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Roy, D.

Publications and source records attributed to Roy, D..

At least 37 records · Page 2Linked to original sources

Evidence that Entomophthora muscae controls the timing of host death via its own circadian clock

Timing in the natural world is a matter of life or death; consequently, nearly all life on Earth has evolved internal circadian clocks. Many behavior-manipulating parasites exhibit striking daily timing, but whether this is clock-driven has remained unclear. Here, we leveraged the laboratory-tractable zombie fruit fly model, Drosophila melanogaster infected by the behavior manipulating fungus Entomophthora muscae, to tackle this long standing mystery. Using an automated behavioral paradigm, we found that the timing of death of wild-type flies continues to occur with [~]21 hour periodicity in the absence of environmental cues, indicating that death is controlled by a system-intrinsic clock. Experiments with circadian and photoreception mutants revealed that death is independent of host genotype, suggesting that the host does not drive this rhythm and raising the possibility that timing is dictated by E. muscae. Transcriptomic analysis of in vitro grown fungus revealed that E. muscae maintains rhythmic gene expression independent of the fly host that peaks at sunset and has a free-running period of [~]22 hours. Among cycling genes, we identified a transcript encoding a protein with high homology to white collar-1, the blue light sensor and core component of the molecular oscillator in the model ascomycete fungus Neurospora crassa. Altogether, our findings suggest that E. muscae has an endogenous circadian clock. Given that the host genetic background does not appear to dictate the timing of death, our results suggest that the E. muscae clock may be the primary driver of this rhythm. Our work supports a model in which a fungal clock influences fly outcomes, suggesting that endogenous parasitic clocks may play a broader role in the temporal coordination of host manipulation.

microbiology↗

Polymorphic α-Glucans as Structural Scaffolds in Cryptococcus Cell Walls for Chitin, Capsule, and Melanin: Insights from 13C and 1H Solid-State NMR

Cryptococcus species are major fungal pathogens responsible for life-threatening infections in approximately a million individuals globally each year, with alarmingly high mortality rates. These fungi are distinguished by a distinctive cell wall architecture further reinforced by two virulence-associated layers, melanin and capsule, rendering them insensitive to antifungal agents targeting the cell wall, such as echinocandins. The molecular interplay between these three biomolecular layers remains poorly understood. Here we employ solid-state NMR spectroscopy to examine intact cells of both wild-type and capsule-deficient strains of C. neoformans, along with its melanized cells. High-resolution 13C and 1H data revealed five distinct structural forms of -1,3-glucans that play versatile roles in forming the rigid cell wall scaffold by interacting with chitin microfibrils and chitosan, and in stabilizing the mobile matrix by associating with {beta}-1,6-glucan and a small fraction of {beta}-1,3-glucan. Two primary forms of -1,3-glucans were distributed throughout the cell wall, hosting melanin deposition in the inner domain and capsule attachment on the cell surface. These findings offer a paradigm shift in understanding the cryptococcal cell wall and its interaction with two key virulence factors on opposite sides, raising critical biochemical questions that could inform the development of more effective antifungal treatments for cryptococcosis.

biochemistry↗

Elucidating tissue and sub-cellular specificity of the entire SUMO network reveals how stress responses are fine-tuned in a eukaryote

SUMOylation is essential in plant and animal cells, but it remains unknown how SUMO components act in concert to modify specific targets in response to environmental stresses. In this study we characterise every SUMO component in the Arabidopsis root to create the first complete SUMO Cell Atlas in eukaryotes. This unique resource reveals wide spatial variation, where SUMO proteins and proteases have sub-functionalized in both their expression and subcellular localisation. During stress SUMO conjugation is mainly driven by tissue specific regulation of the SUMO E2 ligase. Stress-specific modulation of the SUMO pathway reveals unique combinations of Proteases being targeted for regulation in distinct root tissues by salt, osmotic and biotic signals. Our SUMO Cell Atlas resources reveal how this PTM influences cellular and tissue scale adaptations during root development and stress responses. We provide the first comprehensive study elucidating how multiple stress inputs can regulate an entire PTM system.

plant biology↗

A unique serum-free murine cortical astrocyte culture to study endoplasmic reticulum stress in response to amyloid-β

Astrocytes are integral to understand Alzheimers disease (AD) pathology but the existing serum-supplemented in vitro astrocyte culture models are not suitable to study certain stress response mechanisms. Here, we developed a serum-free murine primary cortical astrocyte culture model to study endoplasmic reticulum (ER) stress and inflammation to see the effect of amyloid-beta (A{beta}1-42). Astrocytes were cultured in a controlled serum-free environment to minimize interference from serum components. Serum-free astrocytes were exposed to oligomeric A{beta} to induce ER stress and inflammation. Initially no significant activation of eIF2, a key marker of ER stress, was observed under serum-free condition but with the removal of N-acetyl cysteine ER stress response was enhanced after 24 hours of A{beta} exposure. Subsequently, the inflammatory response, assessed through TNF- expression, was minimal in the presence of growth factors but became pronounced when these factors were withdrawn. Astrocytic reactivity, assessed by GFAP expression, was observed with prolonged A{beta} exposure, indicating a reactive astrogliosis response. Transcript analysis revealed a time-dependent shift in the expression of inflammatory modulators, with early time points showing increased anti-inflammatory markers and late exposure promoting pro-inflammatory responses. These findings highlight the potential of serum-free cultures for studying ER stress and inflammation together in astrocytes and offer insights into the complex role of these cells in AD pathophysiology.

neuroscience↗

The interplay of climate change, urbanization, and species traits shapes European butterfly population trends

Species populations naturally fluctuate, yet long-term trend analysis can reveal patterns of success, decline, or stability under global change pressures. While responses to climate change are well-documented, its synergy with another major global driver, urbanization, remains understudied. Here, we analyzed long-term monitoring data from over 8,400 populations of 145 butterfly species across Europe, representing a high diversity of species traits, to assess population trends in response to climate change and urbanization. We examined how population responses vary between urban and rural contexts, providing insights into the influence of site-specific conditions. Climate warming was associated with population declines, which were more pronounced in urban areas. The effect of precipitation varied between environments: increases in precipitation generally benefited populations in rural areas but had detrimental effects in urban ones. Aridity consistently drove population declines across environments, with slightly stronger effects in urban areas. Species with colder climatic niches declined the most in response to warming, increased aridity, and reduced precipitation, while trophic specialists were particularly vulnerable to aridity and precipitation changes in urban environments. Although increasing urbanization did not explain overall population trends, its effects became evident when considering species traits, with certain traits being more vulnerable to urbanization. Specifically, species with narrow climatic niches declined the most in response to urbanization in rural areas, while those and larger body sizes decline the most in urban environments. Our findings highlight the complex interplay between environmental change, landscape context, and species traits in shaping biodiversity outcomes. Importantly, our results suggest that urbanization generally amplifies the impact of climate change on insect population trends.

ecology↗

Evaporation and pathogenesis of levitated bacteria-laden surrogate respiratory fluid droplets: At different relative humidity and evaporation stages

HypothesisAerosols are the principal cause of airborne infections and respiratory diseases. Droplets ejected from the host can evaporate and form a precipitate in the air (aerosol mode), or evaporate for some time, and fall on the ground (mixed mode) or directly fall on the ground and evaporate as sessile mode. Different evaporation modes, stages of evaporation and the relative humidity (RH) conditions affect the survival and infectivity of the bacteria in the precipitate. ExperimentsWe have investigated three droplet diameter reduction ratio-based stages of evaporation of a bacteria-laden levitated droplet at two different RH settings and evaporation modes (aerosol and mixed) mimicking real-life scenarios. The low RH condition mimics evaporation in arid regions. e.g., Delhi and the high RH conditions imitate cold areas like London. The study analyses the mass transport, micro-characterizes the samples, and investigates the survival and infectivity of bacteria in the sample. FindingsThe bacteria survive more in the high RH condition than in the low RH condition for all diameter reduction ratio-based stages and modes of evaporation. For the aerosol mode, at a fixed RH condition, the evaporation time plays a vital role as the bacteria in early-stage partially dried samples are more viable than the full precipitate. The evaporation rate, and the generation of reactive oxygen species (ROS) cause a remarkable difference in the viability and infectivity of the bacterial samples. Therefore, our findings report that the evaporation history of an infected droplet is an indispensable factor in determining bacterial viability and subsequent infectivity.

microbiology↗

An envelope stress response governs long-chain fatty acid metabolism via a small RNA to maintain redox homeostasis in Escherichia coli

Long-chain fatty acids (LCFAs) are a tremendous source of energy for several bacteria but are complex to use because they induce redox stress. We previously showed that LCFA degradation impedes oxidative protein folding in the Escherichia coli envelope, an issue that arises due to the insufficiency of ubiquinone, a lipid-soluble electron carrier in the electron transport chain (ETC). To maintain redox homeostasis, E. coli activates the CpxAR two-component system; however, the nature of feedback imparted by this envelope stress response (ESR) remained unknown. Here, we show that contrary to the well-recognized remedial mode of Cpx restoring envelope integrity by upregulating protein quality control factors, in LCFA-grown cells, it uses a preventive measure to maintain homeostasis. Cpx increases ubiquinone availability for oxidative protein folding by suppressing LCFA metabolism and directly increasing ubiquinone levels. Further, rather than using its conventional mode of imparting regulation via CpxR working as a transcriptional regulator, during LCFA metabolism, Cpx mainly uses its non-coding arm to counteract envelope redox stress. The Cpx-regulated small RNA CpxQ represses fad genes involved in LCFA transport and {beta}-oxidation, downregulates components of glyoxylate shunt, gluconeogenesis, and ETC, and increases ubiquinone content. Corroborating with its role in repressing LCFA metabolism and maintaining redox homeostasis, CpxQ overexpression impairs growth of E. coli in LCFAs and CpxQ deletion renders LCFA-grown E. coli hypersensitive to a thiol agent. Our foremost work studying the interconnection between LCFA metabolism, redox stress, and ESR in E. coli provides a rationale for investigating similar networks in other LCFA-utilizing bacteria. Significance StatementLong-chain fatty acids (LCFAs) are energy-rich nutrients for Escherichia coli; however, their utilization hampers disulfide bond (DSB) formation in secreted proteins, an essential process that occurs in the envelope compartment. Here, we show that an envelope stress response manipulates LCFA metabolism in E. coli and uses a small RNA (sRNA) to restore homeostasis. Several bacteria with a huge impact on human health use host-derived LCFAs during infection. Because many virulence factors require DSB formation, the present study offers a basis to examine whether sRNAs play a role in governing envelope redox balance during LCFA metabolism in pathogens. The sRNA-mediated control is likely an ideal strategy both for rapid response to and quick recovery from LCFA-induced stress.

microbiology↗

Synergistic control of axon regeneration and functional recovery by let-7 miRNA and Insulin signalling (IIs) pathways

The capability of neurons to regenerate after injury becomes poor in adulthood. Previous studies indicated that loss of either let-7 miRNA or components of Insulin signalling (IIs) can overcome the age-related decline in axon regeneration in C. elegans. In this study, we wanted to understand the relationship between these two pathways in axon regeneration. We found that the simultaneous removal of let-7 and the gene for insulin receptor daf-2 synergistically increased the functional recovery involving posterior touch sensation following axotomy of PLM neuron in adulthood. Conversely, the loss of let-7 could bypass the regeneration block due to the loss of DAF-16, a transcriptional target of DAF-2. Similarly, the loss of daf-2 could bypass the requirement of LIN-41, a transcriptional co-factor of the let-7 pathway. Our analysis revealed that these two pathways synergistically control targeting of the regenerating axon to the ventral nerve cord, which leads to functional recovery. The computational analysis of the gene expression data revealed a large number of genes, their interacting modules, and hub genes under let-7 and IIs pathway are exclusive in nature. Our study highlights a potential to promote neurite regeneration by harnessing the independent gene expression program involving the let-7 and Insulin signalling pathways.

neuroscience↗

Towards optical measurements of membrane potential values in Bacillus subtilis using fluorescence lifetime

Membrane potential (MP) changes can provide a simple readout of bacterial functional and metabolic state or stress levels. While several optical methods exist for measuring fast changes in MP in excitable cells, there is a dearth of such methods for absolute and precise measurements of steady-state membrane potentials (MPs) in bacterial cells. Conventional electrode-based methods for the measurement of MP are not suitable for calibrating optical methods in small bacterial cells. While optical measurement based on Nernstian indicators have been successfully used, they do not provide absolute or precise quantification of MP or its changes. We present a novel, calibrated MP recording approach to address this gap. In this study, we used a fluorescence lifetime-based approach to obtain a single-cell resolved distribution of the membrane potential and its changes upon extracellular chemical perturbation in a population of bacterial cells for the first time. Our method is based on (i) a unique VoltageFluor (VF) optical transducer, whose fluorescence lifetime varies as a function of MP via photoinduced electron transfer (PeT) and (ii) a quantitative phasor-FLIM analysis for high-throughput readout. This method allows MP changes to be easily visualized, recorded and quantified. By artificially modulating potassium concentration gradients across the membrane using an ionophore, we have obtained a Bacillus subtilis-specific MP versus VF lifetime calibration and estimated the MP for unperturbed B. subtilis cells to be -65 mV (in MSgg), -127 mV (in M9) and that for chemically depolarized cells as -14 mV (in MSgg). We observed a population level MP heterogeneity of [~]6-10 mV indicating a considerable degree of diversity of physiological and metabolic states among individual cells. Our work paves the way for deeper insights into bacterial electrophysiology and bioelectricity research.

biophysics↗

Age associated alterations in the cortical representation of cardiac signals: A heartfelt tale

The brain continuously tracks signals from the body, including the heartbeat, which influence internal states such as the perception of time, well-known to accelerate with age and disrupted in disorders such as Parkinsons disease and dementia. The present study examined whether the representation of cardiac events onto spontaneous neural oscillations maps to regions responsible for processing time-perception, show age-related differences, and uncovered the mechanisms that may underlie any such reorganization. From a large cohort (N = 620), cortical heartbeat-evoked responses (HERs) were characterized and their sources were pinned to frontotemporal regions. Phase-based analyses demonstrated that cardiac signals affect phase of ongoing neural oscillations in the theta frequency band, rather than altering overall power, with this effect consolidating in older adults. Advanced statistical analysis further indicated that these changes are primarily driven by enhanced bottom-up heart-to-brain influences, revealing that altered interoceptive signaling can shape the age-related changes in time perception.

neuroscience↗

Hemispheric specialization of functions are tuned by conduction velocities of neuronal propagation in large-scale brain networks

Analogous to the notion of pleiotropy where one gene can influence two or three unrelated traits, shared structural connectome encompassing both hemispheres of human brain gets functionally segregated along left vs right hemispheres during speech and melody processing, respectively. Here, the underlying neural mechanism is explored with a combined empirical and computational approach wherein, context-specific causal outflow of information emerging from primary auditory cortices (PAC) is shown to be guiding the hemispheric specialization of speech and melody processing while human volunteers listened to naturalistic music while their electroencephalogram (EEG) were recorded. Using a detailed whole-brain connectome model guided by diffusion MRI, individual-specific functional lateralization were predicted at cortical sources representing an extended auditory processing network. High levels of accuracy in prediction can be achieved after optimizing conduction velocity - controller of transmission delays of neural information processing. Thus, a tuning-by-delay mechanism is presented, which when triggered by the spectro-temporal complexity of the task context, guides the geometry of lateralization.

neuroscience↗

Aging distorts the representation of emotions by amplifying prefrontal variability

Understanding the mechanisms behind the variability of neural signals holds the key to the characterization of developmental and lifespan aging trajectories. Here we propose that tracking temporally structured neural fluctuations or volatility in brain areas during naturalistic tasks provides a more salient characterization of ageing trajectories compared to measures based on mean and resting-state variability. Compared to other prefrontal regions, the orbitofrontal cortices (OFC) exhibit higher BOLD signal variability in aged individuals. Neural latent state analysis revealed that, in contrast to the stable representations in younger adults, the OFC in older adults exhibited more temporally distorted representations, mirroring their distinct affective experiences. Furthermore, lower OFC volatility during the movie was associated with participants bias toward positive responses in a separate emotional reactivity task. This suggests orbitofrontal neural volatility might be a general adaptive response to affective computations. To investigate this further, a Bayesian learning model of valence dynamics was employed, which revealed that older adults exhibit heightened uncertainty in neural representations while estimating affective states. Collectively, these results indicate that neural volatility identified through BOLD variability carries unique information about older adults affective experiences and how naturalistic neuroimaging can chart a way forward in understanding this better.

neuroscience↗

Explainable Deep Learning Framework: Decoding Brain Task and Prediction of Individual Performance in False-Belief Task at Early Childhood Stage

Decoding of brain tasks aims to identify individuals brain states and brain fingerprints to predict behavior. Deep learning provides an important platform for analyzing brain signals at different developmental stages to understand brain dynamics. Due to their internal architecture and feature extraction techniques, existing machine learning and deep-learning approaches for fMRI-based brain decoding must improve classification performance and explainability. The existing approaches also focus on something other than the behavioral traits that can tell about individuals variability in behavioral traits. In the current study, we hypothesized that even at the early childhood stage (as early as 3 years), connectivity between brain regions could decode brain tasks and predict behavioural performance in false-belief tasks. To this end, we proposed an explainable deep learning framework to decode brain states (Theory of Mind and Pain states) and predict individual performance on ToM-related false-belief tasks in a developmental dataset. We proposed an explainable spatiotemporal connectivity-based Graph Convolutional Neural Network (Ex-stGCNN) model for decoding brain tasks. Here, we consider a dataset (age range: 3-12 yrs and adults, samples: 155) in which participants were watching a short, soundless animated movie, "Partly Cloudy," that activated Theory-of-Mind (ToM) and pain networks. After scanning, the participants underwent a ToMrelated false-belief task, leading to categorization into the pass, fail, and inconsistent groups based on performance. We trained our proposed model using Static Functional Connectivity (SFC) and Inter-Subject Functional Correlations (ISFC) matrices separately. We observed that the stimulus-driven feature set (ISFC) could capture ToM and Pain brain states more accurately with an average accuracy of 94%, whereas it achieved 85% accuracy using SFC matrices. We also validated our results using five-fold cross-validation and achieved an average accuracy of 92%. Besides this study, we applied the SHAP approach to identify neurobiological brain fingerprints that contributed the most to predictions. We hypothesized that ToM network brain connectivity could predict individual performance on false-belief tasks. We proposed an Explainable Convolutional Variational Auto-Encoder model using functional connectivity (FC) to predict individual performance on false-belief tasks and achieved 90% accuracy.

neuroscience↗

ROS responsive Aux/IAA multimerization modulates auxin responses

Reactive oxygen species (ROS) function as key signals in plants to enable adaptation to environmental stresses. Plant roots respond to transient water stress by temporarily ceasing branching using the acclimative response xerobranching1. In this study, we report that a rapid ROS burst regulates Xerobranching by inducing multimerization of auxin repressor protein IAA3/SHY2. Mutations in specific cysteine residues in IAA3/SHY2 disrupt redox-mediated multimerization and interaction with co-repressor TPL, but not with auxin response partner ARF7 and auxin receptor TIR1. ROS-mediated oligomerization of IAA3/SHY2 is required for efficient ARF mediated target gene repression during Xerobranching and lateral root emergence. We demonstrate that AUX/IAA proteins vary in their redox mediated multimerization, revealing a new auxin response regulatory mechanism that directly connects ROS sensing to auxin signalling. Our study reveals how ROS, auxin and water stress intersect to shape acclimative responses in plant roots and maintain their phenotypic plasticity.

plant biology↗

Contributions of sub-community based on short and long-range white matter tracts in personalized age-associated neurocompensatory mechanism

Brain function is shaped by the local and global connections between its dynamical units and biological parameters. With aging, the anatomical connectivity undergoes significant deterioration (e.g., long-range white matter fiber loss), which affects the brains overall function. Despite the structural loss, previous research has shown that normative patterns of functions remain intact across the lifespan, defined as the compensatory mechanism of the aging brain. However, the crucial components in guiding the compensatory preservation of the dynamical complexity and the underlying mechanisms remain uncovered. Moreover, it remains largely unknown how the brain readjusts its biological parameters to maintain optimal brain dynamics with age; in this work, we provide a parsimonious mechanism using a whole-brain generative model to uncover the role of sub-communities comprised of short-range and long-range connectivity in driving the dynamic compensation process in the aging brain. We utilize two neuroimaging datasets to demonstrate how short--and long-range white matter tracts affect compensatory mechanisms. We unveil their modulation of intrinsic global scaling parameters, such as global coupling strength and conduction delay, via a personalized large-scale brain model. Our two key findings suggest that (1) the optimal coupling strength and delay play complementary roles in preserving the brains optimal working state. (2) Short-range tracts predominantly amplify global coupling strength with age, potentially representing an epiphenomenon of the compensatory mechanism. This mechanistically explains the significance of short-range connections in compensating for the major loss of long-range connections during aging. This insight could help identify alternative avenues to address aging-related diseases where long-range connections are significantly deteriorated.

neuroscience↗

Evaporation of bacteria-laden surrogate respiratory fluid droplets: On a hydrophilic substrate versus contact-free environment confers differential bacterial infectivity

The transmission of viruses/ bacteria cause infection predominantly via aerosols. The transmission mechanism of respiratory diseases is complex, including direct or indirect contact, large droplet, and airborne routes apart from close contact transmission. With this pretext, we have investigated two modes of droplet evaporation to understand its significance in airborne disease transmission; a droplet in a contact-free environment, which evaporates and forms droplet nuclei, and a droplet on a hydrophilic substrate (fomite). The study examines mass transport, the deposition pattern of bacteria in the precipitates, and their survival and virulence. The osmotic pressure increases with the salt concentration, inactivating the bacteria embedded in the precipitates with accelerated evaporation. Further, the bacterias degree of survival and enhanced pathogenicity are compared for both evaporation modes. The striking differences in pathogenicity are attributed to the evaporation rate, oxygen availability, and reactive oxygen species (ROS) generation.

microbiology↗

Diet-induced miRNAs regulate adult neurogenesis and functional activity of nascent neurons in the hypothalamus

A high-fat diet (HFD) regulates the feeding circuitry in young-adult mice by stimulating neurogenesis from {beta}2 tanycytes in the hypothalamus. However, the fate of HFD-induced tanycytic neurogenesis, the functional attributes of the nascent neurons, and mechanisms underlying their subsequent integration into the feeding-related neural circuitry remain unclear. microRNAs (miRNAs) are known to play crucial roles in adult neurogenesis. In this study, miRNA profiling of BrdU-labelled neurogenic {beta}2 tanycytes from HFD-fed mice identified a cohort of miRNAs that originate from different chromosomal loci rather than a single genomic cluster. Network analysis of predicted targets for these HFD-induced miRNAs identified key "hub" mRNA targets that influence neurogenesis and the functional integration of newborn neurons. These HFD-induced miRNAs promoted the differentiation of nascent neurons into orexigenic AgRP+ and anorexigenic POMC+ neurons. Interestingly, only AgRP+ newborn neurons were selectively integrated into the functional feeding circuit, as detected by c-Fos immunostaining. This integration was disrupted when HFD-induced miRNA activity was suppressed via hypothalamic miRNA sponge expression. Furthermore, HFD feeding increased body weight in female mice, which was abrogated upon the inhibition of HFD-induced miRNAs. Magnetic resonance imaging (MRI) revealed elevated liver fat in HFD-fed mice, which reverted to normal levels when the HFD-induced miRNAs in hypothalamic tanycytes were blocked. Collectively, the findings from our study highlight a miRNA-mediated paradigm that links HFD-induced neurogenesis from {beta}2 tanycytes to weight gain and liver fat accumulation, and identifies the selective integration of AgRP+ neurons into the feeding circuitry as a possible causality of HFD-induced changes to body weight. Significance StatementThis study highlights a miRNA-network that biases the transcriptional program in hypothalamic tanycytes to promote neurogenesis in young adult mice following their exposure to an acute high-fat diet (HFD) paradigm. These HFD-induced miRNAs have the potential to alter the brains feeding circuitry by promoting neurogenesis and the preferential functional integration of nascent orexigenic (AgRP+) neurons; resulting in weight gain and hepatic fat accumulation. Collective inhibition of this miRNA-network prevents the integration of newborn AgRP+ neurons and reverses the metabolic consequences of high-fat diet. Our study provides an unexplored link between diet, neurogenesis, and remodeling of the feeding circuitry; and reveals potential therapeutic targets for combating hyperphagic obesity.

neuroscience↗