Biology subjects

Collins, K. M.

Publications and source records attributed to Collins, K. M..

12 recordsLinked to original sources

bioRxiv2026

Origin-1: a generative AI platform for de novo antibody design against novel epitopes

0Generative artificial intelligence has advanced antibody discovery, yet de novo design of therapeutic antibodies against targets with "zero-prior" epitopes remains a fundamental challenge. We define "zero-prior" epitopes as target sites lacking structural data from any reported antibody-antigen or protein-protein complex involving the target. Here we present Origin-1, a generative AI platform that overcomes this by integrating epitope-conditioned all-atom structure generation, paired complementarity determining region sequence design, and a specialized co-folding-based scoring protocol to select antibody designs predicted to be high-confidence, specific binders with favorable developability. We evaluated Origin-1 on a panel of ten targets selected to have no available protein-protein complex structures and minimal homology ([≤]60% sequence identity) to proteins with known complexes, creating stringent design conditions. In fewer than one hundred design attempts per target, we identified developable, specific antibodies, validated across multiple biophysical and developability assays, for four targets: COL6A3, AZGP1, CHI3L2, and IL36RA, with functional inhibition demonstrated for IL36RA. Cryogenic electron microscopy confirmed the atomic accuracy of our designs, revealing complexes that closely matched the computational models with high structural fidelity (3.0-3.3 [A] resolution; 0.83-0.91 DockQ). Furthermore, we employed AI-guided affinity maturation to optimize a de novo antibody binder against IL36RA, producing functional antagonists with sub-nanomolar affinities and a top EC50 of 12.3 nM. These results demonstrate a framework for targeting epitopes without structural precedent, expanding the programmable therapeutic antibody landscape.

molecular biology↗

bioRxiv2025

Rho signaling promotes cell excitability and synaptic transmission

Gq signaling through Trio RhoGEF and Phospholipase C effectors promotes neurotransmitter release at synapses. Whether activated Rho and Phospholipase C signaling acts through shared or independent pathways remains unclear. We use the egg-laying circuit of C. elegans, which is regulated positively by Gq signaling and negatively by Go signaling, to determine the role of Rho GTPase in G-protein regulation of neural circuit excitability. We previously showed that Trio signals in both the presynaptic Hermaphrodite-Specific command Neurons (HSNs) and the postsynaptic egg-laying vulval muscles they innervate to promote egg laying. Here we show that its effector Rho similarly signals both pre- and post-synaptically. Expression of constitutively active Rho-1(G14V) in either the HSNs or vulval muscles increased their Ca2+ activity and stimulated egg laying. Conversely, reducing Rho signaling in the HSNs via expression of Rho-1(T19N) or C3 transferase expression inhibited HSN Ca2+ activity and egg laying. Animals lacking Rho function in HSN still had vulval muscle Ca2+ activity that supported contraction and egg release, although this Ca2+ activity lacked the enhancement associated with HSN neurotransmitter release, suggesting it was largely driven by stretch-dependent feedback. Together, these results show that Rho signals in both the HSNs and vulval muscles to promote excitability and egg laying. Article SummaryRho-type G-proteins have been extensively studied for their role in neural development, but accumulating evidence points to a role in regulating synaptic transmission and neural circuit activity. Using powerful in vivo imaging and genetic techniques in the nematode Caenorhabditis elegans, the authors show that Rho signals in both presynaptic neurons and postsynaptic muscles to promote circuit activity and behavior. These findings solidify Rho as a key regulator of neurotransmitter signaling.

neuroscience↗

bioRxiv2025

Arsenic Toxicity in the Drosophila Brain at Single Cell Resolution

Arsenic is an ubiquitous environmental toxicant with harmful physiological effects, including neurotoxicity. Modulation of arsenic-induced gene expression in the brain cannot be readily studied in human subjects. However, Drosophila allows quantification of transcriptional responses to neurotoxins at single cell resolution across the entire brain in a single analysis. We exposed Drosophila melanogaster to a chronic dose of NaAsO that does not cause rapid lethality and measured survival and negative geotaxis as a proxy of sensorimotor integration. Females survive longer than males but show earlier physiological impairment in climbing ability. Single-nuclei RNA sequencing showed widespread sex-antagonistic transcriptional responses with modulation of gene expression in females biased toward neuronal cell populations and in males toward glial cells. However, differentially expressed genes implicated similar biological pathways. Evolutionary conservation of fundamental processes of the nervous system enabled us to translate arsenic-induced changes in transcript abundances from the Drosophila model to orthologous human neurogenetic networks.

genetics↗

bioRxiv2024

Osmolarity regulates C. elegans egg-laying behavior via parallel chemosensory and biophysical mechanisms

Animals alter their behavior in response to changes in the environment. Upon encountering hyperosmotic conditions, the nematode worm C. elegans initiates avoidance and cessation of egg-laying behavior. While the sensory pathway for osmotic avoidance is well-understood, less is known about how egg laying is inhibited. We analyzed egg-laying behavior after acute and chronic shifts to and from hyperosmotic media. Animals on 400 mM sorbitol stop laying eggs immediately but then resume [~]3 hours later, after accumulating additional eggs in the uterus. Surprisingly, the hyperosmotic cessation of egg laying did not require known osmotic avoidance signaling pathways. Acute hyperosmotic shifts in hyperosmotic-resistant mutants overproducing glycerol also blocked egg laying, but these animals resumed egg laying more quickly than similarly treated wild-type animals. These results suggest that hyperosmotic conditions disrupt a high-inside hydrostatic pressure gradient required for egg laying. Consistent with this hypothesis, animals adapted to hyperosmotic conditions laid more eggs after acute shifts back to normosmic conditions. Optogenetic stimulation of the HSN egg-laying command neurons in hyper-osmotic treated animals led to fewer and slower egg-laying events, an effect not seen following direct optogenetic stimulation of the postsynaptic vulval muscles. Hyperosmotic conditions also affected egg-laying circuit activity with the vulval muscles showing reduced Ca2+ transient amplitudes and frequency even after egg-laying resumes. Together, these results indicate that hyperosmotic conditions regulate egg-laying via two parallel mechanisms: a sensory pathway that acts to reduce HSN excitability and neurotransmitter release, and a biophysical mechanism where a hydrostatic pressure gradient reports egg accumulation in the uterus. Summary StatementWe find that hyperosmotic conditions inhibit C. elegans egg laying through both a sensory pathway and a separate biophysical pathway affecting a high-inside hydrostatic pressure gradient.

neuroscience↗

bioRxiv2024

The C. elegans uv1 neuroendocrine cells provide direct mechanosensory feedback of vulval opening

Neuroendocrine cells react to physical, chemical, and synaptic signals originating from tissues and the nervous system, releasing hormones that regulate various body functions beyond the synapse. Neuroendocrine cells are often embedded in complex tissues making direct tests of their activation mechanisms and signaling effects difficult to study. In the nematode worm C. elegans, four uterine-vulval (uv1) neuroendocrine cells sit above the vulval canal next to the egg-laying circuit, releasing tyramine and neuropeptides that feedback to inhibit egg laying. We have previously shown uv1 cells are mechanically deformed during egg laying, driving uv1 Ca2+ transients. However, whether egg-laying circuit activity, vulval opening, and/or egg release triggered uv1 Ca2+ activity was unclear. Here we show uv1 responds directly to mechanical activation. Optogenetic vulval muscle stimulation triggers uv1 Ca2+ activity following muscle contraction even in sterile animals. Direct mechanical prodding with a glass probe placed against the worm cuticle triggers robust uv1 Ca2+ activity similar to that seen during egg laying. Direct mechanical activation of uv1 cells does not require other cells in the egg-laying circuit, synaptic or peptidergic neurotransmission, or TRPV and Piezo channels. EGL-19 L-type Ca2+ channels, but not P/Q/N-type or Ryanodine Receptor Ca2+ channels, promote uv1 Ca2+ activity following mechanical activation. L-type channels also facilitate the coordinated activation of uv1 cells across the vulva, suggesting mechanical stimulation of one uv1 cells cross-activates the other. Our findings show how neuroendocrine cells like uv1 report on the mechanics of tissue deformation and muscle contraction, facilitating feedback to local circuits to coordinate behavior. Significance StatementNeuroendocrine cells respond to diverse physical and chemical signals from the body, releasing hormones that control reproduction, gut motility, and fight or flight responses. Neuroendocrine cells are often found embedded in complex tissues, complicating studies of how they are activated. Using the genetic and experimental accessibility of C. elegans, we find the uv1 neuroendocrine cells of the egg-laying motor behavior circuit respond directly to mechanical stimulation and vulval opening. We show that L-type voltage-gated Ca2+ channels facilitate uv1 mechanical activation and also coordinate cell activation across the vulval opening. In contrast to other mechanically activated cells, uv1 activation does not require Piezo or TRPV channels. This work shows how neuroendocrine cells relay critical mechanosensory feedback to circuits that control reproduction.

neuroscience↗

bioRxiv2024

A novel ClpC adaptor protein that functions in the developing Bacillus subtilis spore

Bacterial protein degradation machinery consists of chaperone-protease complexes that play vital roles in bacterial growth and development and have sparked interest as novel antimicrobial targets. ClpC-ClpP (ClpCP) is one such chaperone-protease, recruited by adaptors to specific functions in the model bacterium Bacillus subtilis and other Gram-positive bacteria including the pathogens Staphylococcus aureus and Mycobacterium tuberculosis. Here we have identified a new ClpCP adaptor protein, MdfA ("Metabolic differentiation factor A", formerly YjbA), in a genetic screen for factors that help drive B. subtilis toward metabolic dormancy during spore formation. A knockout of mdfA stimulates gene expression in the developing spore, while aberrant expression of mdfA during vegetative growth is toxic. MdfA binds directly to ClpC to induce its oligomerization and ATPase activity, and this interaction is required for the in vivo effects of mdfA. Finally, a co-crystal structure reveals that MdfA binds to the ClpC N-terminal domain at a location analogous to that on the M. tuberculosis ClpC1 protein where bactericidal cyclic peptides bind. Altogether our data and that of an accompanying study by Riley, Lyda and colleagues support a model in which MdfA induces ClpCP-mediated degradation of metabolic enzymes in the developing spore, helping drive it toward metabolic dormancy.

microbiology↗

bioRxiv2022

Muscle-directed mechanosensory feedback activates egg-laying circuit activity and behavior in C. elegans

Mechanosensory feedback of internal reproductive state drives decisions about when and where to reproduce.1 For instance, stretch in the Drosophila reproductive tract produced by artificial distention or from accumulated eggs regulates the attraction to acetic acid to ensure optimal oviposition.2 How such mechanosensory feedback modulates neural circuits to coordinate reproductive behaviors is incompletely understood. We previously identified a stretch-dependent homeostat that regulates egg laying in Caenorhabditis elegans. Sterilized animals lacking eggs show reduced Ca2+ transient activity in the presynaptic HSN command motoneurons that drive egg-laying behavior while animals forced to accumulate extra eggs show dramatically increased circuit activity that restores egg laying.3 Interestingly, genetic ablation or electrical silencing of the HSNs delays, but does not abolish, the onset of egg laying3-5 with animals recovering vulval muscle Ca2+ transient activity upon egg accumulation.6 Using an acute gonad microinjection technique to mimic changes in pressure and stretch resulting from germline activity and egg accumulation, we find that injection rapidly stimulates Ca2+ activity in both neurons and muscles of the egg-laying circuit. Injection-induced vulval muscle Ca2+ activity requires L-type Ca2+ channels but is independent of presynaptic input. Conversely, injection-induced neural activity is disrupted in mutants lacking the vulval muscles, suggesting bottom-up feedback from muscles to neurons. Direct mechanical prodding activates the vulval muscles, suggesting they are the proximal targets of the stretch-dependent stimulus. Our results show that egg-laying behavior in C. elegans is regulated by a stretch-dependent homeostat that scales postsynaptic muscle responses with egg accumulation in the uterus.

neuroscience↗

bioRxiv2021

Gαq signals via Trio RhoGEF to modulate synaptic transmission in a model serotonin motor circuit in C. elegans

Activated Gq signals through Phospholipase-C{beta} (PLC{beta}) and Trio, a Rho GTPase exchange factor (RhoGEF), but how these distinct effector pathways promote cellular responses to neurotransmitters like serotonin remains poorly understood. We used the egg-laying behavior circuit of C. elegans to determine whether PLC{beta} and Trio mediate serotonin and Gq signaling through independent or related biochemical pathways. Our genetic rescue experiments suggest that PLC{beta} functions in neurons while Trio RhoGEF functions in both neurons and the postsynaptic vulval muscles. While Gq, PLC{beta}, and Trio RhoGEF mutants all fail to lay eggs in response to serotonin, optogenetic stimulation of the serotonin-releasing HSN neurons restores egg laying only in PLC{beta} mutants. PLC{beta} mutants showed vulval muscle Ca2+ transients while strong Gq and Trio RhoGEF mutants had little or no vulval muscle Ca2+ activity. Treatment with phorbol 12-myristate 13-acetate (PMA) that mimics 1,2-diacylglycerol (DAG), a product of PIP2 hydrolysis, rescued egg-laying circuit activity and behavior defects of Gq signaling mutants, suggesting both Phospholipase-C and Rho signaling promote synaptic transmission and egg laying via modulation of DAG levels. DAG activates effectors including UNC-13, however we find that phorbol esters, but not serotonin, stimulate egg laying in unc-13 and PLC{beta} mutants. These results support a model where serotonin signaling through Gq, PLC{beta}, and UNC-13 promote neurotransmitter release, and that serotonin also signals through Gq, Trio RhoGEF, and an unidentified, PMA-responsive effector to promote postsynaptic muscle excitability. Thus, the same neuromodulator serotonin can signal in distinct cells and effector pathways to coordinate activation of a motor behavior circuit.

neuroscience↗

bioRxiv2020

The female-specific VC neurons are mechanically activated, feed-forward motor neurons that facilitate serotonin-induced egg laying in C. elegans

Successful execution of behavior requires coordinated activity and communication between multiple cell types. Studies using the relatively simple neural circuits of invertebrates have helped to uncover how conserved molecular and cellular signaling events shape animal behavior. To understand the mechanisms underlying neural circuit activity and behavior, we have been studying a simple circuit that drives egg-laying behavior in the nematode worm C. elegans. Here we show that the sex-specific, Ventral C (VC) motor neurons are important for vulval muscle contractility and egg laying in response to serotonin. Ca2+ imaging experiments show the VCs are active during times of vulval muscle contraction and vulval opening, and optogenetic stimulation of the VCs promotes vulval muscle Ca2+ activity. Blocking VC neurotransmission inhibits egg laying in response to serotonin and increases the failure rate of egg-laying attempts, indicating that VC signaling facilitates full vulval muscle contraction and opening of the vulva for efficient egg laying. We also find the VCs are mechanically activated in response to vulval opening. Optogenetic stimulation of the vulval muscles is sufficient to drive VC Ca2+ activity and requires muscle contractility, showing the presynaptic VCs and the postsynaptic vulval muscles can mutually excite each other. Together, our results demonstrate that the VC neurons facilitate efficient execution of egg-laying behavior by coordinating postsynaptic muscle contractility in response to serotonin and mechanosensory feedback. Significance StatementMany animal motor behaviors are modulated by the neurotransmitters serotonin and acetylcholine. Such motor circuits also respond to mechanosensory feedback, but how neurotransmitters and mechanoreceptors work together to coordinate behavior is not well understood. We address these questions using the egg-laying circuit in C. elegans where we can manipulate presynaptic neuron and postsynaptic muscle activity in behaving animals while recording circuit responses through Ca2+ imaging. We find that the cholinergic VC motoneurons are important for proper vulval muscle contractility and egg laying in response to serotonin. Muscle contraction also activates the VCs, forming a positive feedback loop that promotes full contraction for egg release. In all, mechanosensory feedback provides a parallel form of modulation that shapes circuit responses to neurotransmitters.

neuroscience↗

bioRxiv2019

Sequence-to-function deep learning frameworks for synthetic biology

While synthetic biology has revolutionized our approaches to medicine, agriculture, and energy, the design of novel circuit components beyond nature-inspired templates can prove itself challenging without well-established design rules. Toehold switches -- programmable nucleic acid sensors -- face an analogous prediction and design bottleneck: our limited understanding of how sequence impacts functionality can require expensive, time-consuming screens for effective switches. Here, we introduce the Sequence-based Toehold Optimization and Redesign Model (STORM), a deep learning architecture that applies gradient ascent to re-engineer poorly-performing toeholds. Based on a dataset of 91,534 toehold switches, we examined convolutional filters and saliency maps of sequences to interpret our sequence-to-function model, identifying hot spots where mutations change toehold effectiveness and features unique to high-performing switches. Our modeling platform provides frameworks for future toehold selection, augmenting our ability to construct potent synthetic circuit components and precision diagnostics, and enabling straightforward translation of this in silico workflow to other circuitries.

synthetic biology↗

bioRxiv2019

Presynaptic Gαo (GOA-1) signaling depresses command neuron excitability to allow for stretch-dependent modulation of egg-laying behavior in C. elegans

Egg laying in the nematode worm Caenorhabditis elegans is a two-state behavior modulated by internal and external sensory input. We have previously shown that homeostatic feedback of embryo accumulation in the uterus regulates bursting activity of the serotonergic HSN command neurons that sustains the egg-laying active state. How sensory feedback of egg release signals to terminate the egg-laying active state is less understood. We find that Go, a conserved Pertussis Toxin-sensitive G protein, signals within HSN to inhibit egg-laying circuit activity and prevent entry into the active state. Go signaling hyperpolarizes HSN, reducing HSN Ca2+ activity and input onto the postsynaptic vulval muscles. Loss of inhibitory Go signaling uncouples presynaptic HSN activity from a postsynaptic, stretch-dependent homeostat, causing precocious entry into the egg-laying active state when only a few eggs are present in the uterus. Feedback of vulval opening and egg release activates the uv1 neuroendocrine cells which release NLP-7 neuropeptides which signal to inhibit egg laying through Go-independent mechanisms in the HSNs and Go-dependent mechanisms in cells other than the HSNs. Thus, neuropeptide and inhibitory Go signaling maintains a bi-stable state of electrical excitability that dynamically controls circuit activity in response to both external and internal sensory input to drive a two-state behavior output.

neuroscience↗

bioRxiv2017

Homeostatic feedback, not early activity, modulates development of two-state patterned activity in the C. elegans egg-laying circuit

Neuron activity accompanies synapse formation and maintenance, but how early circuit activity contributes to behavior development is not well understood. Here, we use the Caenorhabditis elegans egg-laying motor circuit as a model to understand how coordinated cell and circuit activity develops and drives a robust two-state behavior in adults. Using calcium imaging in behaving animals, we find the serotonergic Hermaphrodite Specific Neurons (HSNs) and vulval muscles show rhythmic calcium transients in L4 larvae before eggs are produced. HSN activity in L4 is tonic and lacks the alternating burst-firing/quiescent pattern seen in egg-laying adults. Vulval muscle activity in L4 is initially uncoordinated but becomes synchronous as the anterior and posterior muscle arms meet at HSN synaptic release sites. However, coordinated muscle activity does not require presynaptic HSN input. Using reversible silencing experiments, we show that neuronal and vulval muscle activity in L4 is not required for the onset of adult behavior. Instead, the accumulation of eggs in the adult uterus renders the muscles sensitive to HSN input. Sterilization or acute electrical silencing of the vulval muscles inhibits presynaptic HSN activity, and reversal of muscle silencing triggers a homeostatic increase in HSN activity and egg release that maintains ~12-15 eggs in the uterus. Feedback of egg accumulation depends upon the vulval muscle postsynaptic terminus, suggesting a retrograde signal sustains HSN synaptic activity and egg release. Our results show that egg-laying behavior in C. elegans is driven by a homeostat that scales serotonin motor neuron activity in response to postsynaptic muscle feedback.\n\nSignificance StatementThe functional importance of early, spontaneous neuron activity in synapse and circuit development is not well understood. Here we show that in the nematode C. elegans, the serotonergic Hermaphrodite Specific Neurons (HSNs) and postsynaptic vulval muscles show activity during circuit development, well before the onset of adult behavior. Surprisingly, early activity is not required for circuit development or the onset of adult behavior, and the circuit remains unable to drive egg laying until fertilized embryos are deposited into the uterus. Egg accumulation potentiates vulval muscle excitability, but ultimately acts to promote burst firing in the presynaptic HSNs during which eggs are laid. Our results suggest that mechanosensory feedback acts at three distinct steps to initiate, sustain, and terminate C. elegans egg-laying circuit activity and behavior.

neuroscience↗