Biology subjects

Agrawal, A.

Publications and source records attributed to Agrawal, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Urbanization and a green corridor do not impact genetic divergence in common milkweed (Asclepias syriaca)

Urbanization is altering landscapes globally at an unprecedented rate. While ecological differences between urban and rural environments often promote phenotypic divergence among populations, it is unclear to what degree these trait differences arise from genetic divergence as opposed to phenotypic plasticity. Furthermore, little is known about how specific landscape elements, such as green corridors, impact genetic divergence in urban environments. We tested the hypotheses that: 1) urbanization, and 2) proximity to an urban green corridor influence genetic divergence in Asclepias syriaca (common milkweed) populations for phenotypic traits. Using seeds from 52 populations along three urban-to-rural subtransects in the Greater Toronto Area, one of which followed a green corridor, we grew [~]1000 plants in a common garden and observed >20 ecologically-important traits associated with plant defense/damage, reproduction, and growth over four years. We found significant heritable variation for eight traits within A. syriaca populations and weak phenotypic divergence among populations. However, neither urbanization nor an urban green corridor influenced genetic divergence in individual traits or multivariate phenotype. These findings contrast with the expanding literature demonstrating that urbanization promotes rapid evolutionary change and offer preliminary insights into the eco- evolutionary role of green corridors in urban environments.

evolutionary biology↗

bioRxiv2023

3D Confinement-enabled Priming of Synaptic Activation Promotes Primary T Cell Expansion

The success of autologous cell therapy, which depends highly on T lymphocyte expansion efficiency, is often hindered by suboptimal interactions between T-cell receptors and peptide-MHC molecules. Here, we demonstrate 3D confinement-enabled priming of T cell-MHC immune synapse junctions based on cytoskeletal forces within minutes, which is 200-fold faster than conventional 24 h bulk shaking method. Using T cell-Dynabead binding skeletons in the starting culture, two- to six-fold greater T cell expansion was achieved over the conventional T cell expansion approach without inducing excessive cell exhaustion. Under 3D force-confinement, T-cell division (G1, S, and G2 phases) was increased to be twice as fast. Creating 3D T cell-Dynabead skeletons as the "booster" material enables highly efficient T cell expansion, without requiring complex surface modification of antigen-presenting cells. This method can be modularly adapted to existing T cell expansion processes for a wide range of applications including adoptive cell therapies. Teaser3D confinement-enabled priming of synaptic activation enables radically faster autologous cell production.

immunology↗

bioRxiv2023

p16-dependent upregulation of PD-L1 impairs immunosurveillance of senescent cells

The accumulation of senescent cells promotes aging, but a molecular mechanism that senescent cells use to evade immune clearance and accumulate remains to be elucidated. Here, we report that p16-positive senescent cells upregulate the immune checkpoint protein programmed death-ligand 1 (PD-L1) to accumulate in aging and chronic inflammation. p16-mediated inhibition of CDK4/6 promotes PD-L1 stability in senescent cells via the downregulation of ubiquitin-dependent degradation. p16 expression in infiltrating macrophages induces an immunosuppressive environment that can contribute to an increased burden of senescent cells. Treatment with immunostimulatory anti-PD-L1 antibody enhances the cytotoxic T cell activity and leads to the elimination of p16, PD-L1-positive cells. Our study uncovers a molecular mechanism of p16-dependent regulation of PD-L1 protein stability in senescent cells and reveals the potential of PD-L1 as a target for treating senescence-mediated age-associated diseases.

cell biology↗

bioRxiv2022

Cell-Sized Lipid Vesicles as Artificial Antigen-Presenting Cells for Antigen-Specific T Cell Activation

In this study, efficient T cell activation is demonstrated using cell-sized artificial antigen-presenting cells (aAPCs) with protein-conjugated bilayer lipid membranes that mimic biological cell membranes. The highly uniform aAPCs are generated by a facile method based on standard droplet microfluidic devices. These aAPCs are able to activate the T cells in peripheral blood mononuclear cells (PBMCs), showing a 28-fold increase in IFN{gamma} secretion, a 233-fold increase in antigen-specific CD8 T cells expansion, and a 16-fold increase of CD4 T cell expansion. The aAPCs do not require repetitive boosting or additional stimulants and can function at a relatively low aAPC-to-T cell ratio (1-to-17). The research presents strong evidence that the surface fluidity and size of the aAPCs are critical to the effective formation of immune synapses essential for T cell activation. The findings demonstrate that the microfluidic-generated aAPCs can be instrumental in investigating the physiological conditions and mechanisms for T cell activation. Finally, this method demonstrates the feasibility of customizable aAPCs for a cost-effective off-the-shelf approach to immunotherapy.

bioengineering↗

bioRxiv2022

Schwann cells promote sensory neuron excitability during development

Excitability--the ability to fire action potentials--is a signature feature of neurons. How neurons become excitable during development, and whether excitability is an intrinsic property of neurons or requires signaling from glial cells, remain unclear. Here we demonstrate that Schwann cells, the most abundant glia in the peripheral nervous system, promote somatosensory neuron excitability during development. We find that Schwann cells secrete prostaglandin E2, which is necessary and sufficient to induce developing somatosensory neurons to express normal levels of voltage-gated sodium channels and fire action potential trains. Inactivating this signaling pathway specifically in Schwann cells selectively impairs the maturation of nociceptor and proprioceptor somatosensory neuron subtypes, leading to corresponding sensory defects in thermoception, inflammatory pain, and proprioception. Our studies thus reveal a cell non-autonomous mechanism by which glia regulate neuronal excitability to enable the development of normal sensory functions.

neuroscience↗

bioRxiv2022

Profiling emergent behaviors from single-cell motility

Cell motility plays an essential role in many biological processes as cells move and interact within their local microenvironments. Current methods for quantifying cell motility typically involve tracking individual cells over time, but the results are often presented as averaged values across cell populations. While informative, these ensemble approaches have limitations in assessing cellular heterogeneity and identifying generalizable patterns of single-cell behaviors, at baseline and in response to perturbations. In this study, we introduce CaMI, a computational framework designed to leverage the single-cell nature of motility data. CaMI identifies and classifies distinct spatio-temporal behaviors of individual cells, enabling robust classification of single-cell motility patterns in a large dataset (n=74,253 cells). This framework allows quantification of spatial and temporal heterogeneities, determination of single-cell motility behaviors across various biological conditions, and provides a visualization scheme for direct interpretation of dynamic cell behaviors. Importantly, CaMI reveals insights that conventional cell motility analyses may overlook, showcasing its utility in uncovering robust biological insights. Together, we present a multivariate framework to classify emergent patterns of single-cell motility, emphasizing the critical role of cellular heterogeneity in shaping cell behaviors across populations. TeaserA computational framework to identify and classify single-cell motility patterns and phenotypic heterogeneity across biological conditions.

bioengineering↗

bioRxiv2022

A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors

Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood due in part to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single cell transcriptomic time course of mouse embryos to identify emerging CPCs and describe their transcriptional profiles. Mesp1, a transiently-expressed mesodermal transcription factor (TF), is canonically described as an early regulator of cardiac specification. However, we observed perdurance of CPC transgene-expressing cells in Mesp1 mutants, albeit mis-localized, prompting us to investigate the scope of Mesp1s role in CPC emergence and differentiation. Mesp1 mutant CPCs failed to robustly activate markers of cardiomyocyte maturity and critical cardiac TFs, yet they exhibited transcriptional profiles resembling cardiac mesoderm progressing towards cardiomyocyte fates. Single cell chromatin accessibility analysis defined a Mesp1-dependent developmental breakpoint in cardiac lineage progression at a shift from mesendoderm transcriptional networks to those necessary for cardiac patterning and morphogenesis. These results reveal Mesp1-independent aspects of early CPC specification and underscore a Mesp1-dependent regulatory landscape required for progression through cardiogenesis.

developmental biology↗

bioRxiv2022

A novel in silico method employs chemical and protein similarity algorithms to accurately identify chemical transformations in the human gut microbiome

Bacteria within the gut microbiota possess the ability to metabolize a wide array of human drugs, foods, and toxins, but the responsible enzymes for these chemical events remain largely uncharacterized due to the time consuming nature of current experimental approaches. Attempts have been made in the past to computationally predict which bacterial species and enzymes are responsible for chemical transformations in the gut environment, but with low accuracy due to minimal chemical representation and sequence similarity search schemes. Here, we present an in silico approach that employs chemical and protein Similarity algorithms that Identify MicrobioMe Enzymatic Reactions (SIMMER). We show that SIMMER predicts the chemistry and responsible species and enzymes for a queried reaction with high accuracy, unlike previous methods. We demonstrate SIMMER use cases in the context of drug metabolism by predicting previously uncharacterized enzymes for 88 drug transformations known to occur in the human gut. Bacterial species containing these enzymes are enriched within human donor stool samples that metabolize the query compound. After demonstrating its utility and accuracy, we chose to make SIMMER available as both a command-line and web tool, with flexible input and output options for determining chemical transformations within the human gut. We present SIMMER as a computational addition to the microbiome researchers toolbox, enabling them to make informed hypotheses before embarking on the lengthy laboratory experiments required to characterize novel bacterial enzymes that can alter human ingested compounds.

bioinformatics↗

bioRxiv2022

Reference compounds for characterizing cellular injury in high-content cellular morphology assays

Robust, generalizable approaches to identify compounds efficiently with undesirable mechanisms of action in complex cellular assays remain elusive. Such a process would be useful for hit triage during high-throughput screening and, ultimately, predictive toxicology during drug development. We generated cell painting and cellular health profiles for 218 prototypical cytotoxic and nuisance compounds in U-2 OS cells in a concentration-response format. A diversity of compounds causing cellular damage produced bioactive cell painting morphologies, including cytoskeletal poisons, genotoxins, nonspecific electrophiles, and redox-active compounds. Further, we show that lower quality lysine acetyltransferase inhibitors and nonspecific electrophiles can be distinguished from more selective counterparts. We propose that the purposeful inclusion of cytotoxic and nuisance reference compounds such as those profiled in this Resource will help with assay optimization and compound prioritization in complex cellular assays like cell painting.

pharmacology and toxicology↗

bioRxiv2022

Dendrite architecture determines mitochondrial distribution patterns in vivo

Mitochondria are critical for neuronal function and must be reliably distributed through complex neuronal architectures. By quantifying in vivo mitochondrial transport and localization patterns in the dendrites of Drosophila visual system neurons, we show that mitochondria make up a dynamic system at steady-state, with significant transport of individual mitochondria within a stable global pattern. Mitochondrial motility patterns are unaffected by visual input, suggesting that neuronal activity does not directly regulate mitochondrial localization in vivo. Instead, we present a mathematical model in which four simple scaling rules enable the robust self-organization of the mitochondrial population. Experimental measurements of dendrite morphology validate key model predictions: to maintain equitable distribution of mitochondria across asymmetrically branched subtrees, dendritic branch points obey a parent-daughter power law that preserves cross-sectional area, and thicker trunks support proportionally bushier subtrees. Altogether, we propose that "housekeeping" requirements, including the need to maintain steady-state mitochondrial distributions, impose constraints on neuronal architecture.

cell biology↗

bioRxiv2022

Comprehensive characterization of the transcriptional response to COVID-19 in multiple organs reveals shared signatures across tissues

Infection by Coronavirus SARS-CoV2 is a severe and often deadly disease that has implications for the respiratory system and multiple organs across the human body. While the effects in the lung have been extensively studied, less is known about COVID-19s cellular impact across other organs. Here we contribute a single-nuclei RNA sequencing atlas comprising six human organs across 20 autopsies where we analyzed the transcriptional changes due to COVID-19 in multiple cell types. Computational cross-organ analysis for endothelial cells and macrophages identified systemic transcriptional changes in these cell types in COVID-19 samples. In addition, analysis of signaling pathways from multiple datasets showed several systemic dysregulations of signaling interaction in different cell types. Altogether, the COVID Tissue Atlas enables the investigation of both cell type-specific and cross-organ transcriptional responses to COVID-19, providing insights into the molecular networks affected by the disease and highlighting novel potential targets for therapies and drug development.

genomics↗

bioRxiv2022

Cell walls are dynamically O-acetylated in the green seaweed, Ulva compressa

We report that cell wall polymers in the chlorophyte algae may be modified by O-acetylation. The importance of cell wall modifications in the green algae is not well understood, although similar modifications play key roles in land plants by modulating the properties of cell wall carbohydrate polymers. Using a combination of biophysical (Fourier-transform infrared and cross-polarisation heteronuclear correlation nuclear magnetic resonance spectroscopy), biochemical (thin-layer chromatography) and molecular approaches (yellow fluorescent protein-tagged transgene localisation), we show that the extractable ulvan fractions of Ulva compressa cell walls contain O-acetyl sidechains, we demonstrate that acetylation is dynamic and decreases reversibly in response to metal-induced stress, we note interactions between acetyl and borate sidechains and we locate two candidate genes that, together, may encode an acetyltransferase. We therefore propose that O-acetylation of ulvan residues is involved in the normal cell wall physiology of at least some chlorophyte algae. To the best of our knowledge, this is the first demonstration of O-acetyl sidechains in green algal cell wall polymers, and of reversible changes in algal cell wall polymer modification in response to stress.

cell biology↗

bioRxiv2022

Histone deacetylase 6 inhibition promotes microtubule acetylation and facilitates autophagosome-lysosome fusion in dystrophin-deficient mdx mice

Duchenne Muscular Dystrophy (DMD) is a severe X-linked genetic disorder. Defective autophagy and disorganized microtubule network contributes to DMD pathogenesis, yet the mechanisms by which microtubule alterations regulate autophagy remain elusive. We show decreased acetylated -tubulin and enhanced histone deacetylase (HDAC6) expression in mdx mice. Pharmacological inhibition of HDAC6 increases tubulin acetylation and enhances Q-SNARE complex formation, leading to improved autophagosome-lysosome fusion. HDAC6 inhibition reduces apoptosis, inflammation, muscle damage and prevents contraction induced force loss. HDAC6 inhibition restores peroxiredoxin (PrxII) by increasing its acetylation and protecting it from hyper-oxidation, hence modulating intracellular redox status in mdx mice. Genetic inhibition of Nox2 activity in mdx mice promotes autophagosome maturation. Our data highlight that autophagy is differentially regulated by redox and acetylation in mdx mice. By restoring tubulin acetylation HDAC6 inhibition enhances autophagy, ameliorates the dystrophic phenotype and improves muscle function, suggesting a potential therapeutic target for treating DMD.

cell biology↗

bioRxiv2022

Multi-omics analyses cannot identify true-positive novel associations from underpowered genome-wide association studies of four brain-related traits

BackgroundThe integration of multi-omics information (e.g., epigenetics and transcriptomics) can be useful for interpreting findings from genome-wide association studies (GWAS). It has additionally been suggested that multi-omics may aid in novel variant discovery, thus circumventing the need to increase GWAS sample sizes. We tested whether incorporating multi-omics information in earlier and smaller sized GWAS boosts true-positive discovery of genes that were later revealed by larger GWAS of the same/similar traits. MethodsWe applied ten different analytic approaches to integrating multi-omics data from twelve sources (e.g., Genotype-Tissue Expression project) to test whether earlier and smaller GWAS of 4 brain-related traits (i.e., alcohol use disorder/problematic alcohol use [AUD/PAU], major depression [MDD], schizophrenia [SCZ], and intracranial volume [ICV]) could detect genes that were revealed by a later and larger GWAS. ResultsMulti-omics data did not reliably identify novel genes in earlier less powered GWAS (PPV<0.2; 80% false-positive associations). Machine learning predictions marginally increased the number of identified novel genes, correctly identifying 1-8 additional genes, but only for well-powered early GWAS of highly heritable traits (i.e., ICV and SCZ). Multi-omics, particularly positional mapping (i.e., fastBAT, MAGMA, and H-MAGMA), was useful for prioritizing genes within genome-wide significant loci (PPVs = 0.5 - 1.0). ConclusionsAlthough the integration of multi-omics information, particularly when multiple methods agree, helps prioritize GWAS findings and translate them into information about disease biology, it does not substantively increase novel gene discovery in brain-related GWAS. To increase power for discovery of novel genes and loci, increasing sample size is a requirement.

genetics↗

bioRxiv2022

Opiate responses are controlled by interactions of Oprm1 and Fgf12 loci in the murine BXD family: Correspondence to human GWAS finding

Exploring the molecular genetic cascades responsible for behavioral responses to opioids can improve our understanding of drug use initiation. We generated high-precision time-series data for 105 morphine-and naloxone-related traits across [~]700 young adult BXD mice (64 diverse strains and both sexes) for 3 hours after a single morphine injection. Variations in responses were mapped using high-precision genome sequencing-based genotypes. The initial locomotor responses to morphine mapped precisely to the {micro} opioid receptor gene (Oprm1) on chromosome (Chr) 10 with a peak linkage of 12.4 (-logP, genome-wide significance level is approximately 3.8). The B allele inherited from C57BL/6J was associated with up to 60% higher activity. This effect climaxed at 75 min but was exhausted by 160 min. A second major modulator of opioid-induced locomotion emerged after approximately 100 min. This locus, also associated with a high B allele, was located on Chr 16 with peak linkage of 10.6 (-logP) in females. This locus included only one compelling candidate, fibroblast growth factor 12 (Fgf12), a 600 Kb gene that controls sodium current kinetics at the axon hillock. A strong and transient epistatic interaction existed between the Oprm1 and Fgf12 loci during a short time window (45-75 min). The combination of a B haplotype at Oprm1 with a D haplotype from DBA/2J at Fgf12 was associated with unusually high activity. In a complementary study in heterogeneous stock rats, we demonstrated that Oprm1 and Fgf12 were co-expressed in one specific subtype of Drd1+ medium spiny neuron. A Bayesian network analysis supported an Oprm1-to-Fgf12 network that involves a MAP kinase cascade that modulates FGF12 phosphorylation and locomotor activation. OPRM1 and FGF12 networks in human GWAS data highlight enrichment of signals associated with substance use disorder. This study represents the first demonstration of a time-dependent epistatic interaction modulating drug response in mammals and the first linkage of Fgf12 to opioid-induced behavior.

genetics↗

bioRxiv2022

Temporal matches and mismatches between monarch butterfly and milkweed population changes over the past 12,000 years

In intimate ecological interactions, the interdependency of species may result in correlated demographic histories. For species of conservation concern, understanding the long-term dynamics of such interactions may shed light on the drivers of population decline. Here we address the demographic history of the monarch butterfly, Danaus plexippus, and its dominant host plant, the common milkweed Asclepias syriaca, using broad-scale sampling and genomic inference. Because genetic resources for milkweed have lagged behind those for monarchs, we first release a chromosome-level genome assembly and annotation for common milkweed. Next, we show that despite its enormous geographic range across eastern North America, A. syriaca is best characterized as a single, roughly panmictic population. Using Approximate Bayesian Computation via Random Forests (ABC-RF), a machine learning method for reconstructing demographic histories, we show that both monarchs and milkweed experienced concurrent range expansion during the most recent recession of North American glaciers [~]12,000 years ago. Our data identify an expansion of milkweed during the large-scale clearing of eastern forests ([~]200 years ago) but was inconclusive as to expansion or contraction of the monarch butterfly population during this time. Finally, our results indicate that neither species experienced a population contraction over the past 75 years. Thus, the well-documented decline of monarch abundance over the past 40 years is not visible in our genomic dataset, reflecting a possible mismatch of the overwintering census population to effective population size in this species.

evolutionary biology↗

bioRxiv2022

Age-Related Impairment of Innate and Adaptive Immune Responses Following Intranasal Herpes Simplex Infection

Immune function declines with age, leading to an increased vulnerability to respiratory viral infections. The mechanisms by which aging negatively impacts the innate and adaptive immune system leading to enhanced susceptibility to infections remain to be fully elucidated. In the present study, we used a mouse model of intranasal infection with herpes simplex virus type 1 (HSV-1), a virus that can enter the lungs through the nasal route causing pneumonia, a serious health concern in the elderly. Following intranasal inoculation of young (6 weeks), adult (36 weeks), and aged (68 weeks) with HSV-1 (KOS strain) we: (i) compared the local and systemic innate and adaptive immune response to infection; and (ii) correlated the level and type of immune response to protection against HSV-1 infection. Compared to young and adult mice, aged mice displayed: (i) increased basal level activation of epithelial cells with a decreased expression of TLR3; (ii) increased activation of dendritic cells with increased expression of MHC-1, MHC-II and CD80/86; and (iii) decreased production of type-I interferons upon stimulation; (iv) a delay in cytokines and chemokines production in the lungs; and (v) an impairment in function (CD107 and IFN-{gamma} production) of HSV-specific CD8+ T cells. These impairment in innate and adaptive immune responses in aged mice following intranasal HSV-1 inoculation was associated with symptomatic herpes infection. The findings suggest an age-related impairment of both innate and adaptive immune responses which may exacerbate herpes infection and disease in the elderly. IMPORTANCEImmune function declines with age, leading to an increased vulnerability of the elderly to respiratory viral infections. The mechanisms by which aging negatively impacts the innate and adaptive immune system leading to enhanced susceptibility to respiratory infections remain to be fully elucidated. The present study showed that, compared to young and adult mice, aged mice displayed increased basal level activation of epithelial cells with a decreased expression of TLR3 increased activation of dendritic cells associated with an impairment of HSV-specific CD8+ T cell responses. These immune dysregulations were associated with to symptomatic herpes infection. The findings suggest an age-related impairment of both innate and adaptive immune responses which may exacerbate herpes infection and disease in the elderly.

immunology↗

bioRxiv2021

Exploring the relationships between autozygosity, educational attainment, and cognitive ability in a contemporary, trans-ancestral American sample

Previous studies have found significant associations between estimated autozygosity - the proportion of an individuals genome contained in homozygous segments due to distant inbreeding - and multiple traits, including educational attainment (EA) and cognitive ability. In one study, estimated autozygosity showed a stronger association with parental EA than the subjects own EA. This was likely driven by parental EAs association with mobility: more educated parents tended to migrate further from their hometown, therefore choosing more genetically diverse partners. We examined the associations between estimated autozygosity, cognitive ability, and parental EA in a contemporary sub-sample of adolescents from the Adolescent Brain and Cognitive Development StudySM (ABCD Study(R)) (analytic N=6,504). We found a negative association between autozygosity and child cognitive ability consistent with previous studies, while the associations between autozygosity and parental EA were in the expected direction of effect (with greater levels of autozygosity being associated with lower EA) but the effect sizes were significantly weaker than those estimated in previous work. We also found a lower mean level of autozygosity in the ABCD sample compared to previous autozygosity studies, which may reflect overall decreasing levels of autozygosity over generations. Variation in migration and mobility patterns in the ABCD study compared to other studies may explain the pattern of associations between estimated autozygosity, EA, and cognitive ability in the current study.

genetics↗