Biology subjects

Nolan, N.

Publications and source records attributed to Nolan, N..

7 recordsLinked to original sources

bioRxiv2026

Model-guided design of single-cargo, dual-attractor gene circuits

Dual-attractor gene networks program distinct states, guiding native cellular decision-making processes such as differentiation. Synthetic dual-attractor circuits (DACs) emulate native gene networks, directing cells to two different states starting from a single, genetically uniform population. However, existing DAC designs for mammalian cells often require multiple genetic cargoes, limiting their application to control cell fate in therapeutically relevant contexts. Here, we leverage model-guided tuning of compact biochemical and biophysical layers of regulation to program two cellular states using a single-cargo DAC. Through activator selection and layering microRNA-mediated mutual repression, we identify and resolve an imbalance between modules that biases states, allowing us to achieve balanced adoption of both states without relying on copy-number variation. Consolidating this optimized DAC into a single cargo, we use gene syntax to minimize bias, generating two balanced states from a single cargo of less than 11 kilobases. Overall, this work establishes design rules for combined biochemical and biophysical tuning of DACs to generate balanced cell states from a single-cargo design, paving the way for programming divergent cell-state trajectories and dual-fate systems.

synthetic biology↗

bioRxiv2026

A synthetic PGC1α co-activator reprograms microglial immunometabolism to preserve cone function in retinal degeneration

Retinitis pigmentosa (RP) is genetically heterogeneous, yet initiating mutations converge on primary rod degeneration followed by cone dysfunction and loss. Activated microglia are implicated in this secondary phase, but whether selective immunometabolic reprogramming of microglia preserves retinal function remains unknown. In human iPSC-derived microglia and retinal CD11b cells, PGC1 induction suppressed LPS-driven interferon signaling and cytokine release, yet Seahorse analysis and isotopologue tracing showed that energy metabolism remained altered. We therefore fused PGC1 to a multivalent p65-HSF1 module, yielding ~2.5-fold higher nuclear receptor output than native PGC1 and coordinated engagement of oxidative and anti-inflammatory programs in mouse retinal CD11b cells. Microglia-restricted expression in humanized RHOP347L mice preserved photopic responses through six months, increased retinal thickness and promoted ramified subretinal IBA1 morphology. Microglial immunometabolism thus represents a potentially genotype-independent neuroprotective target in RP, and engineered PGC1 co-activators provide a means to sustain oxidative metabolism under inflammatory pressure.

immunology↗

bioRxiv2026

A Brain Circuit for Status Epilepticus

Status epilepticus (SE) is a life-threatening persistent epileptic seizure that can arise from various brain structures, leaving its brain circuit unknown. In this study, we utilize brain imaging changes during SE to reveal the brain architecture and circuit of persistent seizures. Multimodal lesion mapping identified that brain imaging changes during SE localize to a specific predisposed brain architecture characterized by increased metabolic rate, high synaptic and mitochondrial density, glutamate (mGLUR5 and NMDA) and GABA receptors. Gene expression patterns within lesion locations revealed a transcriptomic profile enriched for epilepsy pathologies (including SE), neuronal and synaptic processes, and glutamate signaling. Lesion network mapping demonstrated these same lesions map to a common brain circuit, unifying a traditionally heterogeneous patient population. Findings were validated in an independent cohort and the identified SE circuit distinguished brain imaging changes during SE from other lesion etiologies with excellent accuracy (91%), significantly outperforming all other tested maps. With this SE circuit, we identify therapeutic targets for precision therapy that could modulate this circuit. This study demonstrates brain imaging changes in SE converge on a unified brain circuit that could help diagnostic workup of patients in critical care and guide clinical trials of precision therapy for persistent seizures.

neuroscience↗

bioRxiv2026

Chytridiomycosis infection and heat compromises sperm quality in a threatened frog

Environmental change is reshaping wildlife reproduction through increasing temperatures and the spread of emerging infectious diseases, yet the physiological consequences of managing these stressors remain poorly understood. Amphibians are particularly vulnerable due to their ectothermy and high susceptibility to chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd). Here, we examine how Bd infection and thermal treatment interact to influence sperm quality and reproductive investment in male green and golden bell frogs (Ranoidea aurea), a species that has suffered severe population declines. Moderate Bd infection was associated with elevated sperm concentration relative to uninfected and heavily infected males, consistent with increased short-term reproductive investment under elevated mortality risk. However, severe infection led to pronounced reductions in sperm concentration and motility. Thermal treatment successfully eliminated Bd infection but imposed substantial reproductive costs: sperm concentration declined following treatment and remained significantly reduced six months later, despite partial recovery of sperm motility and membrane integrity. These results indicate persistent impairment of spermatogenic capacity rather than transient suppression. Our findings reveal that disease and thermal stress jointly shape amphibian reproductive outcomes through context-dependent trade-offs between immune defence and gamete production. While mild infection may trigger short-lived increases in reproductive output, both severe infection and pathogen clearance via thermal exposure impose lasting constraints on fertility. These results highlight an underappreciated cost of disease mitigation and suggest that increasing thermal extremes associated with climate change may further limit amphibian reproductive resilience, with important implications for conservation management and population persistence.

physiology↗

bioRxiv2024

MicroBayesAge: A Maximum Likelihood Approach to Predict Epigenetic Age Using Microarray Data

Certain epigenetic modifications, such as the methylation of CpG sites, can serve as biomarkers for chronological age. Previously, we introduced our BayesAge frameworks for accurate age prediction through the use of locally weighted scatterplot smoothing (LOWESS) to capture the non-linear relationship between methylation or gene expression and age, and Maximum Likelihood Estimation (MLE) for bulk bisulfite and RNA sequencing data. Here we now introduce MicroBayesAge, a framework that enhances prediction accuracy by subdividing input data into age-specific co-horts and employing a new two-stage process for training and testing. Age prediction for younger patients was significantly improved. MicroBayesAge also exhibited minimal bias in its age predictions. Additionally, we explored the performance of our model for sex-specific age prediction which revealed slight improvements in accuracy for male patients, while no changes were observed for female patients. MicroBayesAge provides more accurate age predictions by accounting for variations in epigenetic markers of aging among different subgroups, which have been over-looked by commonly used models.

bioinformatics↗

bioRxiv2023

Enhancer-driven regulatory network of forebrain human development provides insights into autism

Cell differentiation is orchestrated by transcription factors (TFs) binding to enhancers, shaping gene regulatory networks that drive neuronal lineage specification. Deciphering these enhancer-driven networks in human forebrain development is essential for understanding the genetic basis of neurodevelopmental disorders. Through integrative epigenomic and transcriptomic analyses of human forebrain organoids derived from 10 individuals with autism spectrum disorder (ASD) and their neurotypical fathers, we constructed a comprehensive enhancer-driven gene regulatory network (GRN) of early neurodevelopment. This GRN revealed hierarchical regulatory transitions guiding neuronal differentiation and was experimentally validated via CRISPR interference (CRISPRi) and loss-of-function analyses. A subnetwork linked ASD-associated transcriptomic alterations to dysregulated TF activity, implicating FOXG1, BHLHE22, EOMES, and NEUROD2 as key regulators of excitatory neuron specification in macrocephalic ASD. These findings suggest that ASD disrupts enhancer-driven regulatory frameworks, altering neuronal cell fate decisions in the developing fetal brain.

genomics↗

bioRxiv2023

Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages {lambda} and P1

Phages are one of the key ecological drivers of microbial community dynamics, function and evolution. Despite their importance in bacterial ecology and evolutionary processes, phage genes are poorly characterized, hampering their usage in a variety of biotechnological applications. Methods to characterize such genes, even those critical to the phage life cycle, are labor-intensive and are generally phage-specific. Here, we develop a systematic gene essentiality mapping method scalable to new phage-host combinations that facilitate the identification of non-essential genes. As proof of concept, we use a catalytically inactive Cas12a mediated genome-wide CRISPRi assay to determine the essential genes in the canonical coliphages {lambda} and P1. Results from a single panel of CRISPRi probes largely recapitulate the essential gene roster determined from decades of genetic analysis for lambda and provide new insights into essential and nonessential loci in P1. We present evidence of how CRISPRi polarity can lead to false positive gene essentiality assignments and recommend caution towards interpreting CRISPRi data on gene essentiality when applied to less studied phages. Finally, we show that we can engineer phages by inserting DNA barcodes into newly identified inessential regions, which will empower processes of identification, quantification and tracking of phages in diverse applications.

microbiology↗