Biology subjects

Nelson, T.

Publications and source records attributed to Nelson, T..

14 recordsLinked to original sources

bioRxiv2026

RhoA effectors ROCK and SLK/LOK oppositely regulate VE-cadherin mobility at endothelial junctions

Cellular contractile forces regulate VE-cadherin dynamics, adhesion, and endothelial junction integrity. RhoA controls these forces through two parallel effector kinases: ROCK, which activates non-muscle myosin II motors, and SLK/LOK, which promote actin-membrane attachment through phosphorylation of ezrin, radixin, moesin proteins (ERM). How these two RhoA effector pathways differentially affect VE-cadherin dynamics at junctions is not known. Using single-molecule tracking of Halo-tagged VE-cadherin, we obtained a detailed characterization of VE-cadherin diffusive behavior inside and outside junctional regions in cultured human umbilical vein endothelial cells (HUVEC). VE-cadherin was substantially less mobile and more confined within junctions than in non-junctional membrane. Inhibiting ROCK with Y-27632 increased VE-cadherin mobility both inside and outside junctions, consistent with RhoA/ROCK-driven contractility restraining cadherin diffusion globally. Unexpectedly, inhibiting SLK/LOK produced the opposite effect, selectively reducing VE-cadherin mobility within junctions with no comparable change outside them. This effect was accompanied by an increase in reticular junctions, suggesting that SLK/LOK inhibition alters VE-cadherin mobility indirectly, through a change in junctional architecture, rather than through a direct effect of actin-membrane coupling on VE-cadherin itself. These findings identify SLK/LOK as a regulator of VE-cadherin dynamics acting in parallel to ROCK downstream of RhoA and point to junctional architecture as a previously unappreciated determinant of VE-cadherin mobility at endothelial cell-cell contacts.

biophysics↗

bioRxiv2026

Chronic pain exacerbates nicotine withdrawal severity in a sex-specific and dose-dependent manner

Chronic pain and nicotine use frequently co-occur, and individuals with chronic pain often experience greater difficulty quitting. Therefore, we examined nicotine withdrawal behaviors and analgesic-like effects in pain-naive and chronic pain conditions. Adult male and female rats underwent chronic constriction injury or sham surgery. After pain establishment, rats received twice-daily subcutaneous nicotine (0.3 or 0.7 mg/kg) or saline for 14 days. 24 h after the final injection, withdrawal was assessed, including physical signs and anxiety-like behavior. Depressive-like responses were evaluated at 72 h. Pain sensitivity and nicotines analgesic-like effects were assessed throughout. Chronic pain increased physical signs of withdrawal in both sexes, with greater effects in females. It also induced anxiety-like behavior in controls of both sexes. In rats with comorbid chronic pain and withdrawal, anxiety-like behavior was further enhanced in males, whereas females showed variable responses across assays, with increases or decreases depending on the test. Chronic pain induced depressive-like behavior in males but not in females. During withdrawal, depressive-like responses in males with chronic pain were not greater than those in the chronic pain alone group, while chronic nicotine exposure reduced depressive-like behavior in females. Nicotine produced acute analgesic-like effects that diminished over time in both pain-naive and chronic pain conditions, indicating tolerance. In pain-naive rats, repeated nicotine exposure induced mechanical hypersensitivity. Chronic pain intensified nicotine withdrawal severity in a nicotine concentration- and sex-dependent manner. These findings highlight the importance of considering pain status and sex when developing effective cessation strategies, particularly for individuals with comorbid chronic pain. SummaryChronic pain exacerbates nicotine withdrawal severity. Chronic nicotine exposure induces pain hypersensitivity and tolerance to analgesic effects. These effects vary by nicotine concentration and sex.

pharmacology and toxicology↗

bioRxiv2025

Symbiont virulence is a poor predictor of impacts on host population dynamics

Symbionts are classified as parasites or mutualists based on their impacts on host individuals, but timescale, ecological context, and level of biological organization can all influence symbiosis outcomes, and hence whether they are deemed harmful or beneficial. We designed experiments exposing the key freshwater grazer Daphnia dentifera to two symbionts varying in virulence, to test how well individual-level effects translate into population-level patterns. We found that a seemingly mildly virulent microsporidian strongly reduced host population size, with consequences for primary production, while a yeast that was highly virulent to individuals had no detectable negative effects on host population size. Our experiments show that studies that fail to consider the impacts of symbionts at multiple scales risk focusing mitigation and control measures on the wrong symbionts.

ecology↗

bioRxiv2024

Hypomorphic NOTCH1 Expression Alters Cardiomyocyte Cellular Architecture in Hypoplastic Left Heart Syndrome

NOTCH1 is a protein involved in cardiac development and mutations in NOTCH1 are implicated in left sided congenital heart disease, including hypoplastic left heart syndrome (HLHS). Therapeutic advances for HLHS patients have been hampered by the absence of suitable experimental models. Here, using human induced pluripotent stem cells (hiPSCs), we have generated a series of CRISPR-edited complex heterozygous hypomorphic mutations in NOTCH1 that recapitulate mutations seen in HLHS patients. These cells demonstrate the downregulation of genes associated with mitochondria, the actin cytoskeleton, and cardiomyocyte development. In addition, these hypomorphic NOTCH1 hiPSCs cells showed an increased propensity to differentiate towards non-cardiomyocyte lineages such as fibroblasts and smooth muscle cells, a finding confirmed in HLHS patient-derived myocardial tissue. Abnormalities in sarcomeric and mitochondrial architecture contributed to decreased ATP production, abnormal calcium transients, and reduced contractility. Using a split nano-luciferase system as a NOTCH1 intracellular reporter, we screened a library of FDA-approved compounds. Auranofin, an agent currently employed for rheumatoid arthritis, was identified as a candidate drug that could rescue impaired differentiation and contractility seen in the hypomorphic NOTCH1 model. These findings point to cell-autonomous abnormalities in hypomorphic NOTCH1 pre-cardiomyocyte cells that can be leveraged to identify potential therapeutic strategies for patients with severe congenital cardiac abnormalities. HighlightsO_LICRISPR edited and patient-derived iPSCs with hypomorphic NOTCH1 expression were used to characterize a cell-based model of hypoplastic left heart syndrome. C_LIO_LIHypomorphic NOTCH1 iPSCs have abnormalities in pathways associated with mitochondrial function, actin cytoskeleton, and cardiomyocyte development. C_LIO_LIHypomorphic NOTCH1 iPSCs have less pluripotency and tend to skew differentiation away from cardiomyocytes and towards fibroblasts and smooth muscle cells. C_LIO_LINOTCH1 is required for cardiac cytoskeletal and mitochondrial architecture, and to preserve contractility and ATP production. C_LIO_LIA high-throughput drug screen identified auranofin as an agent that may benefit patients with hypoplastic left heart syndrome. C_LI

cell biology↗

bioRxiv2024

Integrative analysis of single-cell gene expression: A comprehensive database approach

The exponential growth of single-cell datasets provides unprecedented opportunities to advance our understanding of complex biological systems. However, effectively locating and integrating related studies for meaningful insights remains challenging. Traditional databases primarily index basic metadata, which necessitates time-consuming downloading and re-filtering based on gene expression and cell type or tissue composition, followed by computationally intensive aggregation. This process often results in excessively large datasets that are difficult to analyze effectively, further complicated by batch effects. To address these issues, we have developed a computational approach to efficiently extract and index both expression data and annotations. Our comprehensive database incorporates detailed author annotations and gene expression profiles, enabling refined searches and integrated analyses to uncover common biological patterns while accounting for the repeatability of patterns across multiple studies and mitigating batch effects. This approach significantly reduces computational demands and enhances the accessibility and utility of single-cell transcriptomics data for the broader research community. In the first version, we release a human database comprising 244 datasets from 236 cell types, 35 tissues, and 31 conditions.

bioinformatics↗

bioRxiv2024

Automated cell annotation in scRNA-seq data using unique marker gene sets

Single-cell RNA sequencing has revolutionized the study of cellular heterogeneity, yet accurate cell type annotation remains a significant challenge. Inconsistent labels, technological variability, and limitations in transferring annotations from reference datasets hinder precise annotation. This study presents a novel approach for accurate cell type annotation in scRNA-seq data using unique marker gene sets. By manually curating cell type names and markers from 280 publications, we verified marker expression profiles across these datasets and unified the nomenclature to consistently identify 166 cell types and subtypes. Our customized algorithm, which builds on the AUCell method, achieves accurate cell labeling at single-cell resolution and surpasses the performance of reference-based tools like Azimuth, especially in distinguishing closely related subtypes. To enhance accessibility and practical utility for researchers, we have also developed a user-friendly application that automates the cell typing process, enabling efficient verification and supporting comprehensive downstream analyses.

bioinformatics↗

bioRxiv2024

Multimodal illumination platform for 3D single-molecule super-resolution imaging throughout mammalian cells

Single-molecule super-resolution imaging is instrumental for investigating cellular architecture and organization at the nanoscale. Achieving precise 3D nanometric localization when imaging structures throughout mammalian cells, which can be multiple microns thick, requires careful selection of the illumination scheme in order to optimize the fluorescence signal to background ratio (SBR). Thus, an optical platform that combines different wide-field illumination schemes for target-specific SBR optimization would facilitate more precise, 3D nanoscale studies of a wide range of cellular structures. Here we demonstrate a versatile multimodal illumination platform that integrates the sectioning and background reduction capabilities of light sheet illumination with homogeneous, flat-field epi-and TIRF illumination. Using primarily commercially available parts, we combine the fast and convenient switching between illumination modalities with point spread function engineering to enable 3D singlemolecule super-resolution imaging throughout mammalian cells. For targets directly at the coverslip, the homogenous intensity profile and excellent sectioning of our flat-field TIRF illumination scheme improves single-molecule data quality by providing low fluorescence background and uniform fluorophore blinking kinetics, fluorescence signal, and localization precision across the entire field of view. The increased contrast achieved with LS illumination, when compared with epi-illumination, makes this illumination modality an excellent alternative when imaging targets that extend throughout the cell. We validate our microscopy platform for improved 3D super-resolution imaging by two-color imaging of paxillin - a protein located in the focal adhesion complex - and actin in human osteosarcoma cells.

biophysics↗

bioRxiv2024

Microsporidian coinfection reduces fitness of a fungal pathogen due to rapid host mortality

Infection outcomes can be strongly context-dependent, shifting a host-symbiont relationship along a parasitism-mutualism continuum. Numerous studies show that under stressful conditions, symbionts that are typically mutualistic can become parasitic. The reverse possibility - a parasite becoming mutualistic - has received much less study. We investigated whether the parasitic microsporidium Ordospora pajunii can become beneficial for its host Daphnia dentifera in the presence of the more virulent fungal pathogen Metschnikowia bicuspidata. We found that, even though infection with O. pajunii reduces the frequency of penetration of M. bicuspidata spores into the host body cavity, it does not improve the survival or reproduction of the host; conversely, coinfection increased the mortality of Daphnia. However, the shorter lifespan of coinfected hosts disrupted the life cycle of M. bicuspidata, greatly reducing its fitness. Thus, coinfection with both pathogens was detrimental to the host at the individual level, but might be beneficial for the host population as a result of greatly reduced production of M. bicuspidata spores. If so, this would mean that O. pajunii outbreaks should delay or prevent M. bicuspidata outbreaks. In support of this, in an analysis of dynamics of naturally occurring outbreaks in two lakes where these pathogens co-occur, we found a time lag in occurrence between O. pajunii and M. bicuspidata, with M. bicuspidata epidemics only occurring after the collapse of O. pajunii epidemics. Thus, these results suggest that the interaction between co-occurring symbionts - and the net impact of a symbiont on a host - might be qualitatively different at different scales. ImportanceUnderstanding the factors that modify infection probability and virulence is crucial for identifying the drivers of infection outbreaks and modeling disease epidemic progression, and increases our ability to control diseases and reduce the harm they cause. One factor that can strongly influence infection probability and virulence is the presence of other pathogens. However, while coexposures and coinfections are incredibly common, we still have only a limited understanding of how pathogen interactions alter infection outcomes, or whether their impacts are scale-dependent. We used a system of one host and two pathogens to show that sequential coinfection can have a tremendous impact on the host and on the infecting pathogens, and that the outcome of (co-)infection can be negative or positive depending on the focal organization level.

ecology↗

bioRxiv2022

Development and application of a computable genotype model in the GA4GH Variation Representation Specification

As the diversity of genomic variation data increases with our growing understanding of the role of variation in health and disease, it is critical to develop standards for precise inter-system exchange of these data for research and clinical applications. The Global Alliance for Genomics and Health (GA4GH) Variation Representation Specification (VRS) meets this need through a technical terminology and information model for disambiguating and concisely representing variation concepts. Here we discuss the recent Genotype model in VRS, which may be used to represent the allelic composition of a genetic locus. We demonstrate the use of the Genotype model and the constituent Haplotype model for the precise and interoperable representation of pharmacogenomic diplotypes, HGVS variants, and VCF records using VRS and discuss how this can be leveraged to enable interoperable exchange and search operations between assayed variation and genomic knowledgebases.

bioinformatics↗

bioRxiv2021

Pulling on multiple threads of evidence to reveal tree species coexistence

Understanding drivers of species coexistence is a central challenge in ecology (1, 2). Coexistence cannot be observed directly, and while species co-occurrence in time and space is necessary for coexistence, it is not sufficient to prove coexistence (3, 4). Species exclusion from a region is potentially observable, but can take decades to occur, and still might just occur stochastically (5, 6). Thus, ecologists generally use theory to identify indirect observations that are indicative of mechanisms driving coexistence or exclusion (7-9). Various methods have been developed to indirectly infer coexistence, each of which requires different data, none of which are usually conclusive on their own, and are not typically combined (e.g. (9-12)). Here, we combine three different approaches which are normally used in isolation to build a case about a lack of coexistence of multiple hardwood species. Importantly, though each method has its flaws, we find that all three point to the same conclusion which strengthens the case for a lack of coexistence. First, in an experimental planting of three mature tree species we found no relationship between productivity and species diversity, which has been hypothesized to occur due to a lack of niche differences among species. Second, we used modern coexistence theory to calculate niche and fitness differences for each pair of species, which confirmed the high niche overlap among species and competitive dominance of one species. Third, we used the United States Department of Agriculture Forest Inventory and Analysis data to examine co-occurrence patterns of our species across thousands of natural forest stands and found that, these three species were distributed randomly throughout the USA, and do not significantly co-occur as would be expected if coexistence occurred naturally. Given that these independent methods agree; we take this as strong evidence about a lack of coexistence.

ecology↗

bioRxiv2021

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Maximizing the personal, public, research, and clinical value of genomic information will require that clinicians, researchers, and testing laboratories exchange genetic variation data reliably. Developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH), the Variation Representation Specification (VRS, pronounced "verse") is an extensible framework for the semantically precise and computable representation of variation that complements contemporary human-readable and flat file standards for variation representation. VRS objects are designed to be semantically precise representations of variation, and leverage this design to enable unique, federated identification of molecular variation. We describe the components of this framework, including the terminology and information model, schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. The specification, documentation, examples, and community links are available at https://vrs.ga4gh.org/.

bioinformatics↗

bioRxiv2020

The maize Aliphatic Suberin Feruloyl Transferase genes affect leaf water movement but are dispensable for bundle sheath CO2 concentration

C4 grasses often outperform C3 species under hot, arid conditions due to superior water and nitrogen use efficiencies and lower rates of photorespiration. A method of concentrating CO2 around the site of carbon fixation in the bundle sheath (BS) is required to realize these gains. In NADP-malic enzyme (NADP-ME)-type C4 grasses such as maize, suberin deposition in the BS cell wall is hypothesized to act as a diffusion barrier to CO2 escape and O2 entry from surrounding mesophyll cells. Suberin is a heteropolyester comprised of acyl-lipid-derived aliphatic and phenylpropanoid-derived aromatic components. To disrupt BS suberization, we mutated two paralogously duplicated, unlinked maize orthologues of Arabidopsis thaliana ALIPHATIC SUBERIN FERULOYL TRANSFERASE, ZmAsft1 and ZmAsft2, using closely linked Dissociation transposons. Loss-of-function double mutants revealed a 97% reduction in suberin-specific omega-hydroxy fatty acids without a stoichiometric decrease in ferulic acid. However, BS suberin lamellae were deficient in electron opaque material, and cohesion between the suberin lamellae and polysaccharide cell walls was attenuated in double mutants. There were no other morphological phenotypes under ambient conditions. Furthermore, there was no significant effect on net CO2 assimilation at any intercellular CO2 concentration, and no effect on 13C isotope discrimination relative to wild type. Thus, ZmAsft expression is not required to establish a functional CO2 concentrating mechanism in in maize. Double mutant leaves exhibit elevated cell wall elasticity, transpirational, and stomatal conductance relative to WT. Thus, the ZmAsft genes are dispensable for gas exchange barrier function but may be involved in regulation of leaf water movement. One-sentence SummaryDouble mutants of two paralogously duplicated maize Aliphatic Suberin Feruloyl Transferase (ZmAsft) genes exhibit reduced aliphatic suberin content, cell wall cohesion defects, and elevated leaf transpiration, but no changes in CO2 assimilation relative to wild type.

plant biology↗

bioRxiv2020

Modulation of proteasome activity by curcumin and didemethylcurcumin

Modulation of proteasome function by pharmacological interventions and molecular biology tools is an active area of research in cancer biology and neurodegenerative diseases. Curcumin (diferuloylmethane) is a naturally occurring polyphenol that affects multiple signaling pathways and known to modulate PKC activities. The therapeutic significance of curcumin is often considered to reside in its anti-inflammatory, antioxidant, anti-angiogenic, or anti-apoptotic properties. However, recent research suggests that the therapeutic efficacy of curcumin may be due to its activity as a potent inhibitor of the proteasome. In this study, we show that both curcumin and its synthetic polyphenolic derivative (didemethylcurcumin), CUIII modulated proteasome activity in a biphasic manner. Curcumin and CUIII increased proteasome activity at nanomolar concentrations but inhibited proteasome activity at micromolar concentrations. Curcumin was more effective than CUIII in relative proteasome activity increase at nanomolar concentrations. Also, curcumin was more effective than CUIII in relative proteasome activity inhibition at micromolar concentration. The docking study was conducted on the 20S proteasome catalytic subunit. Estimated Kd values for curcumin and didemethylcurcumin are 0.0054M and 1.3167M, respectively. These values correlate well with the results of the effectiveness of modulation by curcumin compare to CUIII. The small size of CUIII makes its dock to the narrow cavity of the active site, but the binding interaction is not strong compare to curcumin. This study suggests that curcumin and its didemethyl derivative can be used to modulate proteasome activity. This communication implicates the reason why curcumin and its didemethyl derivative can be used to two different disease mechanisms, neurodegeneration, and cancer.

neuroscience↗

bioRxiv2019

Quantitative proteomics identifies novel PIAS1 protein substrates involved in cell migration and motility

The Protein Inhibitor of Activated STAT 1 (PIAS1) is an E3 SUMO ligase that plays important roles in various cellular pathways, including STAT signaling, p53 pathway, and the steroid hormone signaling pathway. PIAS1 can SUMOylate PML (at Lys-65 and Lys-160) and PML-RAR promoting their ubiquitin-mediated degradation. Increasing evidence shows that PIAS1 is overexpressed in various human malignancies, including prostate and lung cancers. To understand the mechanism of action of PIAS1, we developed a quantitative SUMO proteomic approach to identify potential substrates of PIAS1 in a system-wide manner. Our analyses enabled the profiling of 983 SUMO sites on 544 proteins, of which 204 SUMO sites on 123 proteins were identified as putative PIAS1 substrates. These substrates are involved in different cellular processes, such as transcriptional regulation, DNA binding and cytoskeleton dynamics. Further functional studies on Vimentin (VIM), a type III intermediate filament protein involved in cytoskeleton organization and cell motility, revealed that PIAS1 exerts its effects on cell migration and cell invasion through the SUMOylation of VIM at Lys-439 and Lys-445 residues. VIM SUMOylation was necessary for its dynamic disassembly, and cells expressing a non-SUMOylatable VIM mutant showed reduced levels of proliferation and migration. Our approach not only provides a novel strategy for the identification of E3 SUMO ligase substrates, but also yields valuable biological insights into the unsuspected role of PIAS1 and VIM SUMOylation on cell motility.

cancer biology↗