Biology subjects

Saunders, D.

Publications and source records attributed to Saunders, D..

13 recordsLinked to original sources

bioRxiv2026

Long-Range Coupling of Posterior Cell Addition and Anterior Vacuolation Provides Robustness in Notochord Elongation.

Robust tissue growth control requires long-range communication between the rate of progenitor addition and tissue expansion. However, the regulatory mechanisms that couple these two processes are unknown. In zebrafish, notochord morphogenesis is a principal driver of axis extension through the combined actions of posterior progenitor addition and anterior vacuolation. To elucidate how progenitor dynamics and vacuole-driven cell expansion interact to shape notochord development, we first generated a mathematical model that links progenitor addition rate to the progressive expansion of cells from anterior-to-posterior to simulate vacuolation rate. Comparing this with empirical measurements, we find that progenitor incorporation together with vacuolation, produces a linear gradient in nearest neighbour distance. We next explored the role of YAP/TAZ in regulating the rate of progenitor addition in mutants for YAP/TAZ inhibitor vgll4b. We find that vgll4b expression and YAP activity are enriched in posterior midline progenitors. Loss of vgll4b elevates YAP signaling, enhances progenitor addition, restricts vacuole expansion, and--after a transient buffering phase--compromises A-P axis elongation. These results support a long-range feedback mechanism linking progenitor recruitment to vacuolation, enabling the notochord to balance cellular input with volumetric expansion, thereby maintaining tissue proportions. Graphical abstract. Proposed working model O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/706348v2_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@6c3c6dorg.highwire.dtl.DTLVardef@1f34eb0org.highwire.dtl.DTLVardef@b33a21org.highwire.dtl.DTLVardef@ad582b_HPS_FORMAT_FIGEXP M_FIG C_FIG A. Schematic representation of the authors proposed model illustrating how increased YAP activation in notochord progenitors of vgll4b mutants leads to enhanced progenitor addition to the notochord. This increased incorporation subsequently compromises the ability of notochord cells to undergo proper vacuolation, resulting in reduced axial elongation compared with control embryos.

developmental biology↗

bioRxiv2025

Novel clonal lineages of wheat stem rust in the Southern Cone of South America

Puccinia graminis f. sp. tritici (Pgt) causes wheat stem rust, a devastating disease of cereals. Recent approaches to examine populations at a genomic level have provided valuable information on the genotypic diversity of Pgt populations in Africa, Europe and North America and evolutionary mechanisms underlying the emergence of new races. However, an in-depth characterisation of Pgt populations in South America has been lacking. To bridge this knowledge gap, 91 Pgt isolates were collected from Argentina and Uruguay in 2020 and 2021 and used to generate transcriptome and whole genome sequence data and pathotype information. Phylogenetic analyses revealed that this South American Pgt population includes three clonal lineages, two of which have not been detected elsewhere. The third lineage is globally dispersed, including isolates from Africa and the Middle East. The predominant lineage, unique to South America, encompassed 90% of the samples and showed related pathotypes differing by virulence on single resistance genes consistent with evolution by stepwise mutation within the clonal lineage. There was no evidence of sexual recombination giving rise to new genetic diversity in this population. These observations urge to routinely incorporate and compare genotypic data from South American Pgt isolates to surveillance data from other geographic regions.

evolutionary biology↗

bioRxiv2025

fgf8a signalling shapes brain divergence between Malawi cichlids

Brain diversification is intimately linked with adaptive radiations, yet the underlying molecular basis remains poorly understood. Here, we examine the mechanisms of neural evolution in two ecologically divergent Lake Malawi cichlid species: a generalist, Astatotilapia calliptera, and a pelagic piscivore, Rhamphochromis sp. chilingali. We demonstrate that forebrain domains diverged independently from other brain regions in these species, consistent with mosaic brain evolution. We identify fibroblast growth factor 8a (fgf8a) as a key factor underlying this neuroanatomical divergence. Species-specific fgf8a expression patterns during critical developmental windows correlate with adult brain differences. Functional knockout experiments confirm fgf8as essential role in cichlid brain patterning, directly linking this conserved developmental gene to interspecific neuroanatomical variation. We identify species-specific transposable element repertoires in the Malawi cichlid fgf8a locus that function as developmental enhancers in brain and sensory systems, providing a potential mechanism for expression divergence between species. Phylogenetic analysis across the radiation reveals elevated transposable element polymorphism at the fgf8a locus in Rhamphochromis, suggesting ongoing regulatory evolution in this clade. Our findings reveal how conserved developmental programmes can accommodate regulatory modification, providing a mechanistic framework for understanding rapid neural diversification during adaptive radiation.

developmental biology↗

bioRxiv2025

Stress-Responsive Transcriptomic Signatures in Human iPSC-Derived Microglia Reveal Links to Alzheimer's Disease Risk Genes

Commercially available human iPSC lines with inducible CRISPR interference (CRISPRi) systems offer scalable platforms for gene function studies. One widely available line, the AICS-0090 dCas9-KRAB iPSC line developed by the Allen Institute, has been extensively validated for genomic integrity and stem cell potency. However, its utility in modeling specialized immune cell types such as microglia -- and in assessing their functional responses to disease-relevant stimuli -- has not been fully established. Here, we evaluated the AICS-0090 line for its ability to differentiate into microglia-like cells, support efficient gene knockdown, and respond to environmental stressors. We assessed its differentiation capacity by qPCR, flow cytometry, and immunocytochemistry, confirming reproducible expression of microglial surface markers at early and late timepoints. Gene knockdown efficiency was validated both at the single-gene level and in pooled CRISPRi screens. Focusing on functional responsiveness, we exposed the microglia-like cells to two distinct stimuli: amyloid-{beta} (A{beta}), a disease-associated trigger in Alzheimers disease, and lipopolysaccharide (LPS), a classical inflammatory signal. Transcriptomic and functional analyses revealed stimulus-specific responses: A{beta} induced limited activation of stress and inflammation pathways, whereas LPS elicited broader transcriptional reprogramming and cytokine release. Signatures from both conditions partially overlapped with ex vivo human and mouse microglial states. Together, these findings support the use of the AICS-0090 dCas9-KRAB iPSC-derived microglia-like cells as a flexible and tractable model for gene function interrogation under defined inflammatory contexts, with potential for future applications in neuroimmune modeling and perturbation-based screening.

neuroscience↗

bioRxiv2024

Spinal Cord Elongation Enables Proportional Regulation of the Zebrafish Posterior Body

Early embryos display a remarkable ability to regulate the patterning of tissues in response to changes in tissue size. However, it is not clear whether this ability continues into post-gastrulation stages upon cell commitment to distinct germ layers. Here, we performed targeted removal of neural fated cells in the zebrafish tailbud using multi-photon ablation. This led to a proportional reduction in the length of both the spinal cord and paraxial mesoderm in the tail, revealing a capacity to regulate tissue morphogenesis across multiple tissues to build a well-proportioned posterior body. Following analysis of cell proliferation, gene expression, signalling and cell movements, we found no evidence of cell fate switching from mesoderm to neural fate to compensate for neural progenitor loss. Furthermore, we found that tail paraxial mesoderm length is not reduced upon direct removal of an equivalent number of mesoderm progenitors, ruling out the hypothesis that neuromesodermal competent cells enable proportional regulation. Instead, reduction in the numbers of cells across the spinal cord reduces both spinal cord and paraxial mesoderm length. We conclude that spinal cord elongation is a driver of paraxial mesoderm elongation in the zebrafish posterior body and that this can explain proportional regulation of both tissues upon neural progenitor reduction.

developmental biology↗

bioRxiv2023

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

Cellular composition and anatomical organization influence normal and aberrant organ functions. Emerging spatial single-cell proteomic assays such as Image Mass Cytometry (IMC) and Co-Detection by Indexing (CODEX) have facilitated the study of cellular composition and organization by enabling high-throughput measurement of cells and their localization directly in intact tissues. However, annotation of cell types and quantification of their relative localization in tissues remain challenging. To address these unmet needs, we developed AnnoSpat (Annotator and Spatial Pattern Finder) that uses neural network and point process algorithms to automatically identify cell types and quantify cell-cell proximity relationships. Our study of data from IMC and CODEX show the superior performance of AnnoSpat in rapid and accurate annotation of cell types compared to alternative approaches. Moreover, the application of AnnoSpat to type 1 diabetic, non-diabetic autoantibody-positive, and non-diabetic organ donor cohorts recapitulated known islet pathobiology and showed differential dynamics of pancreatic polypeptide (PP) cell abundance and CD8+ T cells infiltration in islets during type 1 diabetes progression.

bioinformatics↗

bioRxiv2022

Improving stem cell-derived pancreatic islets using single-cell multiome-inferred regulomes

Pancreatic islet cells derived from human pluripotent stem cells hold great promise for modeling and treating diabetes. Differences between stem cell-derived and primary islets remain, but molecular insights to inform improvements are limited. Here, we acquire single-cell transcriptomes and accessible chromatin profiles during in vitro islet differentiation and pancreas from childhood and adult donors for comparison. We delineate major cell types, define their regulomes, and describe spatiotemporal gene regulatory relationships between transcription factors. CDX2 emerged as a regulator of enterochromaffin-like cells, which we show resemble a transient, previously unrecognized, CDX2+ pre-{beta}-cell population in fetal pancreas, arguing against a proposed non-pancreatic origin. Furthermore, we observe insufficient activation of signal-dependent transcriptional programs during in vitro {beta}-cell maturation and identify sex hormones as drivers of {beta}-cell proliferation in childhood. Altogether, our analysis provides a comprehensive understanding of cell fate acquisition in stem cell-derived islets and a framework for manipulating cell identities and maturity.

cell biology↗

bioRxiv2022

Post-vaccination Omicron infections induce broader immunity across antigenic space than prototype mRNA COVID-19 booster vaccination or primary infection

The rapid emergence of new SARS-CoV-2 variants challenges vaccination strategies. Here, we measured antigenic diversity among variants and interpreted neutralizing antibody responses following single and multiple exposures in longitudinal infection and vaccine cohorts. Antigenic cartography using primary infection antisera showed that BA.2, BA.4/BA.5, and BA.2.12.1 are distinct from BA.1 and closer to the Beta cluster. Three doses of an mRNA COVID-19 vaccine increased breadth to BA.1 more than to BA.4/BA.5 or BA.2.12.1. Omicron BA.1 post-vaccination infection elicited antibody landscapes characterized by broader immunity across antigenic space than three doses alone, although with less breadth than expected to BA.2.12.1 and BA.4/BA.5. Those with Omicron BA.1 infection after two or three vaccinations had similar neutralizing titer magnitude and antigenic breadth. Accounting for antigenic differences among variants of concern when interpreting neutralizing antibody titers aids understanding of complex patterns in humoral immunity and informs selection of future COVID-19 vaccine strains.

microbiology↗

bioRxiv2022

Zebrafish Neuromesodermal Progenitors Undergo a Critical State Transition in vivo

The transition state model of cell differentiation proposes that a transient window of gene expression stochasticity precedes entry into a differentiated state. As this has been assessed primarily in vitro, we sought to explore whether it can also be observed in vivo. Zebrafish neuromesodermal progenitors (NMps) differentiate into spinal cord and paraxial mesoderm at the late somitogenesis stages. We observed an increase in gene expression variability at the 24 somite stage (24ss) prior to their differentiation. From our analysis of a published 18ss scRNA-seq dataset, we showed that the NMp population possesses a signature consistent with a population undergoing a critical transition. By building in silico composite gene expression maps from our image data, we were able to assign an NM index to each in silico NMp based on the cumulative expression of its neural and mesodermal markers. With the NM index distributions, we demonstrated that cell population heterogeneity of the NMps peaked at 24ss. We then incorporated stochasticity and non-autonomy into a genetic toggle switch model and uncovered the existence of rebellious cells, which we then confirmed by reexamining the composite maps. Taken together, our work supports the transition state model within an endogenous cell fate decision making event.

developmental biology↗

bioRxiv2022

Approximated Gene Expression Trajectories (AGETs) for Gene Regulatory Network Inference on Cell Tracks

The study of pattern formation has greatly benefited from our ability to reverse-engineer gene regulatory network (GRN) structure from spatio-temporal quantitative gene expression data. Traditional approaches omit tissue morphogenesis, and focus on systems where the timescales of pattern formation and morphogenesis can be separated. In such systems, pattern forms as an emergent property of the underlying GRN and mechanistic insight can be obtained from the GRNs alone. However, this is not the case in most animal patterning systems, where patterning and morphogenesis are co-occurring and tightly linked. To address the mechanisms driving pattern formation in such systems we need to adapt our GRN inference methodologies to explicitly accommodate cell movements and tissue shape changes. In this work we present a novel framework to reverse-engineer GRNs underlying pattern formation in tissues undergoing morphogenetic changes and cell rearrangements. By integrating quantitative data from live and fixed embryos, we approximate gene expression trajectories (AGETs) in single cells and use a subset to reverse-engineer candidate GRNs using a Markov Chain Monte Carlo approach. GRN fit is assessed by simulating on cell tracks (live-modelling) and comparing the output to quantitative data-sets. This framework generates candidate GRNs that recapitulate pattern formation at the level of the tissue and the single cell. To our knowledge, this inference methodology is the first to integrate cell movements and gene expression data, making it possible to reverse-engineer GRNs patterning tissues undergoing morphogenetic changes.

systems biology↗

bioRxiv2021

Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India

Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively. Pathotypes were found to be highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene family expansion was also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known US, European, African and Asian races. Diagnostic markers developed for the identification of different Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.

bioinformatics↗

bioRxiv2019

Cleavage of a pathogen apoplastic protein by plant subtilases activates immunity

The plant apoplast is a harsh environment in which hydrolytic enzymes, especially proteases, accumulate during pathogen infection. However, the defense functions of most apoplastic proteases remains largely elusive. Here, we show that a newly identified small cysteine-rich secreted protein PC2 from the potato late blight pathogen Phytophthora infestans induces immunity in Solanum plant species only after cleavage by plant apoplastic subtilisin-like proteases, such as tomato P69B. A minimal 61-amino-acid core peptide carrying two key cysteines and widely conserved among most oomycete species is sufficient for PC2 activity. Kazal-like protease inhibitors, such as EPI1 produced by P. infestans can prevent PC2 cleavage and dampen PC2 elicited host immunity. This study reveals that cleavage of pathogen proteins to release immunogenic peptides is an important function of apoplastic proteases but that pathogens interfere with these functions using protease inhibitor effectors.

plant biology↗

bioRxiv2017

SOD1A4V aggregation alters ubiquitin homeostasis in ALS

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving the selective death of upper and lower motor neurons in the primary motor cortex and spinal cord. A hallmark of ALS pathology is the accumulation of ubiquitinated protein inclusions within motor neurons. Previous studies suggest the sequestration of ubiquitin (Ub) into inclusions reduces the availability of free Ub, which is essential for cellular function and survival. However, the dynamics of the Ub landscape in ALS have not yet been described. Here we show that Ub homeostasis is altered in a SOD1 cell model of ALS. Utilising fluorescently tagged Ub, we followed the distribution of Ub in living cells expressing SOD1 and show that Ub is present at the earliest stages of SOD1 aggregation. We also report that cells containing aggregates of mutant SOD1 have greater ubiquitin-proteasome system (UPS) dysfunction as measured by the accumulation of the fluorescent proteasome reporter tdTomatoCL1. Furthermore, SOD1 aggregation is associated with the redistribution of Ub and depletion of the free Ub pool. Ubiquitomics analysis indicates that mutant SOD1 is associated with a shift of Ub to a pool of supersaturated proteins including those associated with oxidative phosphorylation and metabolism, corresponding with altered mitochondrial morphology and function. Taken together, these results suggest misfolded SOD1 contributes to UPS dysfunction and that Ub homeostasis is an important target for monitoring pathological changes in ALS.

molecular biology↗