Robustness of circadian clocks to daylight fluctuations: hints from the picoeucaryote Ostreococcus tauri

The development of systemic approaches in biology has put emphasis on identifying genetic modules whose behavior can be modeled accurately so as to gain insight into their structure and function. However most gene circuits in a cell are under control of external signals and thus quantitative agreement between experimental data and a mathematical model is difficult. Circadian biology has been one notable exception: quantitative models of the internal clock that orchestrates biological processes over the 24-hour diurnal cycle have been constructed for a few organisms, from cyanobacteria to plants and mammals. In most cases, a complex architecture with interlocked feedback loops has been evidenced. Here we present first modeling results for the circadian clock of the green unicellular alga Ostreococcus tauri. Two plant-like clock genes have been shown to play a central role in Ostreococcus clock. We find that their expression time profiles can be accurately reproduced by a minimal model of a two-gene transcriptional feedback loop. Remarkably, best adjustment of data recorded under light/dark alternation is obtained when assuming that the oscillator is not coupled to the diurnal cycle. This suggests that coupling to light is confined to specific time intervals and has no dynamical effect when the oscillator is entrained by the diurnal cycle. This intringuing property may reflect a strategy to minimize the impact of fluctuations in daylight intensity on the core circadian oscillator, a type of perturbation that has been rarely considered when assessing the robustness of circadian clocks

A Geometric Approach to Slot Alignment in Wireless Sensor Networks

Traditionally, slotted communication protocols have employed guard times to delineate and align slots. These guard times may expand the slot duration significantly, especially when clocks are allowed to drift for longer time to reduce clock synchronization overhead. Recently, a new class of lightweight protocols for statistical estimation in wireless sensor networks have been proposed. This new class requires very short transmission durations (jam signals), thus the traditional approach of using guard times would impose significant overhead. We propose a new, more efficient algorithm to align slots. Based on geometrical properties of space, we prove that our approach bounds the slot duration by only a constant factor of what is needed. Furthermore, we show by simulation that this bound is loose and an even smaller slot duration is required, making our approach even more efficient.National Science Foundation (CNS Cybertrust Award 0524477, CNS ITR Award 0205294, EIA RI Award 0202067

Rhythms of Locomotion Expressed by Limulus polyphemus, the American Horseshoe Crab: I. Synchronization by Artificial Tides

Limulus polyphemus, the American horseshoe crab, has an endogenous clock that drives circatidal rhythms of locomotor activity. In this study, we examined the ability of artificial tides to entrain the locomotor rhythms of Limulus in the laboratory. In experiments one and two, the activity of 16 individuals of L. polyphemus was monitored with activity boxes and “running wheels.” When the crabs were exposed to artificial tides created by changes in water depth, circatidal rhythms were observed in animals exposed to 12.4-h “tidal” cycles of either water depth changes (8 of 8 animals) or inundation (7 of 8 animals). In experiment three, an additional 8 animals were exposed to water depth changes under cyclic conditions of light and dark and then monitored for 10 days with no imposed artificial tides. Most animals (5) clearly synchronized their activity to the imposed artificial tidal cycles, and 3 of these animals showed clear evidence of entrainment after the artificial tides were terminated. Overall, these results demonstrate that the endogenous tidal clock that influences locomotion in Limulus can be entrained by imposed artificial tides. In the laboratory, these tidal cues override the influence of light/dark cycles. In their natural habitat, where both tidal and photoperiod inputs are typically always present, their activity rhythms are likely to be much more complex

Minimizing Message Size in Stochastic Communication Patterns: Fast Self-Stabilizing Protocols with 3 bits

This paper considers the basic $\mathcal{PULL}$ model of communication, in which in each round, each agent extracts information from few randomly chosen agents. We seek to identify the smallest amount of information revealed in each interaction (message size) that nevertheless allows for efficient and robust computations of fundamental information dissemination tasks. We focus on the Majority Bit Dissemination problem that considers a population of $n$ agents, with a designated subset of source agents. Each source agent holds an input bit and each agent holds an output bit. The goal is to let all agents converge their output bits on the most frequent input bit of the sources (the majority bit). Note that the particular case of a single source agent corresponds to the classical problem of Broadcast. We concentrate on the severe fault-tolerant context of self-stabilization, in which a correct configuration must be reached eventually, despite all agents starting the execution with arbitrary initial states. We first design a general compiler which can essentially transform any self-stabilizing algorithm with a certain property that uses $\ell$-bits messages to one that uses only $\log \ell$-bits messages, while paying only a small penalty in the running time. By applying this compiler recursively we then obtain a self-stabilizing Clock Synchronization protocol, in which agents synchronize their clocks modulo some given integer $T$, within $\tilde O(\log n\log T)$ rounds w.h.p., and using messages that contain $3$ bits only. We then employ the new Clock Synchronization tool to obtain a self-stabilizing Majority Bit Dissemination protocol which converges in $\tilde O(\log n)$ time, w.h.p., on every initial configuration, provided that the ratio of sources supporting the minority opinion is bounded away from half. Moreover, this protocol also uses only 3 bits per interaction.Comment: 28 pages, 4 figure

In Synch but Not in Step: Circadian Clock Circuits Regulating Plasticity in Daily Rhythms

The suprachiasmatic nucleus (SCN) is a network of neural oscillators that program daily rhythms in mammalian behavior and physiology. Over the last decade much has been learned about how SCN clock neurons coordinate together in time and space to form a cohesive population. Despite this insight, much remains unknown about how SCN neurons communicate with one another to produce emergent properties of the network. Here we review the current understanding of communication among SCN clock cells and highlight a collection of formal assays where changes in SCN interactions provide for plasticity in the waveform of circadian rhythms in behavior. Future studies that pair analytical behavioral assays with modern neuroscience techniques have the potential to provide deeper insight into SCN circuit mechanisms

Philosophical perspectives on time in biology

Although time is a central topic in philosophy, within the philosophy of science discussions of time in biology have largely been neglected. This dissertation argues for the philosophical importance of paying closer attention to the vastly different timescales at which biological phenomenon can be investigated and explained. The importance of timescales for four themes in philosophy of biology is examined: abstractions and manipulations of time in biological practice, metaphysical debates between the mechanistic and process ontology frameworks, the problem of synchronizing molecular clocks and fossil clocks, and reductionism in biology. This dissertation provides the first sustained philosophical examination of the role of time in biology. The first chapter explores how researchers manage the complexities of multiple timescales by abstracting from time physically, procedurally, mathematically, and conceptually. Understanding how researchers abstract from time in their investigations is important for determining what phenomena might be obscured by such practices. Chapter two turns to the debate in philosophy of biology between traditional mechanistic accounts and the new process ontology. While process ontology is an advance, insofar as it has the potential to bring temporal issues to the fore, it is better understood as an epistemological—not metaphysical—framework. A careful consideration of timescales highlights how different metaphysical frameworks can be more epistemologically appropriate in different contexts. The third chapter examines how molecular and fossil clocks are used to measure time in biology. In both cases, researchers use phenomena occurring at one timescale (e.g. DNA mutations) to measure durations across another scale (e.g., the evolutionary occurrence of a last common ancestor). Attempts to synchronize these clocks for key biological events in the deep past pose interesting methodological problems—and suggest new solutions—for how to deal with discordant and interdependent lines of evidence. The final chapter considers the consequences of this analysis of time in biology for debates about reductionism. Reductionism has focused almost exclusively on spatial scales. This chapter shows how a consideration of temporal scales transforms philosophical debates about reductionism in biology and poses new challenges. This dissertation demonstrates the fertility of extending the philosophy of time into the philosophy of biology