Biology subjects

Yan, A.

Publications and source records attributed to Yan, A..

At least 19 recordsLinked to original sources

bioRxiv2026

An implantable sensor network for large-scale cellular force mapping in living embryos

Mechanical forces generated by cells are fundamental regulators of embryonic development, yet how locally generated forces are integrated across tissues to drive large-scale morphogenesis remains poorly understood. Addressing this question requires direct quantitative mapping of intercellular forces across tissue scale with cellular resolution while preserving native tissue architectures and dynamics, a capability not yet achieved. Here, we introduce FORCENET, an implantable force-sensing network that enables quantitative tissue-scale force mapping at cellular resolution within living embryos. FORCENET consists of a microfabricated network of ultrathin elastic sensors whose three-dimensional deformations are tracked over time and converted into intercellular force maps through physics-based reconstruction. FORCENET covers hundreds of cells while occupying a total volume 6- to 20-fold smaller than that of a single cell. Anatomical measurements, three-dimensional fluorescent imaging, and cell density and speed tracking confirmed that FORCENET seamlessly integrates within developing embryos without perturbing cell motion and proliferation, tissue architecture, and embryonic development. Applied to zebrafish gastrulation, FORCENET revealed that intercellular forces are dynamically coordinated across supracellular length scales of ~30-210 m. Inhibition of fibroblast growth factor signaling accelerated force accumulation and shortened the force-coordination length scales despite only modest changes in cell density and kinematics, demonstrating that FORCENET uncovers information not readily inferred from cell tracking alone. FORCENET establishes a scalable platform for in vivo force mapping and reveals that cell-generated forces are coordinated into supracellular mechanical patterns that are regulated by developmental signaling.

developmental biology↗

bioRxiv2026

High-density Lipoprotein Inspired Lipid Nanoparticles for Systemic RNA delivery to the Brain

Systemic delivery of nucleic acids to the central nervous system (CNS) remains fundamentally limited by the blood-brain barrier (BBB) and the lack of cell-type specificity. Inspired by endogenous high-density lipoproteins (HDLs) that naturally traverse the BBB, we engineered a library of 112 HDL-inspired lipid nanoparticles (HLNPs) to deliberately program protein corona composition and direct nanoparticle trafficking across the BBB. High-throughput in vivo screening identified HLNPs with robust brain accumulation and preferential enrichment within distinct neural cell populations. Quantitative proteomic analysis revealed that elevated apolipoprotein A-I/apolipoprotein E and vitronectin/apolipoprotein E ratios correlate with enhanced BBB transport. We further demonstrated that neuron-targeted HLNPs delivering PTEN siRNA produced functional recovery and lesion reduction in a murine traumatic brain injury model, while microglia-targeted HLNPs carrying interleukin-10 mRNA potently suppressed neuroinflammation. Together, these findings establish HLNPs as a versatile RNA delivery platform that leverages protein corona programming for enhanced brain delivery and cell-type-selective targeting.

bioengineering↗

bioRxiv2026

Targeting COL4A1-Related Small Vessel Disease: Repurposed Pharmacotherapies for Genetic Vasculopathies

COL4A1-related disorders cause early-onset stroke, intracerebral haemorrhage, visual impairment and kidney disease, often affecting children and young adults, yet no disease-modifying therapies exist. These disorders arise from pathogenic COL4A1 variants that disrupt type IV collagen and impair small-vessel integrity, leading to cerebral small-vessel disease and endothelial dysfunction. We performed a mechanism-guided screen in human brain endothelial cells using a CRISPR-engineered COL4A1 p.G755R line and patient-specific COL4A1 p.G773R iPSC-derived endothelial cells. Simvastatin, L-carnosine, and XPD-101 restored impaired endothelial proliferation, migration, and other markers of endothelial function, including transendothelial electrical resistance (TEER). In a Col4a1Svc/+ mouse model, simvastatin increased pre-weaning survival, improved functional behaviour and reduced cerebral microhaemorrhage burden. These findings identify mechanism-informed candidates that rescue COL4A1-mutant endothelial dysfunction in vitro, with simvastatin demonstrating in vivo efficacy, supporting prioritisation for further preclinical development.

molecular biology↗

bioRxiv2026

Reverse electron transfer at mitochondrial complex I restrains dopaminergic neuron activity to promote early-life sleep in Drosophila

Sleep is especially abundant during early life, yet the cellular mechanisms that maintain elevated juvenile sleep drive remain poorly understood. To identify cell-intrinsic regulators of juvenile sleep, we profiled gene expression in Drosophila dopaminergic neurons (DANs) at different ages and performed a targeted RNAi screen of genes with enriched juvenile expression. We found that the magnitude of mitochondrial complex I (MCI) disruption produced strikingly distinct physiological outcomes. Severe MCI loss-of-function caused profound mitochondrial dysfunction, reduced dopaminergic activity, and locomotor impairment. In contrast, partial MCI inhibition left overall mitochondrial function intact but instead reduced sleep, with disproportionately strong effects on juvenile sleep fragmentation and depth, consistent with a gain of dopaminergic signaling. Multiple genetic manipulations that deplete the reduced coenzyme Q pool (CoQH2) converged on a phenotype of increased dopaminergic activity and wakefulness, indicating that coenzyme Q redox balance itself regulates dopaminergic output. These findings support a model in which CoQH2-driven reverse electron transfer (RET) at MCI restrains dopaminergic arousal. By dissociating mitochondrial redox signaling from catastrophic mitochondrial failure, our work identifies a physiological role for coenzyme Q-dependent signaling in the regulation of neural activity and behavioral state. More broadly, these findings suggest that sleep phenotypes may serve as sensitive indicators of emerging mitochondrial dysfunction and reveal a potential link between the regulation of early-life sleep and later dopaminergic vulnerability.

neuroscience↗

bioRxiv2025

Visualizing PINK1 Activity Dynamics in Single Cells with a Phase Separation-Based Kinase Activity Reporter

Phosphatase and tensin homologue-induced kinase 1 (PINK1) is a serine/threonine kinase that plays roles in mitophagy, cell death, and regulation of cellular bioenergetics. Current approaches for studying PINK1 function depend on bulk techniques that can only provide snapshots of activity and could miss the dynamics and cell-to-cell heterogeneity of PINK1 activity. Therefore, we sought to develop a novel PINK1 kinase activity reporter to characterize PINK1 activity. Taking advantage of the separation of phases-based activity reporter of kinase (SPARK) design, we developed a phase separation-based PINK1 biosensor (PINK1-SPARK). With PINK1-SPARK, we observe real-time PINK1 activity in single cells treated with mitochondria depolarizing agents or pharmacological activators. We then developed a Halo Tag-based PINK1-SPARK for multiplexed imaging of PINK1 activity with live-cell markers of mitochondrial damage. Thus, PINK1-SPARK is a new tool that enables temporal measurement of PINK1 activity in single live cells, allowing for further elucidation of the role of PINK1 in mitophagy and cell function.

cell biology↗

bioRxiv2025

Phosphate limitation triggers Fe3+-dependent polymyxin resistance in Enterobacteriaceae

Phosphate (Pi) scarcity, a pervasive stressor prevalent in bacterial infections and dysbiotic host environments, potently drives antimicrobial resistance (AMR) against cationic antibiotics like polymyxins across diverse bacterial taxa. While established Pi depletion-induced AMR mechanisms often involve membrane phospholipid remodelling, Enterobacteriaceae largely lack these pathways, leaving their Pi scarcity-driven AMR mechanism unresolved. Here, we reveal that Pi limitation robustly induces polymyxin resistance in Enterobacteriaceae through 4-amino-4-deoxy-L-arabinose (L-Ara4N) modification of the Gram-negative outer membrane component lipid A, reflecting a distinct adaptive strategy. This modification is driven by strong ugd-arn operon induction, mediated by the PmrAB two-component system. We discover that Pi depletion triggers cellular Mg{superscript 2} release, prompting compensatory Fe3 mobilization to the cell envelope that directly activates PmrAB. Crucially, this metal-dependent signaling axis offers a directly targetable mechanism for reversing polymyxin resistance, a significant deviation from the less accessible, PhoBR-regulated phospholipid remodelling strategies in other bacteria. We demonstrate that Mg{superscript 2} supplementation or Fe3 chelation effectively suppresses PmrAB activation and restores polymyxin susceptibility, thereby establishing a novel, metal-centric paradigm for understanding and pharmacological intervention in stress-induced AMR.

microbiology↗

bioRxiv2025

Longitudinal TCR repertoires in ulcerative colitis patients show features distinguishing disease states

ABSTRACT AND KEY WORDSO_ST_ABSBackgroundC_ST_ABSUlcerative colitis (UC) affects an estimated 10 million people worldwide. The exact etiology of the disease is unknown, but T cell dysregulation and aberrant activation is associated with UC--prompting research into T cell receptor (TCR) repertoires in UC patients. However, few studies have compared UC patients TCR repertoires in flare (inflamed) and remission (uninflamed) states. Moreover, this is the first dataset to our knowledge examining multiple repertoires from UC patients over time, enabling longitudinal analyses. MethodsTCR repertoires were obtained for 21 patients across multiple timepoints, yielding a total of 58 samples. Repertoires clonality, diversity, overlap, and gene usage frequencies were compared across all patients. CDR3 sequences were split into K-mers (sequences of length K), and enriched K-mers in flare and remission states were identified using GLIPH2. ResultsAlthough repertoires vary across patients, there were significant differences in the usage of 20 V{beta} genes across flare and remission states. Moreover, calculating the overlap in repertoires with enriched K-mers showed higher overlap scores than when using full TCR sequences. 622 unique enriched K-mers were identified in flare states and 495 in remission states, with only 57 overlapping between the two states. ConclusionsOverall, these results highlight the importance of analyzing V{beta} gene usage and K-mer enrichment in TCR repertoires, particularly given the lack of public clones across patient cohorts. Future studies characterizing the specific antigenic targets associated with these features will pave the way for biomarker discovery in UC. KEY MESSAGESO_LIWhat is already known? UC is a chronic condition characterized by fluctuating periods of flares and remissions, as well as aberrant immune activity. C_LIO_LIWhat is new here? TCR repertoires were obtained from UC patients colonoscopies, with multiple timepoints per patient--enabling the analysis of repertoire characteristics within and across patients over time. C_LIO_LIHow can this study help patient care? Understanding the exact immune mechanisms in UC can pave the way for biomarker discovery and advance the state of care for patients, given that current treatments are non-specific and have adverse side effects. C_LI SummaryThis article presents an analysis of T cell receptor repertoires from ulcerative colitis patient samples collected during colonoscopies, identifying genes and motifs associated with patients flare (inflamed) and remission (uninflamed) states.

immunology↗

bioRxiv2025

Intranasal Dantrolene Nanoparticles for Treatment of Amyotrophic Lateral Sclerosis as a Disease-Modifying Drug

Calcium dysregulation, caused by pathological activation of ryanodine receptors, contributes to motor neuron degeneration, motor dysfunction, and muscle weakness in SOD1-G93A transgenic amyotrophic lateral sclerosis (ALS) mice. This study investigates the therapeutic efficacy of intranasally administered dantrolene nanoparticles, a ryanodine receptor antagonist, on motor neuron function, muscle strength, spinal cord degeneration, and survival outcomes. Male and female C57BL/6SJLF1 non-transgenic control and SOD1-G93A ALS transgenic mice were assigned to one of three experimental groups: 1) NO TX: No treatment control; 2) IN-DAN: Intranasal administration of dantrolene in the Ryanodex formulation vehicle (RFV), at a dosage of 5mg/kg, administered daily from ages 90-120 days; 3) IN-VEH: Intranasal administration of RFV alone (as a vehicle control), following the same dosing schedule as the IN-DAN condition. Body weight and general motor function were monitored weekly, with survival recorded daily throughout the treatment period. At the treatment conclusion, neurological function was comprehensively evaluated using a standardized neurological scoring system. Motor coordination and balance were assessed using the balance beam test (beam widths of 12 mm and 6 mm) and the rotarod test. Muscle strength was evaluated by measuring grip force using the Kondziela inverted screen test. After behavioral testing, spinal cord tissues were collected for analysis. The levels of neurofilament light chain (NFL), a skeletal neuron protein, and spinal cord weight were determined to measure spinal cord degeneration. Compared to non-transgenic control mice, SOD1-G93A mice exhibited significantly elevated neurological scores, indicating severely impaired neurological function. This deterioration was robustly and significantly ameliorated by IN-DAN treatment by 90% (P<0.0001). Similarly, ALS mice demonstrated impairments in motor coordination and balance on the beam balance test, with dramatic and significant increases in crossing time and the number of foot slips. These impairments were greatly and significantly mitigated by IN-DAN treatment, by 78% in crossing time (P<0.0001) and 84% in the number of slips (P<0.0001) on the 12 mm-wide beam, but not by the vehicle control. ALS mice demonstrated progressive body weight loss as well, which was similarly reversed by IN-DAN treatment, but not by the vehicle control. Muscle strength, as measured by grip force, was significantly reduced in ALS mice but robustly preserved IN-DAN treatment, which prevented the decrease by 213% (P<0.0001), while the vehicle control had no effect. Spinal cord weight was significantly reduced in ALS mice, a trend reversed by intranasal dantrolene nanoparticle treatment, but not by the vehicle control. Survival analysis revealed that 100% of control mice survived through the 30-day treatment period (up to 120 days of age), while survival in untreated or vehicle-treated ALS mice dropped to 67%. In contrast, ALS mice treated with intranasal dantrolene nanoparticles demonstrated a significantly improved survival rate of 89%. Thus, intranasal dantrolene nanoparticle treatment significantly and robustly improved neurological outcomes in SOD1-G93A ALS mice, inhibiting neurological impairment, motor dysfunction, balance deficits, and muscle weakness. These improvements were associated with a marked inhibition of spinal cord weight loss. Additionally, dantrolene treatment reversed body weight loss and significantly improved survival probability in ALS mice.

pharmacology and toxicology↗

bioRxiv2025

Refined cell transfer model reveals roles for Ascl2 and Cxcr3 in splenic localization of mouse NK cells during virus infection

Cell transfer experiments complement the rigorous investigation of antiviral and antitumor functions of natural killer (NK) cells. Success in these endeavors is enhanced by expansion of small numbers of input NK cells driven by viral antigens or homeostatic proliferation in immunodeficient hosts. In contrast, analysis of other NK-cell functions, including immunoregulation, are non-proliferative and require an intact immune system in recipient mice. We reveal poor persistence of conventional congenic (CD45.1) BoyJ NK cells following adoptive transfer in comparison to CRISPR-generated CD45.1+ (JAXBoy) NK cells. Reciprocal transfers between C57BL/6 and JAXBoy mice substantially improve seeding and maintenance of donor NK cells. Using this system, we confirm that CXCR3 re-positions NK cells in the white pulp of the spleen after infection, which is vital for immunoregulation. Moreover, we discovered that the transcription factor ASCL2 is required for recruitment of NK cells into the spleen and white pulp. These results provide improved tools and novel insights into NK cell biology. Key pointsO_LIJAXBoy are superior to conventional BoyJ mice for NK cell persistence after transfer. C_LIO_LICXCR3 repositions donor NK cells in T/B-zones of the spleen after infection. C_LIO_LIThe transcription factor ASCL2 is required for NK-cell recruitment to spleen white pulp. C_LI

immunology↗

bioRxiv2024

The Impact of Model Assumptions in Interpreting Cell Kinetic Studies

Author summaryStable isotope labelling is one of the best available methods for quantifying cell dynamics in vivo, particularly in humans where the absence of toxicity makes it preferable over other techniques such as CFSE or BrdU. Interpretation of stable isotope labelling data necessitates simplifying assumptions. Here we investigate the impact of three of the most commonly used simplifying assumptions (that the cell population of interest is closed, that the population of interest is kinetically homogeneous, and that the population is spatially homogeneous) and suggest pragmatic ways in which the resulting errors can be reduced.

immunology↗

bioRxiv2024

A novel approach for simultaneous detection of structural and single-nucleotide variants based on a combination of chromosome conformation capture and exome sequencing

Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type--whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Through several case studies, we demonstrate how Exo-Cs multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

genomics↗

bioRxiv2023

High-resolution ultrastructure and morphology of marine ammonia-oxidizing archaea Nitrosopumilus maritimus SCM1 revealed by Cryo-ET and STEM-EDS

Nitrososphaerota, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their significance in Earths ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant question unanswered of how the machinery of these organisms underpins metabolic functions. In this study, we combined chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaerota. Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules in which one type is possibly composed of polyphosphate, while the other type is polyhydroxyalkanoate. Collectively, these findings provide visual evidence for the resilience of AOA in the vast oligotrophic marine environment.

microbiology↗

bioRxiv2023

Sequence-based drug design using transformers

Protein-ligand interactions play central roles in biological processes and are of key importance in drug design. Deep learning-based approaches are emerging as cost-effective alternatives to high-throughput experimental methods for the screening of large libraries of ligands. Here, to predict the binding affinity between proteins and small molecules, we introduce Ligand-Transformer, a deep learning framework based on the AlphaFold2 transformer architecture. We applied Ligand-Transformer to screen inhibitors targeting the mutant EGFRLTC kinase, identifying compounds with low nanomolar potency. We then used this approach to predict the conformational population shifts induced by ABL kinase inhibitors. To show the applicability of Ligand-Transformer to disordered proteins, we explored the binding of small molecules to the Alzheimers A{beta} peptide, identifying compounds that delayed its aggregation. Overall, Ligand-Transformer illustrates the potential of transformers in accurately predicting the interactions of small molecules with both ordered and disordered proteins, thus uncovering molecular mechanisms and facilitating the initial steps in drug discovery.

bioinformatics↗

bioRxiv2023

Preoptic area controls sleep-related seizure onset in a genetic epilepsy mouse model

In genetic and refractory epileptic patients, seizure activity exhibits sleep-related modulation/regulation and sleep and seizure are intermingled. In this study, by using one het Gabrg2Q390X KI mice as a genetic epilepsy model and optogenetic method in vivo, we found that subcortical POA neurons were active within epileptic network from the het Gabrg2Q390XKI mice and the POA activity preceded epileptic (poly)spike-wave discharges(SWD/PSDs) in the het Gabrg2Q390X KI mice. Meanwhile, as expected, the manipulating of the POA activity relatively altered NREM sleep and wake periods in both wt and the het Gabrg2Q390X KI mice. Most importantly, the short activation of epileptic cortical neurons alone did not effectively trigger seizure activity in the het Gabrg2Q390X KI mice. In contrast, compared to the wt mice, combined the POA nucleus activation and short activation of the epileptic cortical neurons effectively triggered or suppressed epileptic activity in the het Gabrg2Q390X KI mice, indicating that the POA activity can control the brain state to trigger seizure incidence in the het Gabrg2Q390X KI mice in vivo. In addition, the suppression of POA nucleus activity decreased myoclonic jerks in the Gabrg2Q390XKI mice. Overall, this study discloses an operational mechanism for sleep-dependent seizure incidence in the genetic epilepsy model with the implications for refractory epilepsy. This operational mechanism also underlies myoclonic jerk generation, further with translational implications in seizure treatment for genetic/refractory epileptic patients and with contribution to memory/cognitive deficits in epileptic patients.

neuroscience↗

bioRxiv2023

Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations

Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. One Sentence Summary: Preclinical hematopoietic stem cell gene therapy for the treatment of Pompe disease.

neuroscience↗

bioRxiv2023

Pathogenic CD8 T cell responses are driven by neutrophil-mediated hypoxia in cutaneous leishmaniasis.

Cutaneous leishmaniasis caused by Leishmania parasites exhibits a wide range of clinical manifestations. Although parasites influence disease severity, cytolytic CD8 T cell responses mediate disease. While these responses originate in the lymph node, we find that expression of the cytolytic effector molecule granzyme B is restricted to lesional CD8 T cells in Leishmania- infected mice, suggesting that local cues within inflamed skin induce cytolytic function. Expression of Blimp-1 (Prdm1), a transcription factor necessary for cytolytic CD8 T cell differentiation, is driven by hypoxia within the inflamed skin. Hypoxia is further enhanced by the recruitment of neutrophils that consume oxygen to produce reactive oxygen species, ultimately increasing granzyme B expression in CD8 T cells. Importantly, lesions from cutaneous leishmaniasis patients exhibit hypoxia transcription signatures that correlate with the presence of neutrophils. Thus, targeting hypoxia-driven signals that support local differentiation of cytolytic CD8 T cells may improve the prognosis for patients with cutaneous leishmaniasis, as well as other inflammatory skin diseases where cytolytic CD8 T cells contribute to pathogenesis.

immunology↗

bioRxiv2023

IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods

Integration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based preclinical and clinical Gene Therapy (GT). A handful of groups have developed standardized bioinformatics pipelines to process IS sequencing data, to generate reports, and/or to perform comparative studies across different GT trials. Keeping up with the technological advances in the field of IS analysis, different computational pipelines have been published over the past decade. These pipelines focus on identifying integration sites (IS) from single-read sequencing or paired-end sequencing data either using read-based or using sonication fragment-based methods, but there is a lack of a bioinformatics tool that automatically includes unique molecular identifiers (UMI) for IS abundance estimations and allows comparing multiple quantification methods in one integrated pipeline. Here we present IS-seq a bioinformatics pipeline that can process data from paired-end sequencing of both old restriction sites-based IS collection methods and new sonication-based IS retrieval systems while allowing the selection of different abundance estimation methods, including read-based, Fragment-based and UMI-based systems. We validated the performance of IS-Seq testing it against the most widely used analytical workflow available in the literature (INSPIIRED) and using different scenarios. Lastly, by performing a comprehensive wet-lab assessment of our IS-Seq pipeline we could show that in clinically relevant scenarios, UMI quantification provides better accuracy than the currently most widely used sonication fragment counts as a method for IS abundance estimation.

bioinformatics↗

bioRxiv2022

FRET monitoring of transcription factor activities in living bacteria

Bacteria adapt to the constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor the in situ TF-promoter interactions in living bacteria are lacking. Herein, we developed a whole-cell TF-promoter binding assay based on the intermolecular Forster resonance energy transfer (FRET) between a fluorescent unnatural amino acid CouA which is genetically encoded into defined sites in TFs and the live cell fluorescent nucleic acid stain SYTO 9. We show that this new FRET pair monitors the intricate TF-promoter interactions elicited by various types of signal transduction systems with specificity and sensitivity. Furthermore, the assay is applicable to identify novel modulators of the regulatory systems of interest and monitor TF activities in bacteria colonized in C. elegans. In conclusion, we established a tractable and sensitive TF-promoter binding assay in living bacteria which not only complements currently available approaches for DNA-protein interactions but also provides novel opportunities for functional annotation of bacterial signal transduction systems and studies of the bacteria-host interface.

molecular biology↗