Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 181 records · Page 10Linked to original sources

bioRxiv2024

Caloric restriction: A potential approach for mitigating neuronal damage: Lesson from cellular model of Alzheimer Disease

Alzheimers disease is a neurodegenerative disorder and characterized by amyloid beta accumulation, synaptic dysfunction, and oxidative stress, lacks effective therapies. Caloric restriction mimetics such as fisetin and chlorogenic acid, natural polyphenols with antioxidant and autophagy-inducing properties, show promise in mitigating age-related diseases. This study investigates their neuroprotective effects against amyloid beta induced toxicity in differentiated human neuroblastoma SHSY5Y cells. Amyloid beta exposure disrupted redox homeostasis, impaired autophagy, induced mitochondrial dysfunction, and exacerbating neuronal degeneration. Fisetin and chlorogenic acid treatments reversed these deleterious effects by restoring redox balance, suppressing reactive oxygen species and upregulating critical antioxidant enzymes like SOD1, GSR, and catalase. These compounds also attenuated amyloid beta induced mitophagy via reduced PINK1 expression and restored mitochondrial fusion by upregulating Mfn2. Autophagy-related pathways were significantly modulated, evidenced by increased AMPK and decreased mTOR mRNA levels, alongside elevated expression of ATG101, ATG13, ULK1, P62 and reduced ATG5 levels. Docking studies also revealed binding of fisetin and CGA within the binding pockets of AMPK and FKBP12 supporting their interaction. Furthermore, fisetin and CGA improved synaptic integrity by upregulating PSD95 and synaptophysin and reducing acetylcholinesterase expression. These findings highlight their potential in ameliorating amyloid beta induced neuronal toxicity through autophagy activation, synaptic preservation, and mitochondrial function enhancement. While this study demonstrates the transcriptional impact and binding affinities of these caloric restriction mimetics further translational and biophysical analyses are required to elucidate their mechanisms and confirm their therapeutic viability. This research underscores the potential of fisetin and CGA as neuroprotective agents, offering promising therapeutic avenues for combating related Alzheimers disease neuropathies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/628076v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1253dd0org.highwire.dtl.DTLVardef@1fd3ffforg.highwire.dtl.DTLVardef@1749d1dorg.highwire.dtl.DTLVardef@f71415_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

NFAT2 drives both Orai3 transcription and protein degradation by harnessing the differences in epigenetic landscape

The functional significance of any protein in physiological processes and pathological conditions is largely dependent on its expression profile. Therefore, nature has evolved several autonomous mechanisms to regulate protein expression such as transcription, translation, post-translational modifications and epigenetic changes. These processes are typically controlled by distinct molecular players with no overlapping roles. Here, we reveal that same transcription factor, NFAT2 regulates both transcription and lysosomal degradation of Orai3 oncochannel in a context dependent manner. We demonstrate that NFAT2 drives Orai3 transcription and thereby increases Orai3 levels in non-metastatic cancerous cells. While in invasive and metastatic cancerous cells, NFAT2 induces Orai3 lysosomal degradation by transcriptionally enhancing the levels of MARCH8 E3 ubiquitin ligase. Our biochemical and super-resolution microscopy data show that MARCH8 physically interacts with Orai3 eventually resulting in its degradation. Mechanistically, the dichotomy in regulation of Orai3 expression emerges from the differences in the epigenetic landscape of MARCH8. We uncover that the MARCH8 promoter is highly methylated in non-metastatic cancerous cells and hence NFAT2 does not induce MARCH8 mediated Orai3 degradation in these cells. Importantly, we demonstrate that MARCH8 restricts pancreatic cancer metastasis by targeting Orai3 degradation thereby highlighting pathophysiological importance of this signaling module. Taken together, we report a unique and clinically relevant scenario wherein nature has commissioned the same transcription factor to both enhance and curtail the expression of a target protein. Highlights[tpltrtarr] NFAT2 transcriptionally upregulates Orai3 Ca2+ channel in non-metastatic cells [tpltrtarr]NFAT2 induces Orai3 lysosomal degradation via MARCH8 E3 ubiquitin ligase in metastatic cells [tpltrtarr]The dichotomy in NFAT2s function is an outcome of differences in the methylation status of MARCH8 promoter [tpltrtarr]MARCH8 inhibits pancreatic cancer metastasis by driving Orai3 degradation Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/628081v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1292480org.highwire.dtl.DTLVardef@1b5b61org.highwire.dtl.DTLVardef@c4483org.highwire.dtl.DTLVardef@16607f8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

CrGEF1, CrGAP1, and CrGDI2 function as key regulators of ROP-GTPase mediated modulation of alkaloid biosynthesis in Catharanthus roseus

ROP-GTPase Regulatory Proteins (RGRPs) have been shown to control plant morphogenesis, development and immunity, however, their role in specialized metabolism is hitherto not known. Here, we demonstrate that specific RGRPs control monoterpene indole alkaloid (MIA) biosynthesis by interacting with distinct Rho of Plants (ROP) in Catharanthus roseus. Among the five Guanine nucleotide Exchange Factors (GEFs), four GTPase-activating proteins (GAPs), and two GDP dissociation inhibitors (GDIs) identified in the C. roseus genome, only CrGEF1, CrGAP1, and CrGDI2 specifically interacted with CrROP3 and CrROP5. These RGRPs displayed distinct cytosolic and/or membrane localization patterns, with their transcripts predominantly expressed in aerial tissues. Functional studies revealed that CrGEF1 acts as a positive regulator of MIA biosynthesis, as its silencing led to a reduction in MIA production, while overexpression enhanced MIA levels. Conversely, CrGAP1 and CrGDI2 function as negative regulators, with their silencing resulting in increased MIA production and their overexpression causing reduced MIA levels. Notably, terminal truncated forms of these RGRPs showed interaction with CrROP3 or CrROP5 but failed to influence MIA biosynthesis, underscoring the importance of these domains in their regulatory functions. Overall, our findings uncover a previously unexplored mechanism by which distinct RGRPs coordinate with specific ROPs to regulate transcription factors and fine-tune MIA biosynthesis in C. roseus. SignificancePlants fine-tune their metabolic pathways to adapt to environmental and physiological cues, balancing primary and specialized metabolism. Here, we uncover a feedback regulatory mechanism by which ROP-GTPase regulatory proteins (RGRPs) control alkaloid biosynthesis in Catharanthus roseus. We found that CrGEF1, CrGAP1, and CrGDI2 specifically interact with ROP-GTPases CrROP3 and CrROP5, modulating the monoterpene indole alkaloid (MIA) pathway. This RGRP-ROP module plays a crucial role in dynamically regulating MIA levels, where CrGEF1 promotes MIA production while CrGAP1 and CrGDI2 act as negative regulators. These findings highlight the importance of RGRP-ROP circuitry in control of alkaloid biosynthesis in C. roseus, and specialized metabolism in plants.

plant biology↗

bioRxiv2024

Beta burst characteristics and coupling within the sensorimotor cortical-subthalamic nucleus circuit in Parkinson's disease

BackgroundBursts of exaggerated subthalamic nucleus (STN) beta activity contribute to clinical impairments in Parkinsons disease (PD). Few studies have explored the characteristics and coupling of bursts across the sensorimotor cortical-STN circuit. ObjectiveWe sought to (1) establish the characteristics of sensorimotor cortical and STN bursts during naturalistic behaviours, and (2) determine the predictability of STN bursts from motor cortical recordings. MethodsWe analysed 1,478 hours of wirelessly streamed bilateral sensorimotor cortical and STN recordings from 5 PD patients. ResultsSTN bursts were longer than cortical bursts and had shorter inter-burst intervals. Long bursts (>200ms) in both structures displayed temporal overlap (>30%), with an estimated cortico-STN conduction delay of 8ms. Furthermore, approximately 27% of all STN bursts were preceded by a cortical burst. ConclusionCortical beta bursts tend to precede STN beta bursts, with short delays. However, subcortical mechanisms are also likely to contribute to STN burst initiation and propagation.

neuroscience↗

bioRxiv2024

Ezh2 Delays Activation of Differentiation Genes During Normal Cerebellar Granule Neuron Development and in Medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumour in children. The Sonic Hedgehog (SHH)-medulloblastoma subtype arises from the cerebellar granule neuron lineage. Terminally differentiated neurons are incapable of undergoing further cell division, so an effective treatment for this tumour could be to force neuronal differentiation. Differentiation therapy provides a potential alternative for patients with medulloblastoma who harbor mutations that impair cell death pathways (TP53), which is associated a with high mortality. To this end, our goal was to explore epigenetic regulation of cerebellar granule neuron differentiation in medulloblastoma cells. Key regulators were discovered using chromatin immunoprecipitation with high-throughput sequencing. DNA-bound protein and chromatin protein modifications were investigated across all genes. We discovered that Ezh2-mediated tri-methylation of the H3 histone (H3K27me3), occurred on more than half of the 787 genes whose transcription normally increases as granule neurons terminally differentiate. Conditional knockout of Ezh2 led to early initiation of differentiation in granule neuron precursors (GNPs), but only after cell cycle exit had occurred. Similarly, in MB cells, neuronal differentiation could be induced by preventing H3K27me3 modifications using an Ezh2 inhibitor (UNC1999), but only when UNC1999 was combined with forced cell cycle exit driven by a CDK4/6 inhibitor (Palbociclib). Ezh2 emerges as a powerful restraint upon post-mitotic differentiation during normal GNP development and combination of Ezh2 inhibition with cell cycle exit leads to MB cell differentiation.

cancer biology↗

bioRxiv2024

Antibacterial Compounds Against Non-Growing and Intracellular Bacteria

Slow- and non-growing bacterial populations, along with intracellular pathogens, often evade standard antibacterial treatments and are linked to persistent and recurrent infections. This necessitates the development of therapies specifically targeting nonproliferating bacteria. To identify compounds active against non-growing uropathogenic Escherichia coli (UPEC) we performed a drug-repurposing screen of 6,454 approved drugs and drug candidates. Using dilution-regrowth assays, we identified 39 compounds that either kill non-growing UPEC or delay its regrowth post-treatment. The hits include fluoroquinolones, macrolides, rifamycins, biguanide disinfectants, a pleuromutilin, and anti-cancer agents. 29 of the hits have not previously been recognized as active against non-growing bacteria. The hits were further tested against non-growing Pseudomonas aeruginosa and Staphylococcus aureus. Ten compounds - solithromycin, rifabutin, mitomycin C, and seven fluoroquinolones - have strong bactericidal activity against non-growing P. aeruginosa, killing >4 log10 of bacteria at 2.5 {micro}M. Solithromycin, valnemulin, evofosfamide, and satraplatin are unique in their ability to selectively target non-growing bacteria, exhibiting poor efficacy against growing bacteria. Finally, 31 hit compounds inhibit the growth of intracellular Shigella flexneri in a human enterocyte infection model, indicating their ability to permeate the cytoplasm of host cells. The identified compounds hold potential for treating persistent infections, warranting further comparative studies with current standard-of-care antibiotics.

microbiology↗

bioRxiv2024

Modeling American Kestrel Decline Using Spatiotemporal Subsampling to Improve eBird Data Reliability

American Kestrel (Falco sparverius) numbers have plummeted over 40% since 1980, despite many other raptor species, including the closely related Merlin (Falco columbarius) rebounding in the same period, post the ban on the use of DDT. One plausible reason for this decline is the increase in Coopers Hawks (Astur cooperii), a predatory species. To model the impact of Coopers Hawk on American Kestrels, one can use citizen science data such as eBird. However, eBird contains a heavy sampling bias towards recent data in large cities as it has gained popularity over time. A novel framework testing different spatiotemporal subsampling resolutions was employed in seeing how to make the data more reliable and to enjoy a finer time resolution compared to the Breeding Bird Survey (BBS) standard. The ecological relationship between two species is then modeled using a time-series framework that accounts for both current and past interactions, with the model order determined based on criteria such as BIC. The creation and analysis of synthetic data are also tested to verify that our framework reflects the ground truth of the bird abundance trend. Immediate forecast results based on the eBird data suggests a decline of American Kestrels at the current pace.

ecology↗

bioRxiv2024

Glioblastoma Treatment by Systemic Actinium-225 alpha-particle Dendrimer-radioconjugates is Improved by Chemotherapy

RATIONALEThe poor prognosis of glioblastoma is largely due to drug resistance and tumor location that, together, make it difficult to treat aggressively without affecting the rest of the brain. METHODOLOGYHigh-energy, short-range (40-80{micro}m) dendrimer-delivered -particles could address both challenges, because (1) they cause complex, highly cytotoxic double-strand DNA breaks, and (2) irradiation of the neighboring brain is minimal, since dendrimers selectively delivers them to tumors. Since cancer cells that are not directly hit by -particles will likely not be killed, the patterns of tumor irradiation affect efficacy. Systemically injected dendrimers extensively accumulate in glioblastomas, where they are taken up by tumor associated macrophages (TAMs), which tend to infiltrate tumors. We hypothesized that dendrimers labeled with -particle emitters, when being carried by TAMs, could more evenly irradiate glioblastomas, improving survival. In this study, the efficacy of dendrimers radiolabeled with the -particle emitter actinium-225 (dendrimer-radioconjugates) was evaluated when administered alone and/or after temozolomide, in a syngeneic immune-competent orthotopic GL261-C57BL/6 mouse model. RESULTSSystemically-administered dendrimer-radioconjugates, at activities that did not result in long-term toxicities, prolonged survival of mice with orthotopic GL261 tumors, compared to standard-of-care temozolomide (39 vs 31 days mean survival, p=0.0061) and non-treated animals (30 days, p=0.0009). Importantly, injection of temozolomide 24 hours before administration of dendrimer-radioconjugates further improved survival remarkably (44 days). This improvement in efficacy was attributed to: (1) the significant increase (by 33%) in tumor absorbed doses delivered by dendrimer-radioconjugates when injected after chemotherapy, without altering normal organ dosimetry, while sparing the tumor-surrounding healthy brain; (2) the potentially deeper tumor penetration of dendrimer-radioconjugates, suggested by the enhancement of dendrimer penetration within GL261-spheroids, employed as model tumor-avascular regions and/or TAM-free regions; and/or (3) the formation of a more lethal cocktail when both modalities acted on same cancer cells, that was correlated with increased levels of dendrimer-radioconjugates associating with GL261 cells in vitro and with greater incidences of karyomegaly in vivo. CONCLUSIONSThis study demonstrates the potential of a brain tumor targeted systemic actinium-225 radiopharmaceutical therapy that inhibits growth of glioblastoma cells and prolongs survival of mice with orthotopic brain tumors, further improved by standard-of-care temozolomide, without notable toxicities.

bioengineering↗

bioRxiv2024

Building neurovascular tissue from autologous blood for modeling brain-activity

There are no faithful individualized stem cell-based bioengineered neuro-vascularized models that can recapitulate the physiological hemodynamic phenomenon of neuro-vascular coupling (NVC)-the principal behind BOLD (blood oxygen level-dependent) signal in functional neuroimaging, thereby dissuading the research in exploring the brain activity-based investigative studies in neurological/neurosensory diseases. This encouraged us to establish a preclinical optoacoustic (Hb/dHb hemoglobin/deoxyhemoglobin) imaging-competent in vitro neuro-vascularized model by employing a novel cellular reprograming PITTRep (Plasma Induced Transcriptomics/ epi-Transcriptomics Reprograming) approach. The current reprograming approach is based on coaxing autologous blood components to ecto-mesodermal lineage intermediates that can subsequently self-pattern into neurovascular tissue by harnessing the hemorheological properties of RBCs. The nature of blood flow is non-Newtonian and is a function of RBC concentration /haematocrit when they flow through the regions of low shear rates as seen in cerebral microcirculation. The current reprograming approach is a modification of our previous cellular reprograming approach that employed a Newtonian plasma fluid. The autologous blood-derived neurovascular tissue is free from exogenous genetic modification, external growth factors, and induced pluripotent stem cell (iPSC) derivation. This model uniquely integrates functional vasculature and neurogenesis. The current reprogramming approach resulted (in part) serendipitously while testing a potential (yet completely unexplored) hypothesis of haemodynamic reprograming by leveraging the fluid mechanic feature of blood erythrocytes as seen in thrombus formation during cerebral ischemic stroke, that is characterized by physiologically intriguing yet clinically meaningful neurological recovery (neuroplasticity) during an early time window. The current study attempted to induce "a post stroke-like model" of adult neurogenesis with functional synaptogenesis by instructing autologous blood components into thrombus formation through incorporation of erythrocytes in varying concentrations. We tried to instruct adult neurogenesis and neuroplasticity (a relatively non-resilient phenomenon under in vitro conditions) by co-induction of a neuro-vascular niche (NVN). These NVNs are marked by dendrites, synapses, astrogliosis, microglia activation, and growth factor signaling, thus phenocopying molecular and cellular aspects of post-stroke recovery window. The induction of neuro-vascularized niches and functional neuro-vascular coupling (NVC) was characterized by confocal microscopy, scanning electron microscopy, proteomic profiling, and Hb/dHb spectra based optoacoustic imaging. The blood thrombus formation was checked by rotational thromboelastometry (ROTEM), and switching of adult-to-embryonic hemoglobin was confirmed by routine hemoglobin typing. We also attempted to establish patient-specific neuro-vascularized niches from autologous blood of sensorineural hearing loss (SNHL) patients. The individualized neovascularised tissues are intended to be employed for investigating deregulated synaptic plasticity/ long term potentiation underlying poor auditory comprehension outcomes in school going kids suffering from SNHL that greatly compromises their academic performance and socio-behavioural-cognitive development. The attendant multiomics of patient-specific NVNs may have potential implications in developing stem-cell based therapies for neurosensory and cerebrovascular diseases.

neuroscience↗

bioRxiv2024

Mitochondrial DNA Mutations Linking Leigh Syndrome and Carotid Atherosclerosis: A Study of Shared Genetic Pathways

Mitochondrial DNA encodes the genetic information necessary for mitochondrial function. In humans, mitochondrial DNA spans 16,569 base pairs while representing a small fraction of the genetic material in humans. Due to their higher mutation rates compared to nuclear DNA, Mitochondrial DNA mutations are emerging as promising biomarkers for assessing disease predisposition and progression. This in-silico analyzes the correlation between Mitochondrial DNA mutations and two conditions: Leigh syndrome, a severe neurodegenerative disorder, and carotid atherosclerosis, a major cardiovascular disease. We focus on five single nucleotide variants (SNVs) - m.14459G>A, m.13513G>A, m.12315G>A, m.1555A>G, and m.15059G>A - to explore their roles in both diseases. Our findings suggest that mutations m.14459G>A, m.1555A>G, and m.15059G>A contribute to the pathogenesis of both conditions. In contrast, m.12315G>A is linked to MELAS syndrome and carotid atherosclerosis. Interestingly, the m.13513G>A mutation is associated with Leigh syndrome but negatively correlated with atherosclerosis, suggesting a potential protective effect. These SNVs could serve as targets for diagnostic and therapeutic approaches, enhancing our understanding of the genetic basis of these diseases.

bioinformatics↗

bioRxiv2024

Activation of the endoplasmic reticulum stress regulator IRE1α compromises pulmonary host defenses

The endoplasmic reticulum (ER) stress sensor inositol-requiring enzyme 1- (IRE1) is associated with lung infections where innate immune cells are drivers for progression and resolution of inflammation. Yet, the role of IRE1 in pulmonary innate immune host defense during acute respiratory infection remains unexplored. Here, we found that activation of IRE1 in infected lungs compromises immunity against methicillin-resistant Staphylococcus aureus (MRSA)-induced primary and secondary pneumonia. Moreover, activation of IRE1 in MRSA-infected lungs and alveolar macrophages (AMs) leads to exacerbated production of inflammatory mediators followed by cell death. Ablation of myeloid IRE1 or global IRE1 inhibition confers protection against MRSA-induced pneumonia with improves survival, bacterial clearance, cytokine reduction, and lung injury. In addition, loss of myeloid IRE1 protects mice against MRSA-induced secondary to influenza pneumonia by promoting AM survival. Thus, activation of IRE1 is detrimental to pneumonia and therefore, it shows potential as a target to control excessive unresolved lung inflammation.

immunology↗

bioRxiv2024

Cannabis smoke and oral Δ9THC enhance working memory in aged but not young adult subjects

With increased legalization of recreational and medical cannabis, use of this drug is growing rapidly among older adults. As cannabis use can impair cognition in young adults, it is critically important to understand how consumption interacts with the cognitive profile of aged individuals, who are already at increased risk of decline. The current study was designed to determine how cannabis influences multiple forms of cognition in young adult and aged rats of both sexes when delivered via two translationally-relevant routes of administration. Acute exposure to cannabis smoke enhanced prefrontal cortex-dependent working memory accuracy in aged males, but impaired accuracy in aged females, while having no effects in young adults of either sex. In contrast, the same cannabis smoke exposure regimen had minimal effects on a hippocampus-dependent trial-unique non-matching to location mnemonic task, irrespective of age or sex. In a second set of experiments, chronic oral consumption of {Delta}9-tetrahydrocannabinol ({Delta}9THC) enhanced working memory in aged rats of both sexes, while having no effects in young adults. In contrast, the same oral {Delta}9THC regimen did not affect spatial learning and memory in either age group. Minimal age differences were observed in {Delta}9THC pharmacokinetics with either route of administration. Together, these results show that cannabis and {Delta}9THC can attenuate working memory impairments that emerge in aging. While these enhancing effects do not extend to hippocampus-dependent cognition, cannabis does not appear to exacerbate age-associated impairments in this cognitive domain.

neuroscience↗

bioRxiv2024

Unravelling the Proteomic Landscape of Imipenem Resistance in Pseudomonas aeruginosa: A Comparative Investigation between Clinical and Control Strains

The increasing prevalence of antimicrobial resistance (AMR) poses a significant challenge to global health, particularly with bacterial pathogens such as Pseudomonas aeruginosa, a notorious cause of nosocomial infections. This study focuses on the comparative proteomic analysis of an imipenem-resistant strain of P. aeruginosa, a representative of world epidemic clone ST235, and a wildtype control strain, P. aeruginosa ATCC 27853, in response to varying concentrations of imipenem. Using label-free quantification (LFQ) and gene ontology (GO) enrichment analyses, we identified significant differences in the proteomic responses between the two strains (data available via ProteomeXchange with identifier PXD055744.). The clinical strain exhibited a stable proteomic profile across the imipenem gradient, suggesting pre-established and efficient resistance mechanisms that do not require extensive reconfiguration under antibiotic pressure. In contrast, the control strain showed a broader, more reactive proteomic response, particularly in proteins associated with membrane transport, stress response, and biofilm formation. Notably, uncharacterized proteins were significantly upregulated in the clinical strain, indicating potential novel resistance mechanisms. These findings highlight the distinct strategies employed by the two strains, with the clinical strains stable resistance mechanisms contrasting sharply with the control strains reactive approach. The study underscores the importance of further research into the uncharacterized proteins that may play crucial roles in antibiotic resistance, potentially leading to new therapeutic targets in the fight against AMR. HighlightsO_LIStable resistance mechanisms: The clinical strain of Pseudomonas aeruginosa (ST235) exhibited a stable proteomic profile across varying concentrations of imipenem, indicating pre-established and efficient resistance mechanisms. C_LIO_LIReactive proteomic response: The control strain (P. aeruginosa ATCC 27853) showed a broader and more reactive proteomic response, particularly in proteins related to membrane transport, stress response, and biofilm formation. C_LIO_LIUncharacterized proteins: Significant upregulation of uncharacterized proteins in the clinical strain suggests potential novel resistance mechanisms that warrant further investigation. C_LI

microbiology↗

bioRxiv2024

AyurPhenoClusters define common molecular roots for rare diseases and uncover ciliary dysfunctions in syndromic conditions

The heterogeneity of underlying causes and the variability of symptoms across Multiple organs in rare diseases present significant challenges when approached from an organ-centric perspective. Ayurveda, however, takes a multisystem perspective, assessing diseases through kinetic (Vata:V ), metabolic (Pitta:P ), and structural (Kapha:K ) dimensions, each with distinct phenotypic and molecular correlates. This study explores rare diseases from a systems perspective by integrating Ayurveda and unifying terminologies from both disciplines using Human Phenotype Ontology (HPO). Experts categorized 10,610 HPO terms into Ayurvedic phenotypic groups (V/P/K ) and applied the Expectation Maximization (EM) algorithm to cluster 12,678 diseases. This yielded six distinct clusters, termed AyurPhenoClusters, with 2,814 diseases uniquely classified and enriched for V/P/K phenotypes. Functional annotation of these, highlighted key biological processes: (i) embryogenesis and skeletal morphogenesis, (ii) endocrine and ciliary functions, (iii) DNA damage response and cell cycle regulation, (iv) inflammation and immune response, (v) immune function, hemopoiesis, and telomere aging, and (vi) small molecule metabolism and transport. Notably, the K predominant cluster had the highest ciliary gene enrichment (43%), followed by the V predominant cluster (16%), suggesting potential ciliopathies in V cluster. This systems-based approach enhances the understanding of rare diseases by bridging Ayurveda with modern medicine, for improved diagnostics and therapeutics

genetics↗

bioRxiv2024

Diffusion Wavelets on Connectome: Localizing the Sources of Diffusion Mediating Structure-Function Mapping Using Graph Diffusion Wavelets

The intricate link between brain functional connectivity (FC) and structural connectivity (SC) is explored through models performing diffusion on SC to derive FC, using varied methodologies from single to multiple graph diffusion kernels. However, existing studies have not correlated diffusion scales with specific brain regions of interest (RoIs), limiting the applicability of graph diffusion. We propose a novel approach using graph heat diffusion wavelets to learn the appropriate diffusion scale for each RoI to accurately estimate the SC-FC mapping. Using the open HCP dataset, we achieve an average Pearsons correlation value of 0.833, surpassing the state-of-the-art methods for prediction of FC. It is important to note that the proposed architecture is entirely linear, computationally efficient, and notably demonstrates the power-law distribution of diffusion scales. Our results show that the bilateral frontal pole, by virtue of it having large diffusion scale, forms a large community structure. The finding is in line with the current literature on the role of the frontal pole in resting-state networks. Overall, the results underscore the potential of graph diffusion wavelet framework for understanding how the brain structure leads to functional connectivity. AUTHOR SUMMARYIn the network diffusion paradigm for brain structure-to-function mapping, we noticed limitations such as manually decided diffusion scales and the absence of RoI-level analysis. We addressed this problem by independently developing the graph diffusion wavelets having multiscale and multiresolution property. Each brain region is associated with a diffusion scale that defines the extent of spatial communication. Using graph diffusion wavelets, we are able to predict the functional connectome with state-of-the-art (SoTA) results. We observe that the diffusion scales follow a power-law degree distribution, which is indicative of a scale-free process in the brain. The frontal pole is a dominant member of the various resting-state networks, and our model is able to associate higher diffusion scales to this region. The graph diffusion wavelet model is a novel method which not only excels in downstream task but also provides insights into the structure-function relation.

neuroscience↗

bioRxiv2024

NucBalancer: Streamlining Barcode Sequence Selection for Optimal Sample Pooling for Sequencing

Recent advancements in next-generation sequencing (NGS) technologies have brought to the forefront the necessity for versatile, cost-effective tools capable of adapting to a rapidly evolving landscape. The emergence of numerous new sequencing platforms, each with unique sample preparation and sequencing requirements, underscores the importance of efficient barcode balancing for successful pooling and accurate demultiplexing of samples. Recently launched new sequencing systems claim better affordability comparable to more established platforms further exemplifies these challenges, especially when libraries originally prepared for one platform need conversion to another. In response to this dynamic environment, we introduce NucBalancer, a Shiny app developed for the optimal selection of barcode sequences. While initially tailored to meet the nucleotide, composition challenges specific to G400 and T7 series sequencers, NucBalancers utility significantly broadens to accommodate the varied demands of these new sequencing technologies. Its application is particularly crucial in single-cell genomics, enabling the adaptation of libraries, such as those prepared for 10x technology, to various sequencers including G400 and T7 series sequencers. By facilitating the efficient balancing of nucleotide composition and the accommodation of differing sample concentrations, NucBalancer plays a pivotal role in reducing biases in nucleotide composition. This enhances the fidelity and reliability of NGS data across multiple platforms. As the NGS field continues to expand with the introduction of new sequencing technologies, the adaptability and wide-ranging applicability of NucBalancer render it an invaluable asset in genomic research. This tool addresses the current sequencing challenges ensuring that researchers can effectively balance barcodes for sample pooling regardless of the sequencing platform used. Availability and implementationNucBalancer is implemented in R and is available at https://github.com/ersgupta/NucBalancer. Additionally, a shiny interface is made available at https://ersgupta.shinyapps.io/NucBalancer/.

bioinformatics↗

bioRxiv2024

Synchrotron Tomography-Based Finite Element Analysis of Vertebral Endplate Loading Reveals Functional Roles for Architectural Features

Lower back pain is linked to vertebral biomechanics, with vertebral endplates (VEPs) playing a key role. Finite element modelling (FEM) is a powerful tool for studying VEP biomechanics but relies on accurate material property inputs, which remain difficult to obtain. Synchrotron computed tomography (sCT) allows for detailed visualisation of the microstructure of intact VEPs under near-physiological loads and, when coupled with digital volume correlation (DVC), can be used to quantify three-dimensional (3D) strain fields, providing experimental reference data for FEM validation. We developed an inversion pipeline to spatially couple DVC data with an image-based FE model, and thus to estimate the elastic properties of rat VEPs. On the first rat lumbar FEM, the pipeline estimated a VEP elastic modulus of 129 MPa and a Poissons ratio of 0.24. Welchs ANOVA revealed statistically significant differences between FEM and DVC strain distributions (p < 0.001) but with small effect sizes ({superscript 2} = 0.1%-0.6%), indicating high practical similarity. Its efficacy was further validated using Bland-Altman analysis, demonstrating over 95% spatial agreement between the FEM-predicted strains and the DVC measurements across multiple loading steps. The pipelines consistency was further evaluated across multiple rat lumbar FE models (n = 3), yielding an estimated VEP elastic modulus = 145 {+/-} 18 MPa and a Poissons ratio = 0.28 {+/-} 0.04. Statistically significant regional variations of strain distribution in VEPs were also identified (p < 0.05 to p < 0.001, {superscript 2} up to 41.8%). This study highlighted the efficacy of the developed pipeline in estimating the isotropic elastic modulus and Poissons ratio of VEP FEMs in a physiologically relevant, complex load transfer system. Our pipeline may be used in estimating properties of VEP in larger animals and humans.

bioengineering↗

bioRxiv2024

Inflammatory pain in mice induces light cycle-dependent effects on sleep architecture

As a syndrome, chronic pain comprises physical, emotional, and cognitive symptoms such as disability, negative affect, feelings of stress, and fatigue. A rodent model of long-term inflammatory pain, induced by complete Freunds adjuvant (CFA) injection, has previously been shown to cause anhedonia and dysregulated naturalistic behaviors, in a manner similar to animal models of stress. We examined whether this extended to alterations in circadian rhythms and sleep, such as those induced by chronic social defeat stress, using actigraphy and wireless EEG. CFA-induced inflammatory pain profoundly altered sleep architecture in male and female mice. Injection of the hind paw, whether with CFA or saline, reduced some measures of circadian rhythmicity such as variance, period, and amplitude. CFA increased sleep duration primarily in the dark phase, while sleep bout length was decreased in the light and increased in the dark phase. Additionally, CFA reduced wake bout length, especially during the dark phase. Increases in REM and SWS duration and bouts were most significant in the dark phase, regardless of whether CFA had been injected at its onset or 12 hours prior. Taken together, these results indicate that inflammatory pain acutely promotes but also fragments sleep.

neuroscience↗