in both experiments. However, color recall error did not increase for second repeat question condition in Experiment 1 as opposed to the non-repeat condition. On the other hand, in Experiment 2 we observed the expected increase in recall error for both repeat and non repeat condition for color probe at the second question. This maybe due to the fact that participants used an anchoring strategy in Experiment 1 by remembering where they clicked on the color wheel in the first question. The rotation of color wheel in second experiment destroys the anchor leading to the aforementioned result. The results show that trying to recall the same feature again leads to degradation of recall accuracy for both color and location, and human beings may use different strategies for recall in working memory tasks.

animal behavior and cognition↗