Biology subjects

Roy, M.

Publications and source records attributed to Roy, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Promoting intestinal healing by exclusive enteral nutrition with TGF-beta in a mouse model of colitis.

Background and aimsExclusive Enteral Nutrition (EEN) is the first line of treatment for pediatric Crohns disease (CD), but its mechanisms of action remain poorly understood. We studied EEN nutritional composition and TGF-{beta} effect in a mouse model of colitis, as well as the role of intestinal microbiota. MethodsMice were treated with Dextran Sulfate Sodium (DSS) during 5 days to induce colitis, until the inflammatory peak (day 7) or gut restitution (day 14). After DSS treatment, some of them received EEN formula such as Modulen IBD(R) (DM mice) or Infatrini Peptisorb(R) (DINF mice), with TGF-{beta} supplementation or neutralization, and clinical inflammation was evaluated. After sacrifice, macroscopic and microscopic inflammation were analyzed, as well as intestinal permeability (IP). The composition of mucosal colonic microbiota was analyzed and fecal microbiota transplantation was performed to evaluate its capacity to mediate anti-inflammatory and pro-regenerative effect. Colonic crypts from DSS and EEN mice were cultured as 3D organoids and cellular properties were analyzed. ResultsDSS mice developed colitis, as evidenced by the weight loss and clinical inflammation. It was accompanied by macroscopic inflammation such as colon thickness and edemas, and an elevated IP. In contrast, EEN mice with TGF-{beta} formula present faster weight recovery and decreased inflammatory parameters, with a normalized IP, suggesting gut restitution and functionality. These functional improvements were not obtained for EEN mice without TGF-{beta} formula. Moreover, EEN with Modulen IBD(R) (DM mice) modified the microbiota in comparison to DSS condition and attenuated inflammation. In addition, the organoids from DM mice colonic crypts treated had an enhanced survival, and re-epithelialization capacity. ConclusionsBoth EEN formula have anti-inflammatory properties, certainly by the nutritional composition. However, TGF-{beta} plays a significant role in intestinal restitution and restoring barrier function. These beneficial effects are partly mediated by the microbiota to maintain gut homeostasis.

physiology↗

bioRxiv2023

Pain reflects the informational value of nociceptive inputs.

Pain perception and its modulation are fundamental to human learning and adaptive behavior. This study investigated the hypothesis that pain perception is tied to pains learning function. Thirty-one participants performed a threat conditioning task where certain cues were associated with a possibility of receiving a painful electric shock. The cues that signalled potential pain or safety were regularly changed, requiring participants to continually establish new associations. Using computational models, we quantified participants pain expectations and prediction errors throughout the task and assessed their relationship with pain perception and electrophysiological responses. Our findings suggest that subjective pain perception increases with prediction error, that is when pain was unexpected. Prediction errors were also related to physiological nociceptive responses, including the amplitude of the nociceptive flexion reflex and EEG markers of cortical nociceptive processing (N2-P2 evoked potential and gamma-band power). Additionally, higher pain expectations were related to increased late event-related potential responses and alpha/beta decreases in amplitude during cue presentation. These results further strengthen the idea of a crucial link between pain and learning and suggest that understanding the influence of learning mechanisms in pain modulation could help us understand when and why pain perception is modulated in health and disease.

neuroscience↗

bioRxiv2022

Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques

Type-I interferons (IFN-I) are critical mediators of innate control of viral infections, but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, and for the first time, IFN-I signaling was modulated in rhesus macaques (RMs) prior to and during acute SARS-CoV-2 infection using a mutated IFN2 (IFN-modulator; IFNmod), which has previously been shown to reduce the binding and signaling of endogenous IFN-I. In SARS-CoV-2-infected RMs, IFNmod reduced both antiviral and inflammatory ISGs. Notably, IFNmod treatment resulted in a potent reduction in (i) SARS-CoV-2 viral load in Bronchoalveolar lavage (BAL), upper airways, lung, and hilar lymph nodes; (ii) inflammatory cytokines, chemokines, and CD163+MRC1-inflammatory macrophages in BAL; and (iii) expression of Siglec-1, which enhances SARS-CoV-2 infection and predicts disease severity, on circulating monocytes. In the lung, IFNmod also reduced pathogenesis and attenuated pathways of inflammasome activation and stress response during acute SARS-CoV-2 infection. This study, using an intervention targeting both IFN- and IFN-{beta} pathways, shows that excessive inflammation driven by type 1 IFN critically contributes to SARS-CoV-2 pathogenesis in RMs, and demonstrates the potential of IFNmod to limit viral replication, SARS-CoV-2 induced inflammation, and COVID-19 severity.

immunology↗

bioRxiv2022

TCF4 trinucleotide repeat expansions and UV irradiation are associated with ferroptosis susceptibility in Fuchs endothelial corneal dystrophy

Fuchs endothelial corneal dystrophy (FECD), the leading indication for corneal transplantation in the U.S., causes loss of corneal endothelial cells (CECs) and corneal edema leading to vision loss. FECD pathogenesis is linked to impaired response to oxidative stress and environmental ultraviolet A (UVA) exposure. Although UVA is known to cause nonapoptotic oxidative cell death resulting from iron-mediated lipid peroxidation, ferroptosis has not been characterized in FECD. We investigated the roles of genetic background and UVA exposure in causing CEC degeneration in FECD. Using ungenotyped FECD patient surgical samples, we found increased levels of cytosolic ferrous iron (Fe2+) and lipid peroxidation in end-stage diseased tissues compared with healthy controls. Using immortalized and primary cell cultures modeling the TCF4 intronic trinucleotide repeat expansion genotype, we found altered gene and protein expression involved in ferroptosis compared to controls including elevated levels of Fe2+, basal lipid peroxidation, and the ferroptosis-specific marker transferrin receptor 1. Increased cytosolic Fe2+ levels were detected after physiologically relevant doses of UVA exposure, indicating a role for ferroptosis in FECD disease progression. Cultured cells were more prone to ferroptosis induced by RSL3 and UVA than controls, indicating ferroptosis susceptibility is increased by both FECD genetic background and UVA. Finally, cell death was preventable after RSL3 induced ferroptosis using solubilized ubiquinol, indicating a role for anti-ferroptosis therapies in FECD. This investigation demonstrates that genetic background and UVA exposure contribute to iron-mediated lipid peroxidation and cell death in FECD, and provides the basis for future investigations of ferroptosis-mediated disease progression in FECD.

cell biology↗

bioRxiv2022

Deep Learning Based Registration of Serial Whole-slide Histopathology Images in Different Stains

For routine pathology diagnosis and imaging based biomedical research, Whole-Slide Image (WSI) analyses have been largely limited to a 2D tissue image space. For a more definitive tissue representation to support fine-resolution spatial and integrative analyses, it is critical to extend such tissue based investigations to a 3D tissue space with spatially aligned serial tissue WSIs in different stains, such as Hematoxylin and Eosin (H&E) and Immunohistochemistry (IHC) biomarkers. However, such WSI registration is technically challenged by the overwhelming image scale, the complex histology structure change, and the significant difference in tissue appearances in different stains. We propose a novel translation based deep learning registration network CycGANRegNet that spatially aligns serial WSIs stained in H&E and by IHC biomarkers without prior deformation information for the model training. First, synthetic IHC images are produced from H&E slides through a robust image synthesis algorithm. Next, the synthetic and the real IHC images are registered through a Fully Convolutional Network with multi-scaled deformable vector fields and a joint loss optimization. We perform the registration at the full image resolution, retaining the tissue details in the results. Evaluated with a dataset of 76 breast cancer patients with one H&E and two IHC serial WSIs for each patient, CycGANRegNet outperforms multiple state-of-the-art deep learning based and conventional pathology image registration methods. Our results suggest that CycGAN-RegNet can produce promising registration results with serial WSIs in different stains, enabling integrative 3D tissue-based biomedical investigations.

bioinformatics↗

bioRxiv2021

Different brain systems support the aversive and appetitive sides of human pain-avoidance learning

Both unexpected pain and unexpected pain absence can drive avoidance learning, but whether they do so via shared or separate neural and neurochemical systems is largely unknown. To address this issue, we combined an instrumental pain-avoidance learning task with computational modeling, functional magnetic resonance imaging (fMRI) and pharmacological manipulations of the dopaminergic (100 mg levodopa) and opioidergic (50 mg naltrexone) systems (N=83). Computational modeling provided evidence that untreated participants learned more from received than avoided pain. Our dopamine and opioid manipulations negated this learning asymmetry by selectively increasing learning rates for avoided pain. Furthermore, our fMRI analyses revealed that pain prediction errors were encoded in subcortical and limbic brain regions, whereas no-pain prediction errors were encoded in frontal and parietal cortical regions. However, we found no effects of our pharmacological manipulations on the neural encoding of prediction errors. Together, our results suggest that human pain-avoidance learning is supported by separate threat- and safety-learning systems, and that dopamine and endogenous opioids specifically regulate learning from successfully avoided pain.

neuroscience↗

bioRxiv2021

Effect sizes and test-retest reliability of the fMRI-based Neurologic Pain Signature

Identifying biomarkers that predict mental states with large effect sizes and high test-retest reliability is a growing priority for fMRI research. We examined a well-established multivariate brain measure that tracks pain induced by nociceptive input, the Neurologic Pain Signature (NPS). In N = 295 participants across eight studies, NPS responses showed a very large effect size in predicting within-person single-trial pain reports (d = 1.45) and medium effect size in predicting individual differences in pain reports (d = 0.49). The NPS showed excellent shortterm (within-day) test-retest reliability (ICC = 0.84, with average 69.5 trials/person). Reliability scaled with the number of trials within-person, with [≥]60 trials required for excellent test-retest reliability. Reliability was tested in two additional studies across 5-day (N = 29, ICC = 0.74, 30 trials/person) and 1-month (N = 40, ICC = 0.46, 5 trials/person) test-retest intervals. The combination of strong within-person correlations and only modest between-person correlations between the NPS and pain reports indicate that the two measures have different sources of between-person variance. The NPS is not a surrogate for individual differences in pain reports but can serve as a reliable measure of pain-related physiology and mechanistic target for interventions. Significance statementCurrent efforts towards translating brain biomarkers require identifying brain measures that can strongly and reliably predict outcomes of interest. We systematically examined the performance of a well-established brain activity pattern, the Neurological Pain Signature (NPS), in a large and diverse sample of participants. The NPS showed excellent reliability, and the reliability scaled with the number of trials within-person. The NPS responses showed strong correlations with pain reports at the within-person level but only modest correlations at the between-person level. The findings suggest that the NPS is not a surrogate for individual differences in pain reports but can serve as a reliable measure of a pain-related physiological target. Author NoteThis project was supported by grants R01MH076136 (T.D.W.), R01DA046064, R01EB026549, and R01DA035484. Elizabeth A. Reynolds Losin was supported by a Mentored Research Scientist Development award from National Institute On Drug Abuse of the National Institutes of Health (K01DA045735). Lauren Y. Atlas was supported in part by funding from the Intramural Research Program of the National Center for Complementary and Integrative Health. Yoni K. Ashar was supported by NCATS Grant # TL1-TR-002386. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Code for all analyses and figures is available at https://github.com/XiaochunHan/NPS_measurement_properties. Data for all analyses and figures is available at https://osf.io/v9px7/.

neuroscience↗

bioRxiv2021

Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning.

Genomic data analysis is a fundamental system for monitoring pathogen evolution and the outbreak of infectious diseases. Based on bioinformatics and deep learning, this study was designed to identify the genomic variability of SARS-CoV-2 worldwide and predict the impending mutation rate. Analysis of 259044 SARS-CoV-2 isolates identify 3334545 mutations (14.01 mutations per isolate), suggesting a high mutation rate. Strains from India showed the highest no. of mutations (48) followed by Scotland, USA, Netherlands, Norway, and France having up to 36 mutations. Besides the most prominently occurring mutations (D416G, F106F, P314L, and UTR:C241T), we identify L93L, A222V, A199A, V30L, and A220V mutations which are in the top 10 most frequent mutations. Multi-nucleotide mutations GGG>AAC, CC>TT, TG>CA, and AT>TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C>T, A>G, and A>T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T>C, G>A, and G>T mutations, respectively. T>G\A, C>G\A, and A>T\C are not anticipated in the future. Since SARS-CoV-2 is evolving continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide.

bioinformatics↗

bioRxiv2021

Effect of plant tubulin kinetic diversification on microtubule lengths

Microtubules (MTs) are dynamic polymers vital for cellular physiology. Bulk tubulin polymerization is nucleation dependent, while individual filaments exhibit dynamic instability driven by GTP hydrolysis rates. Although MTs assembled from well-studied animal brain tubulins have very comparable nucleation and GTP-hydrolysis rates, the kinetic rates of evolutionarily more distant species could diverge. Here we focus on a plant tubulin, the legume Vigna sp. (mung bean) to test the effect of kinetic diversification on MT polymerization. We activity purify tubulin from seedlings and find MT filaments are fewer and shorter than animal brain tubulin. We find mung tubulin polymerization kinetics is nucleation dependent with a high rate of GTP hydrolysis and a critical concentration lower than previously reported for tubulins. A computational model of the kinetics based on the relative influence of rates of nucleation and hydrolysis demonstrates increased rates of hydrolysis can affect MT filament numbers and their lengths, as compared to increasing nucleation rates. Our approach provides a framework to compare the effect of evolutionary diversification of MT nucleation and elongation.

biophysics↗

bioRxiv2021

Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin

The process wherein dividing cells exhaust proliferative capacity and enter into replicative senescence has become a prominent model for cellular aging in vitro. Despite decades of study, this cellular state is not fully understood in culture and even much less so during aging. Here, we revisit Leonard Hayflicks original observation of replicative senescence in WI-38 human lung fibroblasts equipped with a battery of modern techniques including RNA-seq, single cell RNA-seq, proteomics, metabolomics, and ATAC-seq. We find evidence that the transition to a senescent state manifests early, increases gradually, and corresponds to a concomitant global increase in DNA accessibility in nucleolar and lamin associated domains. Furthermore, we demonstrate that senescent WI-38 cells acquire a striking resemblance to myofibroblasts in a process similar to the epithelial to mesenchymal transition (EMT) that is regulated by the transcription factors YAP1/TEAD1 and TGF-{beta}2. Lastly, we show that verteporfin inhibition of YAP1/TEAD1 activity in aged WI-38 cells robustly attenuates this gene expression program.

genomics↗

bioRxiv2021

The aversive value of pain in human decision-making

According to basic utilitarian principles, people should try to maximize rewards and minimize pain. Here, participants were put in a situation where monetary rewards were paired to electric shocks spanning between pain detection and tolerance thresholds. Monetary offers ranged linearly from $0 to $5 or $10 in Group1 and 2, respectively, and exponentially from $0 to $5 in Group3. The value of pain increased quadratically as a function of the anticipated pain intensity. While increasing the range of monetary offers increased the price requested to accept pain, skewing the distribution of rewards encouraged profit maximization. Participants scoring higher on harm avoidance and lower on persistence scales requested more money to accept pain. Accepting highly painful offers slowed decisions regardless of the value of the concurrent reward. Altogether, pain-related decisions are highly relative to the local range of available rewards and may be under the control of more automatic avoidance mechanisms.

neuroscience↗

bioRxiv2021

West Nile virus in crocodiles and mosquitoes in Zimbabwe

We detected, for the first time, West Nile virus lineages 1 and 2 in Zimbabwe in mosquitoes and crocodile tissue samples, including fluid from egg waste. Our results provide evidence of WNV circulation in Zimbabwe, suggesting that an evaluation of the risk to humans and susceptible animals should be considered.

microbiology↗

bioRxiv2020

Evaluation of optically tailored fluorescent silicon quantum dots for bioimaging of the tear film

This experimental study aimed to investigate the feasibility of using silicon quantum dots doped with transition metals: scandium, copper and zinc as contrast agents for eventual application for the study of the tear film in eyes. Si-QDs were synthesized and characterized by transmission electron microscopy, photoluminescence, absorbance and transient absorption measurements. The fluorescence of Si-QDs was investigated when combined with TheraTears(R) (a balanced electrolyte formula for dry eye therapy). An optical imaging system composed of a modified slit lamp biomicroscope combined with a high-resolution Zyla sCMOS camera, SOLIS software, custom-made optical mounts and emission filters (460 nm, 510 nm and 530 nm) were used for in vitro imaging of Si-QDs with TheraTears(R). The average size of Si-QDs was 2.65 nm. In vitro imaging of Sc-Si-QDs and Cu-Si-QDs indicated their stable and bright fluorescence with TheraTears(R). Sc-Si-QDs were significantly brighter compared to Cu-Si-QDs and Zn-Si-QDs, and the Zn-Si-QDs showed a tendency to clump in TheraTears(R). The fluorescence of the Si-QDs was detected down to a concentration of 0.01 {micro}g/mL within a total volume of 5 {micro}L. Cu-Si-QDs and Sc-Si-QDs showed brighter fluorescence than Zn-Si-QDs. However, Zn-Si-QDs and to a lesser extent, Cu-Si-QDs showed some aggregation at specific concentrations. Sc-Si-QDs are proposed as a better option for further development as an in vivo bioimaging agent to study the tear film dynamics.

biochemistry↗

bioRxiv2020

Bundle-specific associations between white matter microstructure and Aβ and tau pathology at their connecting cortical endpoints in older adults at risk of Alzheimer's disease

Beta-amyloid (A{beta}) and tau proteins, the pathological hallmarks of Alzheimers disease (AD), are believed to spread through connected regions. Combining diffusion imaging and positron emission tomography, we investigated associations between A{beta}, tau and white matter microstructure specifically in bundles connecting brain regions in which AD pathology accumulates. In 126 cognitively normal elderly at risk of AD, we focussed on free-water corrected diffusion measures in the cingulum, posterior cingulum, fornix and uncinate fasciculus. We found higher tissue fractional anisotropy and lower mean and radial diffusivity related to increased A{beta} at the cortical endpoints of the cingulum and fornix. We observed similar but stronger associations in the uncinate fasciculus, but with increased A{beta} and tau at the endpoints of this bundle. This consistent pattern of associations, with opposite directionality to the usual degeneration pattern in symptomatic individuals, suggests more restricted diffusion in bundles vulnerable to preclinical AD pathology.

neuroscience↗

bioRxiv2020

Evoked pain intensity representation is distributed across brain systems: A multistudy mega-analysis

Information is coded in the brain at different scales for different phenomena: locally, distributed across regions and networks, and globally. For pain, the scale of representation is controversial. Although generally believed to be an integrated cognitive and sensory phenomenon implicating diverse brain systems, quantitative characterizations of which regions and networks are sufficient to represent pain are lacking. In this meta-analysis (or mega-analysis) using data from 289 participants across 10 studies, we use model comparison combined with multivariate predictive models to investigate the spatial scale and location of acute pain representation. We compare models based on (a) a single most pain-predictive module, either previously identified elementary regions or a single best large-scale cortical resting-state network module; (b) selected cortical-subcortical systems related to evoked pain in prior literature ( multi-system models); and (c) a model spanning the full brain. We estimate the accuracy of pain intensity predictions using cross validation (7 studies) and subsequently validate in three independent holdout studies. All spatial scales convey information about pain intensity, but distributed, multi-system models better characterize pain representations than any individual region or network (e.g. multisystem models explain >20% more of individual subject pain ratings than the best elementary region). Full brain models showed no predictive advantage over multi-system models. These findings quantify the extent that representation of evoked pain experience is distributed across multiple cortical and subcortical systems, show that pain representation is not circumscribed by any elementary region or conical network, and provide a blueprint for identifying the spatial scale of information in other domains. Significance StatementWe define modular, multisystem and global views of brain function, use multivariate fMRI decoding to characterize pain representations at each level, and provide evidence for a multisystem representation of evoked pain. We further show that local views necessarily exclude important components of pain representation, while a global full brain representation is superfluous, even though both are viable frameworks for representing pain. These findings quantitatively juxtapose and reconcile divergent conclusions from evoked pain studies within a generalized neuroscientific framework, and provide a blueprint for investigating representational architecture for diverse brain processes.

neuroscience↗

bioRxiv2020

A small molecule that binds an RNA repeat expansion stimulates its decay via the exosome complex

We describe the design of a small molecule that binds the structure of a r(CUG) repeat expansion [r(CUG)exp] and reverses molecular defects in two diseases mediated by the RNA - myotonic dystrophy type 1 (DM1) and Fuchs endothelial corneal dystrophy (FECD). Thus, a single structure-specific ligand has potential therapeutic benefit for multiple diseases, in contrast to oligonucleotide-based modalities that are customized for each disease by nature of targeting the gene that harbors the repeat. Indeed, the small molecule binds the target with nanomolar affinity and >100-fold specificity vs. many other RNAs and DNA. Interestingly, the compounds downstream effects are different in the two diseases, owing to the location of the repeat expansion. In DM1, r(CUG)exp is harbored in the 3 untranslated region (UTR) of and mRNA, and the compound has no effect on the RNAs abundance. In FECD, however, r(CUG)exp is located in an intron, and the small molecule, by binding the repeat expansion, facilitates excision of the intron, which is then degraded by the exosome complex exonuclease, hRRP6. Thus, structure-specific, RNA-targeting small molecules can act disease-specifically to affect biology, either by disabling its gain-of-function mechanism (DM1) or by stimulating quality control pathways to rid a disease-affected cell of a toxic RNA (FECD). Significance statementMany different diseases are caused by toxic structured RNAs. Herein, we designed a lead small molecule that binds a toxic structure and rescues disease biology. We show that a structure-specific small molecule can improve disease-associated defects in two diseases that share the common toxic RNA structure. In one disease, the toxic structure is harbored in an intron and causes its retention. The compound facilitates processing of a retained intron, enabling the disease-affected cell to remove the toxic RNA.

cell biology↗

bioRxiv2019

Solo: doublet identification via semi-supervised deep learning

AO_SCPLOWBSTRACTC_SCPLOWSingle cell RNA-seq (scRNA-seq) measurements of gene expression enable an unprecedented high-resolution view into cellular state. However, current methods often result in two or more cells that share the same cell-identifying barcode; these "doublets" violate the fundamental premise of single cell technology and can lead to incorrect inferences. Here, we describe Solo, a semi-supervised deep learning approach that identifies doublets with greater accuracy than existing methods. Solo can be applied in combination with experimental doublet detection methods to further purify scRNA-seq data to true single cells beyond any previous approach.

bioinformatics↗

bioRxiv2019

The effect of blue-blocking lenses on photostress recovery times for low and high contrast chromatic and achromatic stimuli

The selective reduction in visible wavelengths transmitted through commercially available blue-blocking lenses (BBLs) is known to influence the appearance and contrast detection of objects, particularly at low light levels which may impact the human retinal receptor response time to dynamic light changes during phostress events. In the present study, we assessed whether BBLs selectively affect photostress recovery times (PSRTs) in 12 participants for chromatic and achromatic stimuli presented under low and high contrast luminance conditions. Four types of commercially available BBLs were evaluated, and their effects on PSRTs were investigated. Our results showed that PSRTs required to detect high contrast chromatic and achromatic stimuli were unaffected by BBLs when compared to a clear control lens. However, PSRTs were significantly affected by BBLs and were longer when chromatic and achromatic stimuli were of low contrast. In addition, BBLs had the greatest impact on the PSRTs of blue coloured targets, and this was dependent on the spectral transmittance profile. These results indicate that wearing BBLs under low contrast conditions can have serious implications for visual behavior, particularly under low-light levels and in situations in which the observer is directly exposed to bright light sources. For example, during night time driving, the driver might be briefly exposed to bright lights by glancing at the headlights of a passing car. This increases the time required for vision to be restored after bright light exposure, resulting in delayed object detection, and therefore stoppage and reaction times, which might pose a safety risk for a driver.

physiology↗