Biology subjects

Lynch, C.

Publications and source records attributed to Lynch, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Stoichiometric transcription factor partnerships specify GABAergic neuron subtype identity

Combinatorial transcription factor (TF) codes specify neuronal fates, yet how quantitative differences in interacting TFs shape these decisions remains unresolved. We address this in the developing basal ganglia, where a pool of undifferentiated progenitors gives rise to both D1 and D2 medium spiny neurons (MSNs). Combining sparse in vivo CRISPR perturbation, lineage barcoding, and single-cell transcriptomics in mice, we find that loss of Sp9 shifts clonal fate bias from D2 toward D1 MSNs and intercalated cells. Mechanistically, chromatin profiling and biochemical assays show that at GC-rich promoters, SP9 binds DNA directly and activates transcription. At distal enhancers, SP9 binds indirectly, tethered by DLX factors, represses activity, and associates with the NuRD corepressor complex. The relative abundance of SP9 and DLX selects between these modes. These findings extend the combinatorial TF code beyond factor identity to relative proportions, with relevance to neurodevelopmental disorders.

developmental biology↗

bioRxiv2026

An endodermal subpopulation generates neural and mesodermal fates in the posterior chick embryo

Embryogenesis occurs through a progressive narrowing of cell fate potential, initiating with the segregation of three distinct germ layers during gastrulation. Although classically, each germ layer contributes to distinct tissue types as development proceeds, this view has been revised with the discovery of neuromesodermal progenitors (NMPs) -- a bipotent progenitor population in the posterior embryo that gives rise to traditionally ectodermal and mesodermal tissues after gastrulation has concluded. However, until now the notion of lineage restriction of the endoderm to gastrointestinal, respiratory, and endocrine tissues has largely remained intact. Here, we describe a unique subpopulation in the chick endoderm that initially lines the ventral surface of Hensens node (the amniote organizer). As posterior regression of the node ends with termination of the primitive streak, these cells undergo an FGF-dependent epithelial-to-mesenchymal transition, erasing their endodermal identity as they invade the tailbud and subsequently differentiate into a remarkably broad range of cell types including paraxial, lateral plate, and intermediate mesoderm, and to a lesser extent, notochord and neural tube. Disrupting ingression of node endoderm reduced embryonic axis elongation -- a process attributed to mesoderm -- by 50%. Through lineage barcoding, single-cell RNA sequencing, and fate mapping experiments, we conclude that the endodermal compartment of Hensens node harbors a mixed population of fate restricted and multipotent progenitor cells that give rise to clonal populations spanning traditional germ layer boundaries. These findings illustrate a surprising example of germ layer plasticity and fate convergence across distant progenitor populations during amniote development.

developmental biology↗

bioRxiv2025

Minimizing inferential bias in the theory and design of nutritional experiments through the application of the equilateral mixture triangle

Animal nutritionists seek to understand how animals regulate the intake and balance of multiple nutrients, yet the design and analysis of such experiments are often limited by how nutrient spaces are represented. The geometric framework for nutrition (GFN) provides a powerful means to visualize nutrient interactions, but when more than two nutrients are considered, most empirical studies employ right-angled mixture triangles (RMTs). While convenient, this coordinate system can introduce visual artifacts that can bias inference. Here, we reintroduce the equilateral mixture triangle (EMT) as a complementary and biologically meaningful framework that preserves proportional relationships among nutrients and connects directly with the design principles of mixture experiments in engineering disciplines, where it is more commonly known as a simplex. The simplex provides a consistent bridge between theory and experimentation, allowing the same geometric representation to be used for choice and no-choice assays. For choice experiments, we extend GFN theory to show that animal feeding trajectories are bounded by the convex hull of available foods, show how it can scale to higher-dimensional nutrient systems, and develop statistical tests to distinguish between random choice and the defense of an intake target. For no-choice experiments, we demonstrate how simplex mixture designs can be integrated with response surface methodologies to model multivariate performance landscapes, identify optimal nutrient ratios, and avoid biologically unrealistic regions of nutrient space. For both types of experiments, we provide simulated case studies on how to design studies around the simplex. Together, these developments refine both the theoretical and experimental foundations of nutritional ecology, providing clear guidance for designing, visualizing, and interpreting multidimensional studies of nutrient regulation with diverse applications across ecological and agricultural disciplines.

animal behavior and cognition↗

bioRxiv2025

A conserved logic for the development of cortical layering in tetrapods

The cerebral cortex is part of the pallium, a brain region conserved across vertebrates yet remarkably diverse in structure and cellular composition. A defining feature of the cerebral cortex is its organization into neuronal layers with distinct gene expression profiles, input-output connectivity, and function. According to prevailing models, the cerebral cortex emerged in ancestral amniotes (mammals and reptiles) following innovations in pallial development that enabled the generation of diverse neuron types and their laminar organization.1-11 However, little is known about pallial development and architecture in amphibians, the sister group of amniotes. Here we show that in the salamander Pleurodeles waltl, the dorsal pallium is organized in distinct superficial and deep layers with neurons that develop following cellular and molecular principles of mammalian corticogenesis. Using birthdating analysis, barcode-based lineage tracing, and single-cell RNA sequencing, we find that radial glia temporal states and intermediate progenitor cells are conserved across species, while neuronal differentiation trajectories are highly evolvable. Neurons generated at different developmental time points occupy different layers and exhibit distinct molecular and projection identities. Thus, temporally-patterned neurogenesis represents an ancient organizing principle of layered pallia, although mammals display an inverted layer order along the radial axis. Together, these findings demonstrate that the core developmental principles underlying cortical layering - including temporal patterning, intermediate progenitors, and laminar organization - predate the origin of amniotes. Our results suggest that the evolutionary expansion of the mammalian neocortex built upon a deeply conserved developmental framework already present in early tetrapods.

developmental biology↗

bioRxiv2025

Tuning regimes in ant foraging dynamics depend on the existence of bistability

Characterizing how behavior must be tuned to produce useful coordination is key to understanding the evolution and regulation of collective behavior. While computational models can answer this question for specific instances, recurring patterns in model dynamics hint at a more general means of classifying collective dynamics. Using ant foraging models as a foundational example, we investigate mechanisms that can produce symmetry-breaking transitions to bistability as a first basic classification of collective behavior. Collective transitions are functionally important: They lead to sudden changes in collective states, enhanced sensitivity to environmental inputs, and hysteresis. We use bifurcation theory to argue that the point at which discontinuous transitions merge at a continuous transition forms a codimension-2 bifurcation with universal properties, and that this point is functionally equivalent to the critical point of a phase diagram. We show how analogous bistable transitions appear across models of ant foraging with different mechanistic assumptions, and we explore how biologically relevant collective effects play out near the transition. This framework clarifies the difficulty of tuning collective behavior: locating a continuous transition typically requires tuning two parameters, while a discontinuous transition requires tuning only one. Finally, we explore conditions that degrade or destroy bistable transitions: heterogeneity blurs the transitions, while recruitment mechanisms that do not create a positive feedback loop do not display bistability at all.

systems biology↗

bioRxiv2025

Mapping gene expression across the microbiome-gut-brain axis of germ- and specific pathogen-free mice

Perturbation of the gut microbiota has been implicated in neurological diseases via communication across the microbiome-gut-brain axis. As a result, the discovery of mechanisms underlying interaction across this axis are becoming increasingly important. The germ-free (GF) mouse model has enabled an improved understanding of the influence of the gut microbiota on brain development and function. By utilising an advanced spatial profiling approach, we determined transcriptional changes in the brain, improving our understanding of how brain cells function and interact within their microenvironment in the absence of microbiome influence. Targeted regions of interest were selected based on brain regions implicated in neurological disease or reported structural differences between GF mouse brains and those of colonized mice. In the hippocampus 276 differentially expressed genes (DEGs) were identified, 345 DEGs in the thalamus, and 21 DEGs in pons. Contrastingly we identified only 2 DEGs in the midbrain and 4 in the medulla oblongata, with no DEGs in the cerebellum or corpus callosum. This data provides an overview of gut microbiota influence on gene expression in the brain, highlighting multiple genes of interest for further investigation in the context of microbiome influence on brain function and their potential relevance to neurological disease.

microbiology↗

bioRxiv2024

Contrasting Cognitive, Behavioral, and Physiological Responses to Breathwork vs. Naturalistic Stimuli in Reflective Chamber and VR Headset Environments

The MindGym, a novel immersive technology utilizing a reflective chamber environment, was developed to create standardized experiential content, including anxiolytic experiences. This study examined whether therapeutic experiences originally created in the MindGym could maintain their efficacy when delivered via 360-degree recordings through virtual reality (VR) headsets. A randomized controlled trial (N=126) compared anxiety reduction, cognitive performance, and physiological responses across four conditions: MindGym and VR platforms, each delivering either breathwork or rain stimuli. Results demonstrated significant improvements across all conditions in cognitive performance (Trail Making Test RTACC, p.fdr<.001; Architex Total Speed, p.fdr<.001) and anxiety reduction (STAI, p.fdr<.001). Breathwork conditions produced greater decreases in breath rate compared to rain stimuli (p.fdr=.002). Treatment responses were moderated by individual differences, with absorption (MODTAS) predicting both awe (p.fdr=.004) and ego dissolution (p.fdr=.015), while openness to experience interacted with stimuli type to influence anxiety reduction (p.fdr=.038). The anxiolytic effects originally generated in the MindGym maintained full efficacy when translated to VR delivery, with no significant differences in effectiveness or immersion between the original environment and its virtual reproduction. These findings establish the MindGym as a viable content creation platform for immersive, anxiety-reducing experiences that can be successfully adapted to more accessible delivery systems, while highlighting the potential for personalization based on individual differences. Future research should investigate the translation of more complex MindGym-generated experiences to expand accessible anxiety management tools.

neuroscience↗

bioRxiv2024

Predicting rifampicin resistance in M. tuberculosis using machine learning informed by protein structural and chemical features.

BackgroundRifampicin remains a key antibiotic in the treatment of tuberculosis. Despite advances in cataloguing resistance-associated variants (RAVs), novel and rare mutations in the relevent gene, rpoB, will be encountered in clinical samples, complicating the task of using genetics to predict whether a sample is resistant or not to rifampicin. We have trained a series of machine learning models with the aim of complementing genetics-based drug susceptibility testing. MethodsWe built a Test+Train dataset comprising 219 susceptible mutations and 46 RAVs. Features derived from the structure of the RNA polymerase or the change in chemistry introduced by the mutation were considered, however, only a few, notably the distance from the rifampicin binding site, were found to be predictive on their own. Due to the paucity of RAVs we used Monte Carlo cross-validation with 50 repeats to train four different machine learning models. ResultsAll four models behaved similarly with sensitivities and specificities in the range 0.84-0.88 and 0.94-0.97 although we preferred the ensemble of Decision Tree models as they are easy to inspect and understand. We showed that measuring distances from molecular dynamics simulations did not improve performance. ConclusionsIt is possible to predict whether a mutation in rpoB confers resistance to rifampicin using a machine learning model trained on a combination of structural, chemical and evolutionary features, however performance is moderate and training is complicated by the lack of data.

microbiology↗

bioRxiv2024

First endangered black-footed ferrets, Mustela nigripes, cloned for genetic rescue

An endangered black-footed ferret female that died in 1988 with no living descendants in the current population was successfully cloned from cryopreserved cells using cross-species somatic cell nuclear transfer, producing three healthy kits. Incorporating progeny from these clones would provide an 8th founder to the breeding program and increase genetic variation to the species limited gene-pool. This marks the first time a native U.S. endangered species has been cloned.

zoology↗

bioRxiv2024

Repeated Exposure Decreases Aesthetic Chills Likelihood but Increases Intensity

Aesthetic chills are a peak emotional response to affectively charged stimuli such as music, films, or speech. This study investigates the impact of repeated exposure on the frequency and intensity of aesthetic chills. Through a longitudinal approach, we quantified changes in chill likelihood, intensity, and pleasure across multiple exposures, focusing on audio stimuli. Participants (n = 58) were randomly exposed to 6 chill-evoking stimuli pre-validated on the population of interest, in a counterbalanced order. Our findings revealed a significant decrease in the likelihood of experiencing chills with repeated exposure, suggesting habituation to chills itself or potential fatigue in response to aesthetic stimuli. The study also identified distinct demographic and psychophysiological response patterns across different participant groups, indicating variability in chill responses. These results provide insights into the dynamic nature of aesthetic experiences and their underlying neural mechanisms, with implications for understanding emotional and reward processing in psychophysiology.

neuroscience↗

bioRxiv2022

The bone ecosystem facilitates multiple myeloma relapse and the evolution of heterogeneous proteasome inhibitor resistant disease

Multiple myeloma (MM) is an osteolytic plasma cell malignancy that, despite being responsive to therapies such as proteasome inhibitors, frequently relapses. Understanding the mechanism and the niches where resistant disease evolves remains of major clinical importance. Cancer cell intrinsic mechanisms and bone ecosystem factors are known contributors to the evolution of resistant MM but the exact contribution of each is difficult to define with current in vitro and in vivo models. However, mathematical modeling can help address this gap in knowledge. Here, we describe a novel biology-driven hybrid agent-based model that incorporates key cellular species of the bone ecosystem that control normal bone remodeling and, in MM, yields a protective environment under therapy. Critically, the spatiotemporal nature of the model captures two key features: normal bone homeostasis and how MM interacts with the bone ecosystem to induce bone destruction. We next used the model to examine how the bone ecosystem contributes to the evolutionary dynamics of resistant MM under control and proteasome inhibitor treatment. Our data demonstrates that resistant disease cannot develop without MM intrinsic mechanisms. However, protection from the bone microenvironment dramatically increases the likelihood of developing intrinsic resistance and subsequent relapse. The spatial nature of the model also reveals how the bone ecosystem provides a protective niche for drug sensitive MM cells under treatment, consequently leading to the emergence of a heterogenous and drug resistant disease. In conclusion, our data demonstrates a significant role for the bone ecosystem in MM survival and resistance, and suggests that early intervention with bone ecosystem targeting therapies may prevent the emergence of heterogeneous drug resistant MM.

cancer biology↗

bioRxiv2022

Quantitative bioactivity signatures of dietary supplements and natural products

Dietary Supplements and Natural Products have minor oversight of their safety and efficacy. We assembled a collection of Dietary Supplements and Natural Products (DSNP) as well as Traditional Chinese Medicinal (TCM) Plant extracts, which were screened against an in vitro panel of assays, including a liver cytochrome p450 enzyme panel, CAR/PXR signaling pathways, and P-gp transporter assays, to assess their activity. This pipeline facilitated the interrogation of Natural Product-Drug Interaction (NaPDI) through prominent metabolizing pathways. In addition, we compared the activity profiles of the DSNP/TCM substances with those of an approved drug collection. Many of the approved drugs have well-annotated mechanisms of action (MOA) while the MOAs for most of the DSNP and TCM samples remain unknown. Based on the premise that compounds with similar activity profiles tend to share similar targets or MOA, we clustered the library activity profiles to identify overlap with the NCATS Pharmaceutical Collection to predict the MOAs of the DSNP/TCM substances. Overall, we highlight four significant bioactivity profiles (measured by p-values) as examples of this prediction. These results can be used as a starting point for further exploration on the toxicity potential and clinical relevance of these substances.

pharmacology and toxicology↗

bioRxiv2022

Deciphering the roadmap of in vivo reprogramming towards pluripotency

Differentiated cells can be converted to pluripotent stem cells (iPSCs) upon ectopic expression of transcription factors OCT4, SOX2, KLF4 and MYC (OSKM) in a process known as reprogramming. Great efforts have been made to dissect intermediate states of in vitro reprogramming and how they are affected by culture conditions, while the roadmap of in vivo reprogramming remains unexplored. Here, we use single cell RNA sequencing to capture cells undergoing reprogramming in the adult pancreas. We identify markers along the trajectory from acinar identity to pluripotency, which allow in situ visualization of the intermediate states of reprogramming. Importantly, different tissues expressing OSKM, such as pancreas, stomach and colon, share markers of intermediate reprogramming, suggesting a conserved in vivo reprogramming path. Our in vivo roadmap defines landmarks along in vivo reprogramming that could be useful for applications in tissue regeneration and cellular rejuvenation based on intermediate reprogramming states.

developmental biology↗

bioRxiv2021

Integrated computational and in vivo models reveal Key Insights into Macrophage Be-havior during bone healing

Myeloid-derived monocyte and macrophages are key cells in the bone that contribute to remodeling and injury repair. However, their temporal polarization status and control of boneresorbing osteoclasts and bone-forming osteoblasts responses is largely unknown. In this study, we focused on two aspects of monocyte/macrophage dynamics and polarization states over time: 1) the injury-triggered pro- and anti-inflammatory monocytes/macrophages temporal profiles, 2) the contributions of pro-versus anti-inflammatory monocytes/macrophages in coordinating healing response. Bone healing is a complex multicellular dynamic process. While traditional in vitro and in vivo experimentation may capture the behavior of select populations with high resolution, they cannot simultaneously track the behavior of multiple populations. To address this, we have used an integrated a coupled ordinary differential equations (ODEs)-based framework describing multiple cellular species to in vivo bone injury data in order to identify and test various hypotheses regarding bone cell populations dynamics. Our approach allowed us to infer several biological insights including, but not limited to,: 1) anti-inflammatory macrophages are key for early osteoclast inhibition and pro-inflammatory macrophage suppression, 2) pro-inflammatory macrophages are involved in osteoclast bone resorptive activity, whereas osteoblasts promote osteoclast differentiation, 3) Pro-inflammatory monocytes/macrophages rise during two expansion waves, which can be explained by the anti-inflammatory macrophages-mediated inhibition phase between the two waves. In addition, we further tested the robustness of the mathematical model by comparing simulation results to an independent experimental dataset. Taken together, this novel comprehensive mathematical framework allowed us to identify biological mechanisms that best recapitulate bone injury data and that explain the coupled cellular population dynamics involved in the process. Furthermore, our hypothesis testing methodology could be used in other contexts to decipher mechanisms in complex multicellular processes. Author SummaryMyeloid-derived monocytes/macrophages are key cells for bone remodeling and injury repair. However, their temporal polarization status and control of bone-resorbing osteoclasts and boneforming osteoblasts responses is largely unknown. In this study, we focused on two aspects of monocyte/macrophage population dynamics: 1) the injury-triggered pro- and anti-inflammatory monocytes/macrophages temporal profiles, 2) the contributions of pro-versus anti-inflammatory monocytes/macrophages in coordinating healing response. In order to test various hypotheses regarding bone cell populations dynamics, we have integrated a coupled ordinary differential equations-based framework describing multiple cellular species to in vivo bone injury data. Our approach allowed us to infer several biological insights including: 1) anti-inflammatory macrophages are key for early osteoclast inhibition and pro-inflammatory macrophage suppression, 2) pro-inflammatory macrophages are involved in osteoclast bone resorptive activity, whereas osteoblasts promote osteoclast differentiation, 3) Pro-inflammatory monocytes/macrophages rise during two expansion waves, which can be explained by the anti-inflammatory macrophages-mediated inhibition phase between the two waves. Taken together, this mathematical framework allowed us to identify biological mechanisms that recapitulate bone injury data and that explain the coupled cellular population dynamics involved in the process.

immunology↗

bioRxiv2021

Water Nanoconfined in a Hydrophobic Pore: MD Simulations and Water Models

Water molecules within biological ion channels are in a nano-confined environment and therefore exhibit novel behaviours which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously de-wet to form a vapour lock if the pore is sufficiently hydrophobic and/or narrow. Notably, this occurs without steric occlusion of the pore. Using molecular dynamics simulations with both additive and polarisable (AMOEBA) force fields, we investigate this wetting/de-wetting behaviour in the TMEM175 ion channel. We examine how a range of rigid fixed-charge (i.e. additive) and polarisable water models affect wetting/de-wetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/de-wetting behaviours, but that the polarisable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nano-confined water, as it implies that polarisability may need to be included if we are to gain detailed mechanistic insights into wetting/de-wetting processes. These findings are of importance for the design of functionalised biomimetic nanopores (for e.g. sensing or desalination), as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function.

biophysics↗

bioRxiv2021

Conversion of spent CHO cell culture media waste to new fermentation feed efficiently supports production of recombinant protein by Escherichia coli

Deriving new value from waste streams through secondary processes is a central aim of the circular bioeconomy. In this study we investigate whether chemically defined spent media (CDSM) waste from cell culture bioprocess can be recycled and used as a feed in secondary microbial fermentation to produce new recombinant protein products. Our results show that CDSM supplemented with 2% glycerol supported a specific growth rate of E. coli cultures equivalent to that achieved using a nutritionally rich microbiological media (LB). The titre of recombinant protein produced following induction in a 4-hour expression screen was approximately equivalent in the CDSM fed cultures to that of baseline, and this was maintained in a 16-hr preparative fermentation. To understand the protein production achieved in CDSM fed culture we performed a quantitative analysis of proteome changes in the E. coli using mass spectrometry. This analysis revealed significant upregulation of protein synthesis machinery enzymes and significant downregulation of carbohydrate metabolism enzymes. We conclude that spent cell culture media, which represents 100s of millions of litres of waste generated by the bioprocessing industry annually, may be valorized as a feed resource for the production of recombinant proteins in secondary microbial fermentations.

microbiology↗

bioRxiv2020

A Library Of Induced Pluripotent Stem Cells From Clinically Well-Characterized, Diverse Healthy Human Individuals

A library of well-characterized human induced pluripotent stem cell (hiPSC) lines from clinically healthy human subjects could serve as a useful resource of normal controls for in vitro human development, disease modeling, genotype-phenotype association studies, and drug response evaluation. We report generation and extensive characterization of a gender-balanced, racially/ethnically diverse library of hiPSC lines from 40 clinically healthy human individuals who range in age from 22-61. The hiPSCs match the karyotype and short tandem repeat identity of their parental fibroblasts, and have a transcription profile characteristic of pluripotent stem cells. We provide whole genome sequencing data for one hiPSC clone from each individual, genomic ancestry determination, and analysis of Mendelian disease genes and risks. We document similar transcriptomic profiles, single-cell RNA-seq derived cell clusters and physiology of cardiomyocytes differentiated from multiple independent hiPSC lines. This extensive characterization makes this hiPSC library a valuable resource for many studies on human biology.

cell biology↗

bioRxiv2020

White matter hyperintensity-associated structural disconnection, resting state functional connectivity, and cognitive control in older adults

ObjectiveWhite matter hyperintensities (WMH) are linked to deficits in cognitive functioning, including cognitive control and memory; however, the structural and functional mechanisms are largely unknown. We investigated the relationship between estimated regional disruptions to white matter fiber tracts from WMH, resting state functional connectivity (RSFC), and cognitive functions in older adults. DesignCross-sectional study. SettingCommunity. ParticipantsFifty-eight cognitively-healthy older adults. MeasurementsTasks of cognitive control and memory, structural MRI, and resting state fMRI. We estimated the disruption to white matter fiber tracts from WMH and its impact on gray matter regions in the cortical and subcortical frontoparietal network, default mode network, and ventral attention network by overlaying each subjects WMH mask on a normative tractogram dataset. We calculated RSFC between nodes in those same networks. ResultsThe interaction of estimated regional WMH burden and RSFC in cortico-striatal regions of the default mode network and frontoparietal network was associated with memory retrieval. Models predicting working memory, cognitive inhibition, and set-shifting were not significant. ConclusionsFindings highlight the role of circuit-level alterations at the structural and functional levels in resting state networks that are related to WMH and impact memory retrieval in older adults.

neuroscience↗