skip to main content


The NSF Public Access Repository (NSF-PAR) system and access will be unavailable from 10:00 PM ET on Friday, December 8 until 2:00 AM ET on Saturday, December 9 due to maintenance. We apologize for the inconvenience.

Title: Measuring how clocks in single cells of Neurospora crassa communicate in microfluidic devices
Most eukaryotes and cyanobacterial species have a biological clock that allows adaptation to the daily light/dark cycle of the planet. A central problem in the study of the biological clock is understanding the synchro-nization of the stochastic oscillators in different cells and tissues, but this problem is largely unstudied, particularly in the context of circadian rhythms. We developed a novel microfluidic platform to make high-throughput and high-precision measurements of biological clocks on a controlled number of Neurospora crassa (N. crassa) cells. Single cell measurements in this platform enabled us to test whether clocks of individual cells are able to communicate.  more » « less
Award ID(s):
Author(s) / Creator(s):
Date Published:
Journal Name:
MicroTAS 2021
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. null (Ed.)
    Like animals, plants have internal biological clocks that allow them to adapt to daily and yearly changes, such as day-night cycles or seasons turning. Unlike animals, however, plants cannot move when their environment becomes different, so they need to be able to weather these changes by adjusting which genes they switch on and off. To do this, plants keep track of how long days are using external cues such as light or temperature. One of the effects of climate change is that these cues become less reliable, making it harder for plants to adapt to their environment and survive. This is a potential problem for crop species, like Brassica rapa . This plant has many edible forms, including Chinese cabbage, oilseed, pak choi, and turnip. It is also a close relative of the well-studied model plant, Arabidopsis . Since evolving away from Arabidopsis , the genome of B. rapa tripled, meaning it has one, two, or three copies of each gene. This has allowed the extra gene copies to mutate and adapt to different purposes. The question is, what impact has this genome expansion had on the plant's biological clock? One way to find out is to perform RNA-sequencing experiments, which record the genes a plant is using at any one time. Here, Greenham, Sartor et al. report the results of a series of RNA-sequencing experiments performed every two hours across two days. Plants were first exposed to light-dark or temperature cycles and then samples were taken when the plants were in constant light and temperature. This revealed which genes B. rapa turned on and off in response to signals from the internal biological clock. It turns out that the biological clock of B. rapa controls close to three quarters of its genes. These genes showed distinct phases, increasing or decreasing in regular patterns. But the different copies of duplicated and triplicated genes did not necessarily all behave in the same way. Many of the copies had different rhythms, and some increased and decreased in patterns totally opposite to their counterparts. Not only did the daily patterns differ, but responses to stressors like drought were also altered. Comparing these patterns to the patterns seen in Arabidopsis revealed that often, one B. rapa gene behaved just like its Arabidopsis equivalent, while its copies had evolved new behaviors. The different behaviors of the copies of each gene in B. rapa relative to its biological clock allow this plant to grow in different environments with varying temperatures and day lengths. Understanding how these adaptations work opens new avenues of research into how plants detect and respond to environmental signals. This could help to guide future work into targeting genes to improve crop growth and stress resilience. 
    more » « less
  2. Comparisons of high-accuracy optical atomic clocks \cite{Ludlow2015} are essential for precision tests of fundamental physics \cite{Safronova2018}, relativistic geodesy \cite{McGrew2018, Grotti2018, Delva2019}, and the anticipated redefinition of the SI second \cite{Riehle2018}. The scientific reach of these applications is restricted by the statistical precision of interspecies comparison measurements. The instability of individual clocks is limited by the finite coherence time of the optical local oscillator (OLO), which bounds the maximum atomic interrogation time. In this letter, we experimentally demonstrate differential spectroscopy \cite{Hume2016}, a comparison protocol that enables interrogating beyond the OLO coherence time. By phase-coherently linking a zero-dead-time (ZDT) \cite{Schioppo2017} Yb optical lattice clock with an Al+ single-ion clock via an optical frequency comb and performing synchronised Ramsey spectroscopy, we show an improvement in comparison instability relative to our previous result \cite{network2020frequency} of nearly an order of magnitude. To our knowledge, this result represents the most stable interspecies clock comparison to date. 
    more » « less
  3. Biological systems have a variety of time-keeping mechanisms ranging from molecular clocks within cells to a complex interconnected unit across an entire organism. The suprachiasmatic nucleus, comprising interconnected oscillatory neurons, serves as a master-clock in mammals. The ubiquity of such systems indicates an evolutionary benefit that outweighs the cost of establishing and maintaining them, but little is known about the process of evolutionary development. To begin to address this shortfall, we introduce and analyse a new evolutionary game theoretic framework modelling the behaviour and evolution of systems of coupled oscillators. Each oscillator is characterized by a pair of dynamic behavioural dimensions, a phase and a communication strategy, along which evolution occurs. We measure success of mutations by comparing the benefit of synchronization balanced against the cost of connections between the oscillators. Despite the simple set-up, this model exhibits non-trivial behaviours mimicking several different classical games—the Prisoner’s Dilemma, snowdrift games, coordination games—as the landscape of the oscillators changes over time. Across many situations, we find a surprisingly simple characterization of synchronization through connectivity and communication: if the benefit of synchronization is greater than twice the cost, the system will evolve towards complete communication and phase synchronization. 
    more » « less
  4. Many living organisms track the 24-hour cycle of day and night via collections of proteins and other molecules that together act like an internal clock. These clocks, also known as circadian clocks, help these organisms to predict regular changes in their environment, like light and temperature, and adjust their activities according to the time of day. Plants use circadian clocks to predict, for example, when dawn will occur and get ready to harness sunlight to fuel their growth. A plant called Arabidopsis thaliana has a light-sensitive protein called ZEITLUPE (or ZTL for short) that helps it keep its circadian clock in sync with the cycle of night and day. Previous studies have shown that light activates this protein causing part of it to change shape and then revert back after a period of about an hour and a half. However, it was unclear if this timing was important for ZEITLUPE to allow plants to keep track of time. To help answer this question, Pudasaini et al. set out to identify a specific chemical event behind ZEITLUPE’s changes in shape. A chemical bond forms when light activates ZEITLUPE, and it turns out that how long this bond lasts before it breaks plays an important role in allowing plants to maintain a 24-hour circadian clock. This chemical bond controls the shape changes that guide the protein’s activities and, when Pudasaini et al. modified ZEITLUPE so that it took much longer for this bond to break, they could tune how fast the plant’s internal clocks run. In essence, the time between the bond forming and breaking breaks acts like a countdown on a stopwatch, and it must be precisely timed to keep the clock in pace with the environment. These findings improve our understanding of how light can regulate an internal biological clock. This improved understanding could, in the future, allow researchers to manipulate how plants and other organisms respond to their environment. This in turn could change how these organisms develop, and how much they grow. As such, extending these findings into agricultural crops may one day lead to new ways to increase crop yields. 
    more » « less
  5. Abstract

    DNA methylation-based biomarkers of aging have been developed for humans and many other mammals and could be used to assess how stress factors impact aging. Deer mice (Peromyscus) are long-living rodents that have emerged as an informative model to study aging, adaptation to extreme environments, and monogamous behavior. In the present study, we have undertaken an exhaustive, genome-wide analysis of DNA methylation inPeromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We describe DNA methylation-based estimators of age for different species of deer mice based on novel DNA methylation data generated on highly conserved mammalian CpGs measured with a custom array. The multi-tissue epigenetic clock for deer mice was trained on 3 tissues (tail, liver, and brain). Two human-Peromyscusclocks accurately measure age and relative age, respectively. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Overall, this study provides a first step towards studying the epigenetic correlates of monogamous behavior and adaptation to high altitude inPeromyscus. The human-Peromyscusepigenetic clocks are expected to provide a significant boost to the attractiveness ofPeromyscusas a biological model.

    more » « less