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Sharma, S.

Publications and source records attributed to Sharma, S..

At least 145 records · Page 8Linked to original sources

The cytokinesis associated proteins CITK and ASPM-1 regulate neuronal microtubule dynamics and polarity in C. elegans

The polarized architecture of neurons is intricately associated with modulation of microtubule dynamics. Over the years several microtubule-associated-factors that modulate neuronal polarity have been identified. However, the precise details of how microtubule arrangement and stability is established in axon and dendrites is not clearly understood. To uncover relevant factors involved in the biological pathways governing microtubule regulation in neuron, we conducted a suppressor screen using the neuronal ectopic extension phenotype caused due to loss of kinesin-13 family microtubule depolymerizing protein KLP-7 in C. elegans. Interestingly, apart from eleven variants of (mec-12) and {beta} (mec-7) tubulins, we isolated a variant of cytokinesis associated protein, W02B8.2/citk-1, the kinase-less worm orthologue of mammalian citron-rho interacting kinase (CIT). Little is known about the role of CITK in microtubule regulation in post-mitotic neurons. In this study, we found that the kinase-less worm orthologues of CIT, citk-1 and citk-2 redundantly modulate microtubule stability in the axon-like anterior process and maintain the population of plus-end-out microtubules in the dendrite-like posterior process of the PLM mechanosensory neurons in a cell autonomous manner. In the absence of citk-1, PLM neurons exhibit variable morphological defects including defects in migration, growth, and guidance. Moreover, the neuronal and microtubule phenotypes of loss of both citk-1 and citk-2 were phenocopied by the mutant animals of aspm-1, the worm homolog of abnormal spindle-like microcephaly-associated protein (ASPM), suggesting a genetic association, similar to their association in dividing mammalian cells. These observations suggest that the cytokinesis associated citron kinase and ASPM-1 have non-mitotic roles in C. elegans mechanosensory neurons in the regulation of microtubules.

cell biology↗

The PERPETUAL FLOWERING Locus: Necessary But Insufficient for Genomic Prediction of Runnerless and Other Asexual Reproduction Phenotypes in Strawberry

Strawberry (Fragaria x ananassa) reproduces sexually through seeds and asexually through stolons. The ability to cost-effectively clonally propagate hybrid individuals on a large scale has profoundly shaped strawberry breeding and production practices. Despite the technical and economic importance of clonal propagation, little is known about the genetic regulation of runnering in strawberry, other than the photoperiod-dependent pleiotropic effects of PERPETUAL FLOWERING (PF), a dominant, yield-doubling gene introgressed from a wild relative that knocks out temperature-dependent photoperiod sensitivity and partially suppresses runnering. Herewe showthat runnering phenotypes are highly variable and heritable, ranging from runnerless to prolific and unrestrained in both short-day (pfpf) and day-neutral (PF_) plants. We physically mapped the PF locus to Mb 26.4-27.3 on chromosome 4B using high-density SNP haplotypes and historical recombination among 932 individuals. PF was the only runneringassociated locus uncovered by genome-wide association studies among diverse clonal genetic resources and progeny from narrow and wide crosses (1,537 individuals). However, PF explained only 22% of the genetic variance for runnering. Genomic-estimated breeding values for runnering were accurately estimated especially among runnerless to near-runnerless individuals. Genomic prediction accuracies were greater within than between populations, increased when corrected for PF, and are sufficient for implementing genomic selection. These results pave the way for enhancing the productivity of strawberry by creating runnerless cultivars for seed-propagation and near-runnerless and reduced runnering cultivars for clone-propagation through phenotypic or genomic selection. 1 CORE IDEASO_LIGenetic variation for runnering is substantial and heritable C_LIO_LIThe dominant PERPETUAL FLOWERING (PF) allele does not uniformly or ubiquitously suppress asexual reproduction C_LIO_LISubstantial wild donor DNA has persisted in day-neutral and summer-plant cultivars carrying the Wasatch PF allele C_LIO_LIThe accuracy of PF-corrected breeding values for runnering are sufficient for implementing genomic selection C_LIO_LIStrawberry productivity can be improved by introducing cultivars with runnerless or near-runnerless phenotypes C_LI

genetics↗

Expression and In-silico Structural analysis of N-acetylglucosamine transporter, Ngt1 in model fungal pathogen, Candida albicans

IntroductionThe commensal yeast, Candida albicans, has the enormous metabolic flexibility to utilize alternative carbon sources such as N-acetylglucosamine (GlcNAc) at the infection sites, thereby facilitating its adaptive strategies to colonize and thrive within diverse host niches. In Candia, GlcNAc specific transporter (Ngt1) imports GlcNAc at cell surface to induce signaling through the master regulator Ngs1 at the chromatin level. Thus, GlcNAc signaling is responsible for changing its habitat from commensal to pathogenic life style. ObjectiveThe current study aims at understanding the expression, structural and functional intricacies of Ngt1 that determines to GlcNAc sensitivity, specificity and its transport which is a prerogatory step in the GlcNAc signaling process in Candida. MethodThe 3-D structure of Ngt1 was predicted using AlphaFold. We have carried out docking studies using AutoDoc suite for native and Site directed mutant versions of Ngt1 with GlcNAc to determine role of critical amino acids and further, tunnel analysis to reveal the transport mechanism. These findings lead to the designing structure-based Ngt1blockers via virtual screening of natural compound libraries. ResultsOur docking studies on Ngt1 with GlcNAc revealed the useful insights in to mechanism and the role of critical amino acids (Ala 324, Ile 325, Tyr 329, and Asp 332) responsible for interaction. In our analysis, Asn 195, located within transmembrane helix and part of the UNC-93-like transmembrane regulatory protein domain, was identified as critical residue for GlcNAc interaction compared with other mutated residues. Interestingly, the tunnel analysis of Ngt1 transporter revealed presence potential pathways in Ngt1 protein for effective GlcNAc transport. ConclusionThis study provides basic insights in to the structural aspects of Ngt1 and its interaction with GlcNAc that can be further explored for the development effective therapeutic agents for control of infection caused by the Candida. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/648653v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1dbd0eforg.highwire.dtl.DTLVardef@721896org.highwire.dtl.DTLVardef@ac2742org.highwire.dtl.DTLVardef@4591b0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Structural and functional analysis of Ngt1 protein. Flow chart depicting Ngt1 3D modeling (AlphaFold2), docking studies Ngt1-wild type and SDM proteins with GlcNAc ligand, tunnel analysis reflecting transport of GlcNAc, and virtual screening to identify potential inhibitors (Brucine). C_FIG

bioinformatics↗

Leveraging foundation models to dissect the genetic basis of cluster compactness and yield in grapevine

Grape cluster compactness is a key trait that influence fruit quality, yield, and disease susceptibility. Understanding the genetic basis of this trait is essential for optimizing vineyard management and improving grapevine cultivars. In this study, we performed quantitative trait locus (QTL) mapping to identify genomic regions associated with cluster architecture and yield components in a bi-parental population derived from Vitis vinifera cv. Riesling x Cabernet Sauvignon. A total of 138 full-sibling progeny were evaluated over two growing seasons at Oakville, Napa Valley, California. Traditional yield-related traits were measured, including cluster number, total cluster weight, and average cluster weight. Additionally, an image-based phenotyping pipeline leveraging the foundation model Segment Anything Model (SAM) was employed to segment individual berries, measure their size and shape, and compute cluster compactness with minimal manual intervention. Trait correlations revealed that compact clusters tended to have a higher berry count but smaller berry size, highlighting the role of compactness in modulating cluster structure. Heritability estimates varied across traits, with berry dimensions and compactness displaying moderate to high heritability, indicating strong genetic control. Two parental linkage maps were constructed using a pseudo-test cross strategy. QTL mapping identified multiple loci associated with cluster architecture and yield components, with several stable QTLs detected across both years. Notably, a QTL for cluster compactness was found in both seasons on chromosome 1 in Cabernet Sauvignon. Other stable QTLs were associated with berry size (chromosomes 6 and 17) and berry count (chromosome 5 in Cabernet Sauvignon and chromosome 7 in Riesling). Additional QTLs were detected in a single year, reflecting the influence of environmental variation. Our findings provide valuable insights into the application of foundation models requiring no prior training and minimal intervention for high-quality segmentation and enhance our understanding of the genetic architecture of cluster compactness and yield traits. The genomic regions identified in this study offer promising targets for breeding programs aimed at improving grape quality and disease resistance.

genetics↗

High fat diet but not glucocorticoid-induced obesity results in fatty liver

Chronic stress, modeled by flattened circadian glucocorticoid (GC) oscillations, is increasingly implicated in obesity. We investigated the underlying mechanisms by disrupting GC rhythms in mice, elevating normally low GC levels during the rest period. This disruption induced substantial obesity, comparable to a 60% high-fat diet (HFD), with additive effects on fat mass, suggesting distinct mechanisms driving adiposity. Despite similar adiposity, GC-flattening and HFD produced profoundly different metabolic outcomes. HFD led to hepatic steatosis and elevated fasting glucose/fatty acid levels, reflecting typical diet-induced dysfunction. In contrast, GC-flattening maintained low fasting glucose/fatty acid levels and prevented hepatic lipid accumulation, with increased adiposity driven by a shift of glucose uptake from muscle to fat and suppression of lipolysis. This reveals a previously unrecognized mechanism of obesity development where excess fat accumulation occurs independently of the mechanisms driving metabolic dysfunction observed in diet-induced obesity. The dissociation between obesity and metabolic dysfunction in GC-flattening challenges the view that increased adiposity and persistent hyperinsulinemia inevitably leads to fatty liver disease. Understanding this pathway opens avenues for novel therapeutic interventions targeting stress-related metabolic disorders.

physiology↗

Inactivation of CDK4/6, CDK2, and ERK in G1-phase triggers differentiation commitment

Terminal cell differentiation, a process vital for tissue development and regeneration where progenitor cells acquire specialized functions and permanently exit the cell cycle, is still poorly understood at the molecular level. Using live-cell imaging and adipogenesis as a model, we demonstrate that the initial stage involves a variable number of cell divisions driven by redundant CDK4/6 or CDK2 activation.. Subsequently, a delayed decrease in cyclin D1 and an increase in p27 levels leads to the attenuation of CDK4/6 and CDK2 activity. This results in G1 lengthening and the induction of PPARG, the master regulator of adipogenesis. PPARG then induces p21, and later p18, culminating in the irreversible inactivation of CDK4/6 and CDK2, and thus, permanent cell cycle exit. However, contrary to expectation, CDK inactivation alone is not sufficient to trigger commitment to differentiation and functional specialization; ERK inactivation is also required. Our study establishes that the coordinated activation and subsequent delayed inactivation of CDK4/6, CDK2, and ERK are crucial determinants for irreversible cell cycle exit and differentiation commitment in terminal cell differentiation.

cell biology↗

Hyperspectral Sensing for High-Throughput Screening of Boron Tolerance in Grapevines

Boron (B) is an essential micronutrient for grapevine growth, yet excessive levels can impair photosynthesis, reduce yields, and diminish fruit quality. In this study, we evaluated the potential of hyperspectral radiometry combined with machine learning to identify B-tolerant rootstocks rapidly and cost-effectively. We screened both commercial grapevine rootstocks and wild Vitis germplasm under B treatments ranging from 0.5 to 8 ppm, measuring leaf B accumulation, stomatal conductance, photosystem II efficiency, and leaf reflectance (R380-R1100 nm). Our results revealed substantial genotypic variation in B exclusion, with some genotypes maintaining low leaf B content despite high external concentrations. Classification models (Partial Least Squares Discriminant Analysis and Random Forest classification) outperformed regression models (Partial Least Squares Regression and Random Forest regression) in distinguishing B-excluding genotypes, achieving moderate to high accuracy within just eight days after stress initiation. Vegetation indices such as Normalized Difference Vegetation Index (NDVI), Photochemical Reflectance Index (PRI), Structure Insensitive Pigment Index (SIPI), and Chlorophyll Index (CI) indicated that B stress reduces chlorophyll levels and may induce carotenoid accumulation, suggesting a photosynthetic tolerance mechanism. Although quantitative prediction of leaf B content proved more challenging, simulations showed that even modest prediction accuracies can substantially boost genetic gains if larger populations are screened, and selection intensities are increased. These findings underscore the value of hyperspectral radiometry for high-throughput phenotyping, allowing breeders to rapidly identify and advance B-tolerant rootstocks.

plant biology↗

TGF-β inhibitor SB431542 suppresses coronavirus replication through multistep inhibition

The COVID-19 pandemic highlighted the critical need for broad-spectrum antivirals with high resistance barriers. Here, we demonstrate that SB431542, a selective TGF-{beta} receptor I (ALK5) inhibitor, exhibits potent antiviral activity against SARS-CoV-2 through unprecedented multitargeted mechanisms. Through comprehensive in vitro, and in silico analyses, we identified that SB431542 directly binds to SARS-CoV-2 ORF3a and disrupt its canonical function in inhibiting autophagosome-lysosome fusion. This interaction restored lysosomal acidification and normalized perinuclear LAMP-1 localization, significantly impairing virion assembly as evidenced by disrupted nucleocapsid-RNA association and reduced intracellular viral titers. Additionally, SB431542 downregulated the CLEAR network genes responsible for lysosomal biogenesis, further restricting viral egress pathways. Our temporal analyses revealed that at later infection stages (36-48 hpi), SARS-CoV-2 exploits TGF-{beta}-induced lysosomal membrane permeabilization (LMP) and apoptosis for viral release--processes effectively inhibited by SB431542 through suppression of GADD45b and BAX expression. These multiple mechanisms resulted in an exceptional EC50 of 515 nM against SARS-CoV-2. In vivo efficacy was demonstrated in embryonated chicken eggs, where SB431542 conferred dose-dependent protection against lethal infectious bronchitis virus (IBV) challenge, with a favourable therapeutic index of 34.54. Remarkably, sequential passaging of SARS-CoV-2 for 50 generations under SB431542 selection pressure failed to generate resistant variants, contrasting sharply with the rapid resistance emergence typical of direct-acting antivirals. These findings establish SB431542 as a promising broad-spectrum coronavirus inhibitor with a unique triple-mechanism approach that simultaneously targets viral entry via TGF-{beta}/Smad modulation, disrupts ORF3a-mediated lysosomal dysfunction affecting assembly, and attenuates TGF-{beta}-induced apoptosis during late-stage infection-- collectively imposing multiple selective constraints that impede escape mutation development. ImportanceThe COVID-19 pandemic highlighted the urgent need for antiviral drugs with high barriers to resistance. This study reveals that SB431542, a drug previously developed to inhibit TGF-{beta} signaling, exhibits remarkable effectiveness against SARS-CoV-2 through an unprecedented triple-mechanism approach. Unlike conventional antivirals that target a single viral component, SB431542 simultaneously disrupts viral entry, assembly, and release by binding to the viral ORF3a protein and modulating host cellular processes. Most importantly, SARS-CoV-2 failed to develop resistance against SB431542 even after 50 generations of exposure--a significant advantage over current therapeutics that quickly lose effectiveness due to viral mutations. Our findings also uncover that coronaviruses exploit both lysosomal dysfunction and programmed cell death to spread efficiently, providing new targets for therapeutic intervention. This research establishes SB431542 as a promising broad-spectrum coronavirus inhibitor and demonstrates the value of targeting host-virus interactions to overcome antiviral resistance.

microbiology↗

IL-1β/IRAK4 Axis Promotes Ovarian Tumor Development at the Mesothelium Injury Sites

Epithelial ovarian cancer (EOC) cells seed at mesothelial inflammation or injury sites. Lack of animal models recapitulating tumor cells seeding at inflamed sites in EOC hinders mechanistic studies and therapy developments. Here, we developed a non-surgical MIM (Mesothelium Inflammation/Injury Metastasis) model that recapitulates tumor cell seeding at inflamed sites. This model captures temporal changes in tumor immune microenvironment and tumor growth allowing for deeper mechanistic and preclinical therapeutic studies of EOC in-vivo. We show here that HGS-3 high-grade murine serous EOC cells seed at needle-induced injury sites in mesothelium/peritoneal wall, forming tumors both internally and protruding outward. Using MIM model, we found that deletion of IL1R1 in mice reduced EOC cell seeding at mesothelium injury/inflamed site in WT but not IL1ra-deficient mice. Treatment of MiM mice with a novel IRAK4 inhibitor we recently developed (UR241-2) revealed an essential role for IRAK4 signaling downstream IL-1{beta}/IL-1R1 in fostering an anti-tumor inflammatory environment, and reduced tumor burden. We conclude that IRAK4 inhibitors can be more effective than IL-1/IL-1R1 targeting agents to control metastasis and peritoneal tumors, an unmet medical need in EOC recurrence. Downregulation of extracellular matrix (ECM), upregulation of neutrophil activation genes, reduced cell adhesion and migration exhibit how UR241-2 corrects ECM and immune disorders in EOC, making it less conducive to metastasis and tumorigenesis.

cancer biology↗

Monkey See, Model Knew: Large Language Models Accurately Predict Visual Brain Responses in Humans and Non-Human Primates

AO_SCPLOWBSTRACTC_SCPLOWRecent progress in multimodal AI and language-aligned visual representation learning has rekindled debates about the role of language in shaping the human visual system. In particular, the emergent ability of language-aligned vision models (e.g. CLIP) - and even pure language models (e.g. BERT) - to predict image-evoked brain activity has led some to suggest that human visual cortex itself may be language-aligned in comparable ways. But what would we make of this claim if the same procedures could model visual activity in a species without language? Here, we conducted controlled comparisons of pure-vision, pure-language, and multimodal vision-language models in their prediction of human (N=4) and rhesus macaque (N=6, 5:IT, 1:V1) ventral visual activity to the same set of 1000 captioned natural images (the NSD1000). The results revealed markedly similar patterns in model predictivity of early and late ventral visual cortex across both species. This suggests that language model predictivity of the human visual system is not necessarily due to the evolution or learning of language perse, but rather to the statistical structure of the visual world that is reflected in natural language.

neuroscience↗

Antibody-Free Immunopeptide Nano-Conjugates for Brain-Targeted Drug Delivery in Glioblastoma Multiforme

Glioblastoma Multiforme (GBM) represents a significant clinical challenge amongst central nervous system (CNS) tumors, with a dismal mean survival rate of less than 8 months, a statistic that has remained largely unchanged for decades (National Brain Society, 2022). The specialized intricate anatomical features of the brain, notably the blood-brain barrier (BBB), pose significant challenges to effective therapeutic interventions, limiting the potential reach of modern advancements in immunotherapy to impact these types of tumors. This study introduces an innovative, actively targeted immunotherapeutic nanoconjugate (P12/AP-2/NCs) designed to serve as an immunotherapeutic agent capable of traversing the BBB via LRP-1 receptor-mediated transcytosis. P12/AP-2/NCs exert its immune-modulating effects by inhibiting the PD-1/PD-L1 axis through a small-size PD-L1/ PD-L2 antagonist peptide Aurigene NP-12 (P12). P12/AP-2/NCs are synthesized from completely biodegradable, functionalized high molecular weight {beta}-poly(L-malic acid) (PMLA) polymer, conjugated with P12 and Angiopep-2 (AP2) to yield P12/AP-2/NCs. Evaluating nanoconjugates for BBB permeability and 3-D tumor model efficacy using an in vitro BBB-Transwell spheroid based model demonstrating successful crossing of the BBB and internalization in brain 3D tumor environments. In addition, the nanoconjugate mediated T cells cytotoxicity on 3D tumor region death in a U87 GBM 3-D spheroid model. AP2/P12/NCs is selectively inhibited in PD1/PDL1 interaction on T cells and tumor site, increasing inflammatory cytokine secretion and T cell proliferation. In an in-vivo murine brain environment, rhodamine fluorophore-labeled AP2/P12/NCs displayed significantly increased accumulation in the brain during 2-6 h time intervals post-injection with a prolonged bioavailability over unconjugated peptides. AP2/P12/NCs demonstrated a safety profile at both low and high doses based on major organ histopathology evaluations. Our findings introduce a novel, programmable nanoconjugate platform capable of penetrating the BBB for directed delivery of small peptides and significant immune environment modulation without utilizing antibodies, offering promise for treating challenging brain diseases like glioblastoma multiforme and beyond.

immunology↗

DZNep-induced single point mutation (M236I) in poxviral 2'-O-methyltransferase enhances mRNA stability and translation efficiency

Poxviruses encode two highly conserved S-adenosylmethionine (SAM)-dependent methyltransferases for mRNA capping. While D1L facilitates translation via cap-0 formation, the role of VP39-mediated cap-1 modification has been canonically restricted to shield viral mRNA from cytoplasmic pattern-recognition receptors (PRRs). Here, we uncover a novel function of VP39 by demonstrating that prolonged exposure to the SAM cycle inhibitor DZNep selected a virus escape mutant harbouring a point mutation (M236I) in VP39. VP39_mut bypasses S-adenosylhomocysteine (SAH)-mediated feedback inhibition, enhancing 2-O-methylation of viral transcripts and promoting their association with active translation machinery. Consequently, VP39_mut significantly improves viral protein translation, replicative fitness, and yields across species. Notably, VP39_mut-capped in vitro transcribed (IVT) mRNA exhibited [~]2.7-fold higher protein expression compared to VP39_wt, the standard tool for IVT applications. These findings reveal a unique resistance mechanism and provide critical insights into poxvirus mRNA biology while underscoring the potential of optimized VP39 for advancing mRNA-based therapeutics and vaccine production.

microbiology↗

Single Cell RNA Sequencing Analysis of Human Melanoma Reveals A Distinct Prognostic Myeloid Cell

Abstract/SummaryMyeloid-derived cells and tumor-associated macrophages (TAMs) represent an emerging field in melanoma research. Single-cell sequencing has enhanced our understanding of interactions within the tumor microenvironment (TME). Although there is no current consensus, several solid-tumor associated TAM subtypes have been identified by single-cell RNA sequencing (scRNA-seq). Due to the lack of agreement across models and tumor types, we aimed to characterize the myeloid sub-compartment in melanoma by analyzing compiled public scRNA-seq datasets. In this study, we identified six myeloid cell clusters, designated M_C1 through M_C6, with distinct gene expression profiles indicating differences in structure and function. The frequency of the M_C1 subtype was found to be predictive of overall survival (OS) in brain metastatic melanoma. This finding was externally validated by deconvolution of publicly available bulk RNA sequencing data from a clinical trial of advanced melanoma patients treated with nivolumab, as well as data from The Cancer Genome Atlas (TCGA) for melanoma stages I-IV. The M_C1 cell type appears to be a hybrid of dendritic cells and macrophages, demonstrating prognostic relevance across all melanoma stages and predictive potential for immunotherapy response. These data suggest that M_C1 may have utility as a prognostic biomarker in melanoma and as a target for future cell-based therapies.

immunology↗

The Genetic Basis of Chloride Exclusion in Grapevines

Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting vine growth and fruit quality. Despite the critical role of chloride exclusion in salinity tolerance, the genetic mechanisms underlying this trait remain poorly understood. In this study, we leveraged one of the largest Vitis germplasm collections, comprising 335 accessions from 18 wild and cultivated Vitis species, to characterize natural variation in chloride exclusion. This diverse panel, which includes accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress, providing an unprecedented opportunity to investigate the genetic basis of salinity tolerance. Using genome-wide association (GWA) and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8 containing candidate genes encoding cation/H exchangers (CHX), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from V. acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed key non-synonymous substitutions within CHX genes, suggesting potential functional roles in salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating extensive phenotypic and genomic data across a diverse Vitis collection, this study provides novel insights into the genetic architecture of chloride exclusion and identifies valuable candidate genes for breeding salt-tolerant rootstocks.

genetics↗

The modifiers that cause changes in gene essentiality

The phenotype of a mutation often differs across genetically distinct individuals. In the most extreme case, a gene can be essential for viability in one genetic background, but dispensable in another. Although genetic context-dependency of mutant phenotypes is frequently observed, the underlying causes often remain elusive. Here, we investigated the genetic changes responsible for differences in gene essentiality across 18 genetically diverse natural yeast strains. First, we identified 39 genes that were essential in the laboratory reference strain but not required for viability in at least one other genetic background, suggesting that the natural strain contained suppressor variants that could bypass the need for the essential gene. We then mapped and validated the causal bypass suppressor variants using bulk segregant analysis and allele replacements. Bypass suppression was generally driven by a single modifier gene that tended to differ between genetic backgrounds. The suppressors often indirectly counteracted the effect of deleting the essential gene, for instance by changing the transcriptome of a cell. Context-dependent essential genes and their bypass suppressors were frequently co-mutated across 1,011 yeast isolates and identified naturally occurring evolutionary trajectories. Overall, our results highlight the relatively high frequency of bypass suppression in natural populations, as well as the underlying variants and mechanisms. A thorough understanding of the causes of genetic background effects is crucial for the interpretation of genotype-to-phenotype relationships, including those associated with human disease.

genomics↗

Novel function of Contactin associated protein 1 (Caspr 1)/ Paranodin in embryonic cortical neurons: hypoxia modulated neurite development.

Hypoxia, a condition of inadequate oxygen supply, is a common phenomenon affecting neurons and brain tissue, leading to significant implications for neuronal health and function. The prevalence of hypoxia in the brain is associated with various neurological conditions, making it a critical area of study. Neuritogenesis, the process of neurite outgrowth, is an essential aspect of neuronal development and connectivity and is particularly sensitive to hypoxic stress. Investigating how hypoxia affects neurite outgrowth is vital for understanding neuronal response and adaptation under low oxygen conditions. This study explores how hypoxic stress affects neurite regulation mediated by Contactin Associated Protein-1 (Caspr1) in primary mouse embryonic cortical neurons. Hypoxia, induced by culturing neurons in a 2% oxygen environment, significantly reduced neurite length and induced notable changes in growth cone morphology. Concurrently, we observed an upregulation in the expression of Caspr1 and its transcriptional regulator C/EBP, suggesting a compensatory role for Caspr1 in neurite extension under low oxygen conditions. Shorter hypoxia exposure periods revealed a dynamic biphasic response in Caspr1 levels, with an initial decrease followed by a substantial increase, correlating with corresponding changes in neurite length. This pattern emphasizes the critical involvement of Caspr1 in adapting neurite growth to fluctuating hypoxia duration. Furthermore, comparative analyses using wild-type and Caspr1 knockout Neuro2a cells demonstrated that the absence of Caspr1 mitigates hypoxia-induced neurite shortening, indicating a potential protective role against hypoxic stress. Additionally, hypoxia profoundly impacted mitochondrial morphology and function. Under hypoxic conditions, mitochondria transitioned to a more spherical shape. Mitochondrial respiration analysis revealed significant reductions in oxygen consumption rates (OCR), highlighting compromised mitochondrial function during hypoxia. These findings underscore the multifaceted role of Caspr1 in neurite regulation and mitochondrial adaptation to hypoxic stress. The study provides insights into the molecular mechanisms underpinning hypoxia-induced changes in neuronal morphology and function. Understanding these processes opens avenues for therapeutic strategies targeting Caspr1 in treating neurological disorders characterized by hypoxic stress. Future research will benefit from extending these investigations to more complex models, such as brain organoids, to further elucidate the metabolic and structural changes under hypoxia and their implications for neurodegenerative diseases.

neuroscience↗

Distinct roles for thymic stromal lymphopoietin (TSLP) and IL-33 in experimental eosinophilic esophagitis

RationaleThymic stromal lymphopoietin (TSLP) and IL-33 are alarmins implicated in EoE pathogenesis by activating multiple cells including mast cells (MCs). Whether TSLP or IL-33 have a role in EoE and whether their activities are distinct requires further investigation. MethodsExperimental EoE was induced in wild type (WT) Il33-/-and Crlf2-/- mice. TSLP or IL-5 were neutralized using antibodies. Esophageal histopathology was determined by H&E, anti-Ki67, anti-CD31 and anti-MBP staining. Esophageal RNA was subjected to RNA sequencing. Bone marrow-derived MCs were activated with TSLP and IL-13 was determined (ELISA) ResultsTSLP and IL-33 were overexpressed in human and experimental EoE. Human and mouse esophageal MCs displayed the highest level of Crlf2 (TSLPR) compared to other immune cells. Crlf2-/- mice were nearly-completely protected from EoE, and TSLP neutralization resulted in decreased basal cell proliferation, eosinophilia, lamina propria thickening and vascularization. Induction of experimental EoE in Il33-/- mice resulted in reduced eosinophilia but no alterations in tissue remodeling were observed compared to WT mice. RNA sequencing revealed that TSLP regulates the expression of key genes associated with human EoE (e.g. eotaxins, Il19, Klk5, Flg, Il36rn, Il1r2) and suggest a role for TSLP in regulating IL-1 signaling, barrier integrity and epithelial cell differentiation. Experimental EoE was characterized by a MC-associated gene signature and elevated MCs. Activation of MCs with TSLP resulted in secretion of IL-13. ConclusionTSLP and IL-33 have non-redundant functions in experimental EoE. This study highlights TSLP as an upstream regulator of IL-13 and a potential therapeutic target for EoE.

immunology↗

Divergent granulopoiesis at extramedullary sites safeguards host defense

Extramedullary organs such as the spleen can assume granulopoiesis as a supportive mechanism to cope with the demands during persistent inflammation. However, the quantitative output of extramedullary granulopoiesis is limited, thus raising the question if the spleen in fact provides neutrophils of a qualitative difference rather than merely contributing to neutrophil numbers. Here we report splenic stress granulopoiesis with distinct production and differentiation trajectories. Myeloid progenitors in the spleen engage in accelerated production of neutrophils with an immature phenotype. Yet, neutrophils generated during persistent stress granulopoiesis are fully competent to exert antimicrobial functions and are necessary to contain bacterial invasion. Activation of type I interferon signaling in the spleen is required for splenic neutrophil production and its loss impairs host defense. Thus, the spleen provides an immunological environment for stress-induced rapid production and priming of highly active neutrophils to meet the demands during infection.

immunology↗