Biology subjects

Rankin, C. H.

Publications and source records attributed to Rankin, C. H..

8 recordsLinked to original sources

bioRxiv2025

Neuropeptides Involved in Elicited Reversal Speed Plasticity in C. elegans During Mechanosensory Habituation

Caenorhabditis elegans respond to mechanosensory taps with brief reversal responses. In past research, speed of the response was averaged over the entire reversal for each tap to analyze reversal speed habituation; however, with this measure, only a modest decrement in speed was observed. Using a more detailed breakdown of reversal speed, we found that speed is most plastic early in the reversal and stable later on. Using this analysis, we found that worms with mutations in neuropeptide genes show reduced speed plasticity during the first second of reversals, indicating peptidergic signaling may be involved in reversal speed plasticity.

animal behavior and cognition↗

bioRxiv2025

The Challenge of Choosing a Negative Control: A Behavioural and Morphological Characterization of Various unc-43 LOF Alleles in the Model Organism C. elegans

Loss-of-Function (LOF) analyses have been pivotal in the discovery of genetic function in biological processes. However, phenotypic variation can occur between different supposedly LOF alleles of the same gene. We investigated the body of research surrounding the nematode ortholog of the Calcium/Calmodulin-dependent protein Kinase II (CAMKII), unc-43, because of its relevance in a large range of biological functions. Our analysis shows that published findings on unc-43 function were obtained from studies using numerous loss-of-function alleles, leading to potential challenges in aligning research findings. We investigated the similarity of these putative loss-of-function (LOF) mutations by using the Multi-Worm Tracker (Swierczek et al., 2011) to phenotype nine LOF alleles across 27 phenotypes, spanning morphology, baseline locomotion and habituation learning and memory. Interestingly, our study reveals significant differences in phenotypes for these LOF alleles. From our data, we have identified the three putative LOF alleles with the most severe and similar phenotypes propose for two of them (n498n1186 and js125) to be regarded as reference alleles to streamline future research on unc-43 function. This data will help future researchers optimise their research of unc-43 function and determine how to choose a strain/strains to use as a negative control.

genetics↗

bioRxiv2024

Ethanol alters mechanosensory habituation in C. elegans by way of the BK potassium channel through a novel mechanism

In this research, we investigated how alcohol modulates the simplest form of learning, habituation, in Caenorhabditis elegans. We used our high throughput Multi-Worm Tracker to conduct a large scale study of more than 21,000 wild-type worms to assess the effects of different doses of alcohol on habituation of the well-characterized tap withdrawal response. We found that the effect of alcohol on habituation of the reversal response to repeated mechanosensory stimuli (taps) differed depending on the component of the reversal response assessed. Furthermore, we discovered that alcohol shifted the dominant response to tap from a backward reversal to a brief forward movement. Because the large conductance potassium (BK) channel has been shown to be important for alcohols effects on behaviour in a variety of organisms, including C. elegans, we investigated whether the C. elegans BK channel ortholog, SLO-1, mediated the effects of alcohol on habituation. We tested several different strains of worms with mutations in slo-1 along with wild-type controls; null mutations in slo-1 made animals resistant to alcohol induced changes in learning. However, a mutation in the putative ethanol binding site on SLO-1 did not disrupt ethanols impact on habituation. Finally, by degrading SLO-1 in different parts of the nervous system we found that SLO-1s function in ethanols impact on habituation is likely distributed throughout the neural circuit that responds to tap. Based on these results, our main conclusions are 1) ethanol is not a general facilitator or inhibitor of habituation but rather a complex modulator, 2) SLO-1 is required for ethanols effect on habituation, 3) ethanol is interacting (directly or indirectly) with SLO-1 through a novel unidentified mechanism to influence response plasticity.

neuroscience↗

bioRxiv2023

A Familial Alzheimers Disease Associated Mutation in Presenilin-1 Mediates Amyloid-Beta Independent Cell Specific Neurodegeneration

Mutations in the presenilin (PS) genes are a predominant cause of familial Alzheimers disease (fAD). An ortholog of PS in the genetic model organism Caenorhabditis elegans (C. elegans) is sel-12. Mutations in the presenilin genes are commonly thought to lead to fAD by upregulating the expression of amyloid beta (A{beta}), however this hypothesis has been challenged by recent evidence. As C. elegans lack amyloid beta (A{beta}), the goal of this work was to examine A{beta}-independent effects of mutations in sel-12 and PS1/PS2 on behaviour and sensory neuron morphology across the lifespan in a C. elegans model. Olfactory chemotaxis experiments were conducted on sel-12(ok2078) loss-of-function mutant worms. Adult sel-12 mutant worms showed significantly lower levels of chemotaxis to odorants compared to wild-type worms throughout their lifespan, and this deficit increased with age. The chemotaxis phenotype in sel-12 mutant worms is rescued by transgenic over-expression of human wild-type PS1, but not the classic fAD-associated variant PS1C410Y, when expression was driven by either the endogenous sel-12 promoter (Psel-12), a pan-neuronal promoter (Primb-1), or by a promoter whose primary expression was in the sensory neurons responsible for the chemotaxis behavior (Psra-6, Podr-10). The behavioural phenotype was also rescued by over-expressing an atypical fAD-linked mutation in PS1 (PS1{Delta}S169) that has been reported to leave the Notch pathway intact. An examination of the morphology of polymodal nociceptive (ASH) neurons responsible for the chemotaxis behavior also showed increased neurodegeneration over time in sel-12 mutant worms that could be rescued by the same transgenes that rescued the behaviour, demonstrating a parallel with the observed behavioral deficits. Thus, we report an A{beta}-independent neurodegeneration in C. elegans that was rescued by cell specific over-expression of wild-type human presenilin.

neuroscience↗

bioRxiv2021

Rapid Assessment of the Temporal Function and Phenotypic Reversibility of Neurodevelopmental Disorder Risk Genes in C. elegans

Hundreds of genes have been implicated in neurodevelopmental disorders. Previous studies have indicated that some phenotypes caused by decreased developmental function of select risk genes can be reversed by restoring gene function in adulthood. However, very few risk genes have been assessed for adult reversibility. We developed a strategy to rapidly assess the temporal requirements and phenotypic reversibility of neurodevelopmental disorder risk gene orthologs using a conditional protein degradation system and machine vision phenotypic profiling in Caenorhabditis elegans. Using this approach, we measured the effects of degrading and re- expressing orthologs of 3 neurodevelopmental risk genes EBF3, BRN3A, and DYNC1H1 across 30 morphological, locomotor, sensory, and learning phenotypes at multiple timepoints throughout development. We found some degree of phenotypic reversibility was possible for each gene studied. However, the temporal requirements of gene function and degree of phenotypic reversibility varied by gene and phenotype. The data reflects the dynamic nature of gene function and the importance of using multiple time windows of degradation and re-expression to understand the many roles a gene can play over developmental time. This work also demonstrates a strategy of using a high-throughput model system to investigate temporal requirements of gene function across a large number of phenotypes to rapidly prioritize neurodevelopmental disorder genes for re-expression studies in other organisms. SUMMARY STATEMENTWe developed a strategy that combines a conditional and reversible protein degradation system with our high-throughput machine vision tracking system to assess the temporal windows of gene function and reversibility of phenotypic disruptions associated with neurodevelopmental disorder risk gene orthologs using C. elegans. Using this approach, we assessed 3 genes (unc- 3, unc-86, and dhc-1) and found that post-embryonic rescue was possible for each gene and each phenotypic feature class assessed. Re-activation of certain genes was able to reverse multiple phenotypic disruptions late into development without inducing novel phenotypes, prioritizing them for further study.

neuroscience↗

bioRxiv2019

Systematic phenomics analysis of ASD-associated genes reveals shared functions and parallel networks underlying reversible impairments in habituation learning

A major challenge facing the genetics of Autism Spectrum Disorders (ASD) is the large and growing number of candidate risk genes and gene variants of unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated genes in vivo. Using our custom machine vision system we quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, and habituation learning in 87 strains each carrying a mutation in an ortholog of an ASD-associated gene. We identified hundreds of novel genotype-phenotype relationships ranging from severe developmental delays and uncoordinated movement to subtle deficits in sensory and learning behaviors. We clustered genes by similarity in phenomic profiles and used epistasis analysis to discover parallel networks centered on CHD8*chd-7 and NLGN3*nlg-1 that underlie mechanosensory hyper-responsivity and impaired habituation learning. We then leveraged our data for in vivo functional assays to gauge missense variant effect. Expression of wild-type NLG-1 in nlg-1 mutant C. elegans rescued their sensory and learning impairments. Testing the rescuing ability of all conserved ASD-associated neuroligin variants revealed varied partial loss-of-function despite proper subcellular localization. Finally, we used CRISPR-Cas9 auxin inducible degradation to determine that phenotypic abnormalities caused by developmental loss of NLG-1 can be reversed by adult expression. This work charts the phenotypic landscape of ASD-associated genes, offers novel in vivo variant functional assays, and potential therapeutic targets for ASD.

neuroscience↗

bioRxiv2018

CRISPR-Cas9 human gene replacement and phenomic characterization in Caenorhabditis elegans to understand the functional conservation of human genes and decipher variants of uncertain significance

Our ability to sequence genomes has vastly surpassed our ability to interpret the genetic variation we discover. This presents a major challenge in the clinical setting, where the recent application of whole exome and whole genome sequencing has uncovered thousands of genetic variants of uncertain significance. Here, we present a strategy for targeted human gene replacement and phenomic characterization based on CRISPR-Cas9 genome engineering in the genetic model organism Caenorhabditis elegans that will facilitate assessment of the functional conservation of human genes and structure-function analysis of disease-associated variants with unprecedented precision. We validate our strategy by demonstrating that direct single-copy replacement of the C. elegans ortholog (daf-18) with the critical human disease-associated gene Phosphatase and Tensin Homolog (PTEN) is sufficient to rescue multiple phenotypic abnormalities caused by complete deletion of daf-18, including complex chemosensory and mechanosenory impairments. In addition, we used our strategy to generate animals harboring a single copy of the known pathogenic lipid phosphatase inactive PTEN variant (PTEN-G129E) and showed that our automated in vivo phenotypic assays could accurately and efficiently classify this missense variant as loss-of-function. The integrated nature of the human transgenes allows for analysis of both homozygous and heterozygous variants and greatly facilitates high-throughput precision medicine drug screens. By combining genome engineering with rapid and automated phenotypic characterization, our strategy streamlines identification of novel conserved gene functions in complex sensory and learning phenotypes that can be used as in vivo functional assays to decipher variants of uncertain significance.

molecular biology↗

bioRxiv2017

CaMK (CMK-1) and O-GlcNAc transferase (OGT-1) modulate mechanosensory responding and habituation in an interstimulus interval-dependent manner in Caenorhabditis elegans

The ability to learn is an evolutionarily conserved adaptation that remains incompletely understood. Genetically tractable model organisms facilitate mechanistic explanations of learning that span genetic, neural circuit, and behavioural levels. Many aspects of neural physiology, including processes that underlie learning (e.g. neurotransmitter release and long-lasting changes in synaptic strength), are regulated by brief and local changes in [m] levels of free intracellular Ca2+. On this scale, changes in [Ca2+] activate many Ca2+-sensors, including the Ca2+/calmodulin-dependent kinases (CaMKs). Here we reveal that the Caenorhabditis elegans ortholog of CaMK1/4, CMK-1, functions in primary sensory neurons to regulate responses to mechanical stimuli and behavioral plasticity, specifically habituation, a conserved form of non-associative learning. The habituation phenotypes of cmk-1 mutants were dependent on interstimulus interval (ISI), such that CMK-1 slows habituation at short ISIs, but promotes it at long ISIs. We predicted potential CaMK phosphorylation targets from catalytic site analysis of the human and C. elegans CaMKs and mutant analysis of these candidates implicated O-linked N-acetylglucosamine (O-GlcNAc) transferase, OGT-1, in mechanosensitivity and learning. Cell specific rescue and knockdown experiments showed that both CMK-1 and OGT-1 function cell autonomously in mechanosensory neurons to modulate learning. Interestingly, despite their similar mutant phenotypes, detailed behavioral analysis of double mutants demonstrated that CMK-1 and OGT-1 act in parallel genetic pathways. Our research identifies CMK-1 and OGT-1 as co-expressed yet independent regulators of mechanosensitivity and learning.

animal behavior and cognition↗