Biology subjects

Shah, M.

Publications and source records attributed to Shah, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Glycolytic compensation rather than NAD+/NADH balance sustains neuronal function during mitochondrial stress

Neurons engage compensatory pathways that promote survival when confronted with mitochondrial dysfunction. Indeed, we recently showed that Drosophila neurons upregulate Ldh transcription to help survive the loss of the key mitochondrial fusion gene Opa1. Here, we further characterize this metabolic flexibility and show that it reflects a more general increase in glycolytic activity. A distinct mitochondrial perturbation, TFAM overexpression, similarly induces glycolytic gene expression including Ldh and also elevates lactate levels. LDH is also required to maintain neuronal function under TFAM overexpression. Notably, raising NAD+/NADH ratio by expressing the bacterial NADH oxidase LbNOX does not substitute for LDH function. On the contrary, it further compromises neuronal function in Opa1-deficient and TFAM-overexpressing neurons. Moreover, mitochondria-targeted LbNOX expression alone induces mitochondrial dysfunction and the compensatory glycolytic response. Together, these findings indicate that LDH-mediated rescue does not reflect an increase in NAD+/NADH ratio but is part of a broader neuroprotective metabolic reprogramming which enables neurons to withstand diverse forms of mitochondrial impairment.

neuroscience↗

bioRxiv2026

Split intein vectors permit oversize FLIM-FRET biosensor neuronal expression

Adeno-associated virus (AAV) packaging limits constrain the design, performance, and in vivo application of genetically encoded biosensors. We developed a split intein-mediated reconstitution strategy enabling modular delivery and reassembly of oversized fluorescence lifetime-based biosensors. Using this platform, we engineered an oversized cAMP sensor compatible with one-photon fluorescence lifetime measurements, enabling monitoring of intracellular signaling dynamics in distinct neuronal subtypes in freely behaving mice.

bioengineering↗

bioRxiv2026

The mechanosensitive channel MscS links lipoteichoic acid synthesis alterations to beta-lactam sensitivity in Staphylococcus aureus

Lipoteichoic acid is an essential cell envelope polymer in Staphylococcus aureus and contributes to beta-lactam resistance in methicillin-resistant S. aureus. Mutations that alter lipoteichoic acid synthesis sensitize MRSA to beta-lactam antibiotics, but the mechanism connecting envelope polymer defects to antibiotic susceptibility has remained unclear. Here, we used suppressor genetics, genome sequencing, transcriptomics, inducible gene expression, antibiotic susceptibility assays, and measurements of intracellular potassium, cyclic di-AMP, and penicillin-binding protein production to define this connection. We found that lipoteichoic acid synthesis defects increased expression of a ParB-like protein and the mechanosensitive channel MscS. Repression of this locus in RNA polymerase suppressor mutants restored beta-lactam resistance, whereas induced expression of both genes reduced resistance. Increased ParBL-MscS expression was associated with decreased intracellular potassium and reduced cyclic di-AMP, linking altered membrane-envelope physiology to second messenger signaling. Lipoteichoic acid synthesis mutants also showed reduced production of penicillin-binding protein 4, an important determinant of beta-lactam resistance. Modest restoration of penicillin-binding protein 4 improved resistance in the mutant with reduced lipoteichoic acid abundance, whereas the mutant producing elongated lipoteichoic acid showed a distinct response, indicating that different lipoteichoic acid defects impose different envelope stresses. Together, these findings identify a potassium-dependent pathway connecting lipoteichoic acid synthesis, mechanosensitive channel activity, cyclic di-AMP signaling, penicillin-binding protein 4 production, and beta-lactam resistance. This work reveals how cell envelope perturbations are converted into cytoplasmic regulatory responses that control antibiotic susceptibility and suggests that ion homeostasis and cyclic di-AMP signaling may be exploitable pathways for restoring beta-lactam efficacy against MRSA. Author SummaryAntibiotic-resistant Staphylococcus aureus, including methicillin-resistant S. aureus, is difficult to treat because it can withstand many beta-lactam antibiotics, a widely used class of drugs. Previous work showed that changes in lipoteichoic acid, an important molecule in the bacterial cell envelope, make these bacteria more sensitive to beta-lactams. However, it was not clear how a change at the cell surface affects antibiotic resistance inside the cell. In this study, we found that defects in lipoteichoic acid production activate a pathway involving a predicted membrane channel. This pathway changes the level of potassium inside the bacterial cell and affects a small signaling molecule that helps coordinate cell wall maintenance. These changes also reduce the amount of an enzyme involved in building the cell wall, making the bacteria more vulnerable to beta-lactam antibiotics. Our findings suggest that antibiotic resistance depends not only on the direct targets of antibiotics, but also on how bacteria maintain the balance between their cell envelope, ion levels, and internal signaling. Understanding this connection may help identify new ways to make resistant bacteria more sensitive to existing antibiotics.

microbiology↗

bioRxiv2026

Decades of Parkinson's disease neuropathology yield a sparse and underpowered map of neuronal vulnerability: a systematic review and meta-analysis

Selective vulnerability is widely assumed in Parkinson's disease (PD), but whether dopaminergic neurons of the substantia nigra are uniquely vulnerable has not been established. Explanations of neuronal degeneration in Parkinson's disease often centre on the distinctive properties of substantia nigra dopaminergic neurons. Whether these properties are necessary for substantial neuronal loss remains unclear. We preregistered a systematic review of 166 post-mortem case-control studies published between 1963 and 2025 and synthesised neuronal counts and densities from 152 studies using a multilevel meta-analysis. After six decades, only 18% of countable brain atlas labels had been examined, and most populations were represented by a single study. Substantial loss beyond dopaminergic and classically pigmented populations shows that neither dopaminergic identity nor neuromelanin is necessary for marked degeneration, challenging key tenets of selective vulnerability in PD. Comparisons across other anatomical and physiological features remain limited by sparse sampling and uncertainty. We identify less-studied populations with substantial estimated loss and estimate the additional sampling needed to improve precision under specified assumptions. These findings direct replication and comparative counting towards uncertainties that limit explanations of neuronal loss across affected and potentially spared populations.

neuroscience↗

bioRxiv2026

Nmur1 and Cckar fail to support functional genetic access in adult dopamine neurons and challenge GPCR atlas assignments

Apuschkin et al. (2024) proposed a GPCR-based transcriptomic atlas for midbrain dopamine (DA) neuron subpopulations, including candidates such as Nmur1, Cckar, and Ffar4. To guide genetic targeting, these markers must reflect functional expression in adult DA neurons. Using in situ hybridization, Cre-dependent reporter lines, and both intracranial and systemic viral approaches, we find no evidence of adult Nmur1-mediated recombination in DA neurons, while Cckar-driven recombination is consistent with developmental expression only. Notably, Ffar4 expression overlaps extensively with Ntsr1 midbrain populations, indicating that it does not define a distinct DA neuron class. Furthermore, analysis of independent spatial transcriptomic datasets together with our MERFISH data shows that many proposed GPCR markers are not detectably expressed in adult DA neurons. These findings demonstrate that transcriptomic enrichment does not always yield reliable adult markers and highlight the need for functional validation prior to use in circuit targeting.

neuroscience↗

bioRxiv2026

Plant LETM1 homologs are required for fungus-induced antibiotic resistance and biostimulation

Our findings confirm that CIRA15A / LEUCINE ZIPPER-EF-HAND CONTAINING TRANSMEMBRANE PROTEIN1 (LETM1) is critical for Trichoderma-induced growth biostimulation in sugar beet and the Cellulase-Induced Resistance to Alamethicin (CIRA) response in Arabidopsis. Notably, this plant homolog of a gene associated with human disease plays a vital role in both defense against Trichoderma antimicrobial peptides and the biostimulation of plant growth. We identified AtCIRA15A/LETM1 and AtCIRA15B/LETM2 as key genetic determinants of CIRA through Arabidopsis analysis and comparative studies of sugar beet inbred lines. BvLETM1 allelic variations correlated with differential biostimulation responses, and complementation confirmed functional LETM1 alleles restore CIRA in Arabidopsis mutants. These findings highlight LETM1 as a crucial factor in Trichoderma-plant interactions, with potential applications in breeding for enhanced microbial-induced plant biostimulation and agricultural productivity.

plant biology↗

bioRxiv2025

Visual features underlying neural selectivity for natural stimuli

Neural activity is selective for the identity and semantic category of natural visual stimuli. In human neuroimaging, this selectivity can be investigated using multivariate pattern analysis. The resulting neural information is thought to reflect neural processes underlying object recognition. However, due to the complexity of natural stimuli, it remains unclear to what extent different visual features drive this information. To address this, we presented natural stimuli from different categories as well as several degraded versions, in which specific visual features were selectively manipulated, to human participants while recording magnetoencephalography (MEG). We applied multivariate pattern analysis and decomposed the resulting high-dimensional neural representational geometry into its distinct contributions from retinotopy, total spatial frequency and orientation energy, global shape, local shape, and textural correlation structure. These features contributed differentially to the neural information, with retinotopy and global shape being the strongest features underlying image and category information, respectively. Our results demonstrate how multiple statistical features of visual stimuli jointly and dynamically account for neural image and category selectivity, providing a basis for a better understanding of human object recognition.

neuroscience↗

bioRxiv2025

Structure-based engineering of a nutrient acquisition protein enhances neutralizing antibodies and protection for the development of a gonococcal vaccine

Gonorrhea is increasingly resistant to treatment and has been labelled an urgent threat due to the diminishing effectiveness of existing therapeutics. To address this challenge, we targeted the Neisseria gonorrhoeae transferrin binding protein B (TbpB), which is critical for iron acquisition and neisserial growth, as a vaccine target. Building on previous studies investigating the application of TbpB as an immunogen against various bacterial pathogens, we aimed to optimize this antigen for a broad protective effect. We compared the efficacy of wild type TbpB immunogens with engineered TbpB mutants that do not bind human transferrin (hTf) using infection studies in transgenic mice expressing hTf, which were required because the strict specificity of neisserial TbpB precludes its complexing with non-human transferrin. Comprehensive biophysical analyses confirmed that the introduced single residue mutations abolished hTf binding without compromising antigen structure. Immunization with the mutant antigens conferred increased resistance to infection by N. gonorrhoeae relative to that provided by the wild-type antigen in the humanized mice. When considering effector functions of the humoral response, we observed that the mutated antigen elicited more effective bactericidal and function-neutralizing activity. Through strategic mutations, we therefore enhanced vaccine effectiveness in a physiologically relevant model without significantly affecting the structure or immunogenicity of the antigen. This study highlights the use of rational structure-guided antigen design to drive effective immune responses and the potential interference of immunogen binding to host factors, and reinforces the utility of targeting TbpB in a gonococcal vaccine.

immunology↗

bioRxiv2025

A post-transcriptional regulatory checkpoint controls the response of tumor-infiltrating cytotoxic CD4+ T cells to immunotherapy

Acquisition of cytotoxic activity in CD4+ T cells (TCTX) can promote potent anti-tumor activity thus holding promise as a therapeutic approach. However, how this activity is regulated remains poorly understood. Here, we demonstrate that tumor-infiltrating CD4+ TCTX activity is restrained by a post-transcriptional regulatory checkpoint. In untreated tumors, CD4+ TCTX exist in a poised state, characterized by abundant Gzmb mRNA but limited Granzyme B (GzmB) protein. Differentiation into poised TCTX is regulated by the Blimp-1-Bcl6 axis and requires type-I interferon signaling. Treatment with anti-CTLA-4 or anti-LAG-3 plus anti-PD-1 removed the block to GzmB protein production by repressing expression of the post-transcriptional regulator Zfp36l1. Constitutive Zfp36l1 expression abrogated the effects of anti-CTLA-4 while deletion of Zfp36l1 and its paralog Zfp36 triggered GzmB protein production and promoted tumor control. These data identify ZFP36/ZFP36L1 as a key post-transcriptional regulatory checkpoint of CD4+ TCTX activity and a potential immunotherapy target in cancer.

immunology↗

bioRxiv2025

Mitochondria structurally remodel near synapses to fuel the sustained energy demands of plasticity

Brain synapses are hotspots of energy consumption, and the synaptic plasticity underlying learning sharply increases this demand. Because most synapses lie far from their cell body, their energy demands must be met locally. A dendritic mitochondrion can extend ~30 m and span many spines, yet ramps up ATP synthesis only near spines undergoing plasticity, providing immediate and sustained energy. Whether structural changes in these juxtaspinal mitochondrial regions (2 m segments at spine bases) support this response is unknown; resolving their energy-producing architecture poses substantial challenges. Compared with the lamellar cristae of axonal mitochondria, dendritic mitochondrial cristae form complex, tubular, and interconnected networks that require multiple high-resolution tomograms to characterize. We therefore developed a correlative light and electron microscopy (CLEM) pipeline with a custom deep-learning model that simultaneously segments five distinct 3D suborganellar structures from limited training data, enabling quantitative analysis across 42 tomograms at 2 nm pixel resolution. We find that juxtaspinal mitochondrial regions are larger than non-juxtaspinal regions within the same mitochondrion and enlarge further during synaptic plasticity. Juxtaspinal mitochondrial ATP synthesis and spine ATP levels rise in parallel; during single-spine plasticity, ATP rises within minutes, before detectable enlargement, indicating that juxtaspinal mitochondrial enlargement sustains rather than initiates the local energy response. The enlarged regions exhibit increased cristae membrane surface area, crista junction number, and membrane area with high curvature, together with increased MIC60 and ATP synthase copies, endoplasmic reticulum contacts, and more proximal ribosomes. Matrix-targeted PKA inhibition reduces MIC60 phosphorylation and impairs juxtaspinal mitochondrial enlargement, plasticity-associated ATP increase, and single-spine plasticity. Together, our findings support a model in which spine-specific remodeling within an individual mitochondrion boosts local metabolic capacity to sustain ATP synthesis and fuel synaptic plasticity.

neuroscience↗

bioRxiv2025

Phagosome Maturation in Macrophages is Enhanced by p38α MAPK Signaling

In macrophages, it is generally assumed that without active escape mechanisms, all phagocytosed cargo eventually reaches lysosomes. Yet, the influence of specific ligands, like lipopolysaccharide (LPS), on phagosome maturation is unclear. Here, using sterile, non-immunogenic particles as model cargo phagocytosed by macrophages, we show that in the absence of an external signal, less than half the phagosomes fuse with lysosomes. By quantifying phagosome maturation in terms of lysosomal localization and mapping lumenal pH dynamics, we find that early events triggered by LPS-induced signaling enhance both cargo delivery to lysosomes and phagosome acidification rates. We demonstrate that stress-activated p38 alpha mitogen-activated protein kinase (p38 MAPK) is important for this signaling event. Other signals known to activate p38 MAPK such as flagellin, IgG and albumin also enhance lysosomal delivery of phagocytosed cargo. Our work indicates that the maturation of phagosomes in macrophages is enhanced by the presence of specific ligands on the cargo, which activate cell surface receptors that signal via p38 MAPK.

cell biology↗

bioRxiv2025

Spatial and single-cell transcriptomics capture two distinct cell states in plant immunity

Unlike animals, plants are sessile organisms that must adapt to localized and fluctuating environmental stimuli, including abiotic and biotic stresses. While animals use mobile immune cells to eliminate pathogens, plants rely on localized cells in contact with the pathogen to detect and mount immune responses. Although bulk RNA sequencing (RNA-seq) has enabled the assessment of plant responses to pathogen infection at the whole transcriptome level, the spatial coordination of plant immune responses remains elusive. In this study, we performed both spatial and single-nuclei transcriptomic experiments to capture the spatial pattern of soybean plant responses to Asian soybean rust infection caused by the pathogen Phakopsora pachyrhizi. Through the analysis of both spatial and single-nuclei transcriptomics data, we identified two distinct host cell states with specific spatial localization in response to pathogen infection: the infected regions with the presence of the pathogen and the surrounding regions bordering the infected regions. Importantly, the surrounding regions exhibited higher expression of defense response-related genes than the infected regions, despite having minimal presence of the pathogen, indicating a cell non-autonomous defense response in the surrounding regions. Additionally, gene co-expression network analysis with single-cell resolution identified a key immune response-related gene module activated in the stressed cells captured in our single-nuclei RNA-seq data. This study reveals the intricate spatial coordination of plant defense responses against pathogen infection and enhances our understanding of the importance of localized cell non-autonomous defense responses in plant-pathogen interactions.

plant biology↗

bioRxiv2025

Pan-Cancer PDOs Preserve Tumor Heterogeneity and Uncover Therapeutic Vulnerabilities

We developed a tumor-matched, pan-cancer patient-derived organoid (PDO) platform comprising 220 PDOs from 190 patients across 15 cancer types to advance functional precision oncology. Our comprehensively characterized PDOs showed 93% histopathology concordance, 80% median genomic concordance for driver mutations, and a 0.85 median gene expression correlation with parent tumors. Gene expression in PDOs remained stable across [≥] 10 passages, supporting reproducibility for long-term drug screening. Even PDOs with low genomic concordance retained oncogenic drivers, supporting their use as disease models. Clonality analysis revealed that 85% of PDOs preserved dominant tumor clones. Higher genomic concordance was associated with greater clonal similarity, while lower genomic concordance was associated with clonal divergence. Functional assays showed that 58% of PDOs from a subset of patients ineligible for FDA-approved PARP inhibitors responded to Talazoparib, with sensitivity linked to alterations in DNA damage repair. Combination screens revealed drugs that effectively overcame resistance, especially in TP53-mutant PDOs. In summary, our platform supports investigation of targeted therapies, identification of molecular features linked to drug sensitivity, and translational discovery, offering insights into personalized cancer treatment beyond current biomarker guidelines.

cancer biology↗

bioRxiv2025

Response of Escherichia coli chemotaxis pathway to pyrimidine deoxyribonucleosides

Nucleosides are essential components of all living cells. Bacteria use salvage pathways to import nucleosides from their environment and to utilize them for nucleic acid biosynthesis, but also as alternative sources of carbon, nitrogen and energy. Motile bacteria commonly show chemoattraction towards nutritionally valuable compounds, and in this work, we demonstrate that the chemotaxis pathway of Escherichia coli exhibits specific attractant response to pyrimidine nucleosides. Particularly sensitive response, in the sub-micromolar range, was observed for deoxyribonucleosides thymidine and deoxycytidine. In contrast, ribonucleosides elicited weaker and less sensitive response, and no response to pyrimidine nucleobases was observed in the micromolar range of concentrations. Our subsequent analysis revealed that the pathway response to pyrimidine deoxyribonucleosides is mediated by the minor E. coli chemoreceptor Tap. The observed narrow dynamic range of this response indicates that sensing of deoxyribonucleosides is indirect, likely via an unknown periplasmic binding protein that interacts with Tap.

microbiology↗

bioRxiv2025

Synapses drive local mitochondrial ATP synthesis to fuel plasticity

Our brain constantly forms new memories and stabilizes existing memories. To achieve such cognitive flexibility, the brain is wired by plastic synapses that are hotspots of energy consumption. Supplying energy to distant synapses is challenging as they are distributed throughout dendrites and axons, spanning hundreds of microns from their cell body. Synapses, therefore, require an instant and local energy supply provided by mitochondria stabilized near dendritic spines. However, the mechanisms by which synapses communicate their energy demands to locally stable mitochondria to drive local energy production and sustain synaptic plasticity is unknown. Using highly sensitive spine- and mitochondrial ATP reporters and two-photon glutamate uncaging to stimulate individual spines, we find that synaptic plasticity input drives instant and sustained increase in spine ATP levels, provided by local ATP synthesis in [~]10-20 m spatially confined compartments within mitochondria. This spatially localized mitochondrial ATP generation is driven by a spatially localized mitochondrial calcium influx independent of the endoplasmic reticulum. Notably, the initial spine ATP increase, supported by local mitochondrial ATP synthesis, is independent of CaMKII and the energy demands of spine structural plasticity. Without local calcium signaling and mitochondrial stabilization, synapses do not meet their instant and sustained energy needs, resulting in synaptic plasticity defects, as observed in neurological disorders.

neuroscience↗

bioRxiv2025

Population and adaptation history of 739 Thlaspi arvense natural accessions

Pennycress (Thlaspi arvense) is a promising intermediate oilseed crop, producing oil suitable for conversion to biofuels--including aviation fuels. While domestication efforts are ongoing, a deeper understanding of the genetic architecture of traits is crucial for informing future breeding efforts. Here, we conducted the largest genomic and phenotypic survey of pennycress to date, analyzing 739 accessions collected across four continents. Leveraging whole-genome sequencing and field-collected phenotypes, we characterized the standing genetic variation underlying key agronomic traits and climate resilience. Our findings revealed multiple independent migration events to North America, with substantial genetic admixture. We identified homologs of Arabidopsis thaliana flowering-time genes that contribute to adaptation and demonstrated the agronomic benefits of winter-type pennycress. Furthermore, through multi-season field trials, we identified a genomic region containing a cluster of mTERF genes strongly associated with green canopy coverage, a critical trait for biomass retention and yield stability. These insights provide a genomic roadmap for accelerating pennycress domestication and improving its resilience to climate variability.

genomics↗

bioRxiv2025

Extracellular matrix proteolysis maintains synapse plasticity during brain development

Maintaining a dynamic neuronal synapse pool is critical to brain development. The extracellular matrix (ECM) regulates synaptic plasticity via mechanisms that are still being defined and are studied predominantly in adulthood. Using live imaging of excitatory synapses in zebrafish hindbrain we observed a bimodal distribution of short-lived (dynamic) and longer-lived (stable) synapses. Disruption of ECM via digestion or brevican deletion destabilized dynamic but not stable synapses and led to decreased synapse density. Conversely, loss of matrix metalloproteinase 14 (MMP14) led to accumulation of brevican and increased the stable synapse pool, resulting in increased synapse density. Microglial MMP14 was essential to these effects in both fish and human iPSC-derived cultures. Both MMP14 and brevican were required for experience-dependent synapse plasticity in a motor learning assay. These data, complemented by mathematical modeling, define an essential role of ECM remodeling in maintaining a dynamic subset of synapses during brain development.

neuroscience↗

bioRxiv2024

A surface lipoprotein on Pasteurella multocida binds complement factor I to promote immune evasion.

Pasteurella multocida is the leading cause of wound infections in humans following animals bites or scratches. This bacterium is also commonly found in the respiratory tract of many mammals and can cause serious diseases resulting in the brutal rapid death of infected animals, especially cattle. To prevent these infections in cattle, a subunit-based vaccine utilizing the surface lipoprotein PmSLP was developed and showed remarkable protection with a single dose administration. Here, we report that PmSLP binds host complement factor I (FI) and facilitates cleavage of complement components C3b and C4b independently of any cofactors (e.g FH, C4BP), thereby allowing the pathogen to evade host defence. Cryo-EM structure of PmSLP bound to FI reveals that PmSLP stimulates FI enzymatic activity by stabilizing the catalytic domain. This is the first time that a bacterial protein has been shown to directly activate FI independent of complement cofactors and target all arms of the complement cascade.

microbiology↗