arXiv subjects

Thomas S. Shimizu

Publications and source records attributed to Thomas S. Shimizu.

4 recordsLinked to original sources

arXiv2024

Statistics of C. elegans turning behavior reveals optimality under biasing constraints

Animal locomotion is often subject to constraints arising from anatomical/physiological asymmetries. We use the nematode C.~elegans as a minimal model system to ask whether such constraints might shape locomotion patterns optimized during evolution. We focus on turning behaviours in two contrasting environmental contexts: (i) random exploration in the absence of strong stimuli and (ii) acute avoidance (escape) navigation upon encountering a strong aversive stimulus. We characterise the full repertoire of reorientation behaviours, including gradual reorientations and various posturally distinct sharp turns. During exploration, our measurements and theoretical modelling indicate that orientation fluctuations on short timescales are, on average, optimized to compensate the constraining gradual turn bias on long timescales. During escape, our data suggests that the reorientation is controlled not by an analog logic of continuous turn-amplitude modulations, but rather through the digital logic of selecting discrete turn types, leading to a symmetric escape performance despite strongly asymmetric turning biases.

q-bio.NC↗

arXiv2020

Functional modules from variable genes: Leveraging percolation to analyze noisy, high-dimensional data

While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to variation of both biological and experimental origin. Complimentary to perturbation approaches, we extract functionally related groups of genes by analyzing the standing variation within a sampled population. To distinguish biologically meaningful patterns from uninterpretable noise, we focus on correlated variation and develop a novel density-based clustering approach that takes advantage of a percolation transition generically arising in random, uncorrelated data. We apply our approach to two contrasting RNA sequencing data sets that sample individual variation -- across single cells of fission yeast and whole animals of C. elegans worms -- and demonstrate robust applicability and versatility in revealing correlated gene clusters of diverse biological origin, including cell cycle phase, development/reproduction, tissue-specific functions, and feeding history. Our technique exploits generic features of noisy high-dimensional data and is applicable, beyond gene expression, to feature-rich data that sample population-level variability in the presence of noise.

q-bio.GN↗

arXiv2019

Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species

A quantitative understanding of organism-level behavior requires predictive models that can capture the richness of behavioral phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here we investigate the motile behavior of nematodes at the level of their translational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioral repertoire by measuring motile trajectories of the canonical lab strain $C. elegans$ N2 as well as wild strains and distant species. We focus on trajectory dynamics over timescales spanning the transition from ballistic (straight) to diffusive (random) movement and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bearing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioral control and a trade-off between exploration and exploitation. The distribution of phenotypes along this primary mode of variation reveals that not only the mean but also the variance varies considerably across strains, suggesting that these nematode lineages employ contrasting ``bet-hedging'' strategies for foraging.

q-bio.NC↗

arXiv2013

Salmonella chemoreceptors McpB and McpC mediate a repellent response to L-cystine: a potential mechanism to avoid oxidative conditions

Chemoreceptors McpB and McpC in Salmonella enterica have been reported to promote chemotaxis in LB motility-plate assays. Of the chemicals tested as potential effectors of these receptors, the only response was towards L-cysteine and its oxidized form, L-cystine. Although enhanced radial migration in plates suggested positive chemotaxis to both amino acids, capillary assays failed to show an attractant response to either, in cells expressing only these two chemoreceptors. In vivo fluorescence resonance energy transfer (FRET) measurements of kinase activity revealed that in wild-type bacteria, cysteine and cystine are chemoeffectors of opposing sign, the reduced form being a chemoattractant and the oxidized form a repellent. The attractant response to cysteine was mediated primarily by Tsr, as reported earlier for E. coli. The repellent response to cystine was mediated by McpB / C. Adaptive recovery upon cystine exposure required the methyl-transferase/-esterase pair, CheR / CheB, but restoration of kinase activity was never complete (i.e. imperfect adaptation). We provide a plausible explanation for the attractant-like responses to both cystine and cysteine motility plates, and speculate that the opposing signs of response to this redox pair might afford Salmonella a mechanism to gauge and avoid oxidative environments.

q-bio.MN↗