Biology subjects

Noble, J.

Publications and source records attributed to Noble, J..

9 recordsLinked to original sources

bioRxiv2025

Not all alloantibodies are created equal: IgG glycosylation and severity of antibody-mediated rejection in kidney transplantation

IntroductionAntibody-mediated rejection (AMR) is a leading cause of kidney transplant (KT) failure, driven by donor-specific anti-HLA antibodies (DSA). However, not all patients with DSA experience accelerated graft loss, suggesting that factors beyond antibody presence influence AMR severity. Post-translational modifications, particularly glycosylation of Immunoglobulin-G (IgG), play a critical role in modulating antibody function. This study investigates the association between IgG glycosylation profiles and the risk and severity of AMR in KT recipients. MethodsWe prospectively analyzed 65 KT patients, including 26 with acute AMR (aAMR), 27 with chronic-active AMR (caAMR), and 12 controls without rejection. IgG glycosylation was quantified using lectin-based ELISA, focusing on mannose, fucose, sialic acid, and bisecting N-acetylglucosamine (GlcNAc) levels. ResultsResults showed that bisecting GlcNAc levels of total IgG were significantly higher in caAMR patients than controls (p=0.019) and aAMR patients (p=0.045). Multivariable analysis revealed that higher bisecting GlcNAc levels of IgG were independently associated with glomerulitis [g-score, OR: 2.7 (95%CI: 1.2-6.7), p=0.019] and chronic glomerulopathy [cg-score, OR: 2.8 (95%CI: 1.3-7.5), p=0.021], independent of DSA presence. ConclusionsThese findings indicate an association between IgG glycosylation, particularly bisecting GlcNAc, and AMR severity. IgG glycosylation profiles could serve as biomarkers for AMR risk and severity, offering new insights into the mechanisms of AMR and potential therapeutic targets.

immunology↗

bioRxiv2025

A proteogenomic tool uncovers protein markers for human microglial states

Human microglial heterogeneity has been largely described using transcriptomic data. Here, we introduce a microglial proteomic data resource and a Cellular Indexing of Transcriptomes and Epitopes by Sequencing panel enhanced with antibodies targeting 17 microglial cell surface proteins (mCITE-Seq). We evaluated mCITE-Seq on HMC3 microglia-like cells, induced-pluripotent stem cell-derived microglia (iMG), and freshly isolated primary human microglia. We identified novel protein microglial markers such as CD51 and relate expression of 101 cell surface proteins to transcriptional programs. This results in the identification and validation of three protein marker combinations with which to purify microglia enriched with each of 23 transcriptional programs; for example, CD49D, HLA-DR and CD32 enrich for GPNMBhigh ("disease associated") microglia. Further, we identify and validate proteins - SIRPA, PDPN and CD162 - that differentiate microglia from infiltrating macrophages. The mCITE-Seq panel enables the transition from RNA-based classification and facilitates the functional characterization and harmonization of model systems.

neuroscience↗

bioRxiv2025

Allosteric Modulation of Pathological Ataxin-3 Aggregation: A Path to Spinocerebellar Ataxia Type-3 Therapies

Spinocerebellar ataxia type 3 (SCA3) is a rare inherited neurodegenerative disease caused by the expansion of a polyglutamine repeat in the protease ataxin-3 (Atx3). Despite extensive knowledge of the downstream pathophysiology, no disease-modifying therapies are currently available to halt disease progression. The accumulation of protein inclusions enriched in the polyQ-expanded Atx3 in neurons suggests that inhibiting its self-assembly may yield targeted therapeutic approaches. Here it is shown that a supramolecular tweezer, CLR01, binds to a lysine residue on a positively charged surface patch of the Atx3 catalytic Josephin domain. At this site, the binding of CLR01 decreases the conformational fluctuations of the distal flexible hairpin. This results in reduced exposure of the nearby aggregation-prone region, which overlaps with the substrate ubiquitin binding site and primes Atx3 self-assembly, ultimately delaying Atx3 amyloid fibril formation and reducing the secondary nucleation rate, a process linked to fibril proliferation and toxicity. These effects translate into the reversal of synapse loss in a SCA3 cultured cortical neuron model, an improved locomotor function in a C. elegans SCA3 model, and a delay in disease onset, accompanied by reduced severity of motor symptoms in a SCA3 mouse model. This study provides critical insights into Atx3 self-assembly, revealing a novel allosteric site for designing CLR01-inspired therapies targeting pathological aggregation pathways while sparing essential functional sites. These findings emphasize that targeting allosteric sites in amyloid-forming proteins may offer unique opportunities to develop safe therapeutic strategies for various protein misfolding disorders.

biophysics↗

bioRxiv2024

Transformation of an olfactory placode-derived cell into one with stem cell characteristics by disrupting epigenetic barriers

The mammalian olfactory neuronal lineage is regenerative, and accordingly, maintains a population of pluripotent cells that replenish olfactory sensory neurons and other olfactory cell types during the life of the animal. Moreover, in response to acute injury, the early transit amplifying cells along the olfactory sensory neuronal lineage are able to de-differentiate to shift resources in support of tissue restoration. In order to further explore plasticity of various cellular stages along the olfactory sensory neuronal lineage, we challenged the epigenetic stability of two olfactory placode-derived cell lines that model immature olfactory sensory neuronal stages. We found that perturbation of the Ehmt2 chromatin modifier transformed the growth properties, morphology, and gene expression profiles towards states with several stem cell characteristics. This transformation was dependent on continued expression of the large T-antigen, and was enhanced by Sox2 over-expression. These findings may provide momentum for exploring inherent cellular plasticity within early cell types of the olfactory lineage, as well as potentially add to our knowledge of cellular reprogramming. SUMMARY STATEMENTDiscovering how epigenetic modifications influence olfactory neuronal lineage plasticity offers insights into regenerative potential and cellular reprogramming.

molecular biology↗

bioRxiv2023

All-optical voltage imaging-guided postsynaptic single-cell transcriptome profiling with Voltage-Seq

Neuronal pathways recruit large postsynaptic populations and maintain connections via distinct postsynaptic response types (PRTs). Until recently, PRTs were only accessible as a selection criterion for single-cell RNA-sequencing (scRNA-seq) through probing by low-throughput whole-cell electrophysiology. To overcome these limitations and target neurons based on specific PRTs for soma collection and subsequent scRNA-seq, we developed Voltage-Seq. An on-site analysis tool, VoltView, was created to guide soma harvesting of specific PRTs using a classifier based on a previously acquired connectome database from multiple animals. Here, we present a detailed step-by-step protocol, including setting up the optical path, the imaging setup, detailing the imaging procedure, and analysis, the reagents and protocols, complete procedure for sequencing library preparation, and provide other tips and pitfalls to assist researchers in conducting high-throughput all-optical voltage imaging, and to obtain the single-cell transcriptomic data from selected postsynaptic neurons. Voltage-seq workflow can be completed in [~]6 weeks including 4-5 weeks of viral expression of the Voltron sensor. The approach allows researchers to resolve the connectivity ratio of a specific pathway and explore the diversity of PRTs within that connectome. Furthermore, the high throughput in conjunction with quick analysis gives unique access to find specific connections within a large postsynaptic connectome. Voltage-seq also allows the investigation of correlations between connectivity and gene expression changes in a postsynaptic cell-type-specific manner in both excitatory and inhibitory connections.

neuroscience↗

bioRxiv2023

JAGGER localization and function is dependent on GPI anchor addition

In flowering plants, successful double fertilization requires the correct delivery of two sperm cells to the female gametophyte inside the ovule. The delivery of a single pair of sperm cells is achieved by the entrance of a single pollen tube into one female gametophyte. To prevent polyspermy, Arabidopsis ovules avoid the attraction of multiples pollen tubes to one ovule - polytubey block. In Arabidopsis jagger mutants, a significant number of ovules attract more than one pollen tube to an ovule due to an impairment in synergid degeneration. JAGGER encodes a putative arabinogalactan protein (AGP) which is predicted to be anchored to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor. Here, we show that JAGGER fused to citrine yellow fluorescent protein (JAGGER-cYFP) is functional and localizes mostly to the periphery of ovule integuments and transmitting tract cells. We further investigated the importance of GPI-anchor addition domains for JAGGER localization and function. Different JAGGER proteins with deletions in predicted {omega}-site regions and GAS (GPI attachment signal) domain, expected to compromise the addition of the GPI anchor, led to disruption of JAGGER localization in the cell periphery. All JAGGER proteins with disrupted localization were also not able to rescue the polytubey phenotype, pointing to the importance of GPI-anchor addition to in vivo function of the JAGGER protein.

plant biology↗

bioRxiv2023

Quantifying the performance benefits of middle distance running super spikes

BackgroundQuantifying the potential benefits of advanced footwear technology (AFT) track shoes (i.e., "spikes") in middle-distance events is challenging, because repeated maximal effort trials (as in sprinting) or aerobic running economy trials (as in long-distance running) are not feasible. MethodsWe introduce a novel approach to assess the benefits of AFT spikes, consisting of a series of 200 m runs at self-perceived middle-distance race pace with 10 min recovery and conducted four experiments to evaluate its validity, sensitivity, reproducibility, and utility. ResultsIn experiment 1, participants ran 1.2% slower in spikes with 200 g added mass vs. control spikes, exactly equal to the known effects of shoe mass on running performance. In experiment 2, participants ran significantly faster in AFT prototype spikes vs. traditional spikes. In experiment 3, we compared two other AFT prototype spikes against traditional spikes, on three separate days. Group-level results were consistent across days, but our data indicates that at least two separate sessions are needed to evaluate individual responses. In experiment 4, participants ran significantly faster in two AFT spike models vs. traditional spikes (2.1% and 1.6%). Speed was similar between a third AFT spike model and the traditional spikes. These speed results were mirrored by changes in step length, as participants took significantly longer steps in the two faster AFT spike models (2.3% and 1.9%), while step length was similar between the other spikes. ConclusionOur novel, interval-based approach is a valid and reliable method to quantify differences between spikes at middle-distance running intensity.

physiology↗

bioRxiv2023

Phenotypic variations of primary metabolites yield during alcoholic fermentation in the Saccharomyces cerevisiae species

Saccharomyces cerevisiae is a major actor in winemaking that converts sugars from the grape must into ethanol and CO2 with outstanding efficiency. Primary metabolites produced during fermentation have a great importance in wine. While ethanol content contributes to the overall profile, other metabolites like glycerol, succinate, etc., also have significant impacts, even when present in lower concentrations. S. cerevisiae is known for its great genetic diversity that is related to its natural or technological environment. However, its range of metabolic diversity which can be exploited to enhance wine quality depends on the pathway considered. Our experiment assessed the diversity of primary metabolites production in a set of 51 S. cerevisiae strains from various genetic backgrounds. Results pointed out great yield differences depending on the metabolite considered, with ethanol having the least variation. A negative correlation between ethanol and glycerol was observed, confirming glycerol synthesis as a suitable lever to reduce ethanol yield. Genetic groups were linked to specific metabolic yields such as -ketoglutarate or acetate. This research highlights the potential of using natural yeast diversity in winemaking and provides detailed data set on metabolite production of well known (ethanol, glycerol, acetate) or little-known (lactate) primary metabolites production.

microbiology↗

bioRxiv2020

Dynamic Laser Speckle Imaging meets Machine Learning to enable Rapid Antibacterial Susceptibility Testing (DyRAST)

Rapid antibacterial susceptibility testing (RAST) methods which measure change of a bacterial phenotype in response to a given treatment are of significant importance in healthcare, as they can assist care-givers in timely administration of the right treatment. Various RAST techniques have been reported for tracking bacterial phenotypes, such as size, shape, motion, and metabolic activity. However, they still require bulky and expensive instruments (which hinders their application in resource-limited environments) and/or utilize labeling reagents (which can interfere with antibiotics and add to cost). Furthermore, the existing ultra-rapid methods do not address possible adaptation of gradual adaptation of bacteria to antibiotics, which can lead to false interpretation of resistance when using ultra-rapid methods. In this work, we present a RAST approach leveraging machine learning analysis of time-resolved dynamic laser speckle imaging (DLSI) results to accurately predict the minimum inhibitory concentration (MIC) of a model strain of Escherichia coli in 60 minutes, compared to 6 hours using the currently FDA-approved phenotype-based RAST technique. To demonstrate the DLSI performance, we studied the effect of a {beta}-lactam ampicillin and an aminoglycoside gentamicin on Escherichia coli strain K-12. DLSI captures change of bacterial motion/division in response to treatment. The machine learning algorithm was trained and validated using the overnight results of gold standard, broth microdilution method. Empowered by machine learning, DyRAST can predict MIC with high accuracy comparable to gold standard methods through a voting strategy.

microbiology↗