Biology subjects

Ramdas, T.

Publications and source records attributed to Ramdas, T..

4 recordsLinked to original sources

bioRxiv2026

An improved Stentor coeruleus genome and time-resolved transcriptomics link cyclic nucleotide-dependent kinase signaling to single-cell habituation

The giant ciliate Stentor coeruleus is a single cell capable of modifying its behavior through experience. When repeatedly disturbed, it undergoes habituation, a simple and widely conserved form of non-associative learning, despite lacking a nervous system. How a single cell achieves such behavioral plasticity at the molecular level remains poorly understood. Here, we report a compact, contiguous macronuclear reference genome for S. coeruleus, substantially improving genome continuity and annotation quality while resolving two successive rounds of whole-genome duplication and extensive lineage-specific gene-family expansion. Anchoring time-resolved transcriptomics to this reference, we profiled pooled RNA from behaviorally tracked cells collected at defined points during a mechanical stimulation paradigm and identified 341 genes with significant temporal expression dynamics during habituation. The dominant transcriptional signature of habituation was the coordinated, sustained up-regulation of a conserved cyclic nucleotide, calcium, and phosphatase signaling module centered on five cGMP-dependent protein kinase (PKG) paralogs together with a voltage-gated calcium channel and a protein phosphatase 2A regulatory subunit, representing conserved intracellular components of the neuronal long-term depression (LTD) pathway. By integrating an improved genome with time-resolved transcriptomics of habituation, this work provides a community resource for Stentor and identifies a conserved signaling program as a candidate molecular framework underlying single-cell habituation.

molecular biology↗

bioRxiv2026

A quantitative portrait of habituation in Stentor coeruleus

Habituation--the decrement in response to a series of stimuli--is a widespread form of learning observed across many organisms, including the unicellular organism Stentor coeruleus. A lesser-known feature of Stentor habituation, shared with animals, is potentiation: faster habituation to a second stimulus series despite partial or complete recovery of responsiveness before that series begins. This suggests that although the first-order habituation memory can decay during the recovery period between the two series, a persistent second-order memory mediates faster relearning. We investigate the response profile of Stentor across a range of stimulation frequencies and recovery periods to identify the timescales at which these memory traces operate. We introduce a statistical framework to infer both population and single-cell learning parameters, allowing us to quantify prior qualitative findings and examine relationships among parameters across cells. Two key findings are that potentiation is frequency-sensitive, and that recovery and potentiation are decoupled, consistent with a serial and hierarchical cascade of leaky integrator units underlying these processes. This quantitative portrait provides a foundation for mechanistic modeling of intracellular memory in Stentor.

cell biology↗

bioRxiv2026

Associative learning in the protozoan Stentor coeruleus

The capacity for associative learning in protozoa has been a matter of longstanding controversy. In a series of Pavlovian conditioning experiments with the ciliate Stentor coeruleus, we show that temporally pairing weak and strong mechanical stimuli results in a transiently enhanced contraction response to the weak stimulus. Control experiments rule out several alternative explanations, such as non-associative sensitization or arousal. Parametric manipulation of the conditioning protocol's temporal structure revealed a systematic dependence of learning on the inter-trial and inter-stimulus intervals, though not in the form classically observed in animals. A simple mathematical model, combining associative learning with habituation, can explain why enhancement is transient, and accurately fits the learning curve at the aggregate level. We conclude that Stentor coeruleus appears capable of associative learning, suggesting an ancient evolutionary origin that preceded the emergence of multicellular nervous systems.

cell biology↗

bioRxiv2025

Storing long-lived memories via molecular error correction: a minimal mathematical model of Crick's memory switch

Cells store information in part by attaching molecular marks to proteins and DNA. But because marks can be randomly removed (e.g., due to ambient phosphatase activity) and added (e.g., due to ambient kinase activity), information encoding may be poor, and in the worst case marks may only store information on the time scale of molecular turnover. We identify a high-level strategy cells use to maintain encoding fidelity beyond the time scale of turnover-- which we call molecular error correction--and find that it closely resembles an underexplored theoretical proposal by Francis Crick. To assess the effectiveness of molecular error correction, we construct and analyze several minimal mathematical models of molecular memory switches. We find that Crick-like error correction provides an efficient way to improve the lifetime of stored memories, especially compared to redundantly encoding information using a large number of molecules, but that it can yield false positives (and hence low information fidelity) when there is ambient marking activity; given these two competing concerns, the optimal level of error correction is moderate rather than arbitrarily high. We also find that combining error correction with redundant encoding can efficiently and robustly produce memories that last between ten and one hundred times longer than the turnover time scale. Our work provides insight regarding how to model and interrogate noisy molecular memory systems, and suggests that error correction is a design principle of performant molecular memory.

systems biology↗