skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Attention:

The NSF Public Access Repository (PAR) system and access will be unavailable from 11:00 PM ET on Friday, July 11 until 2:00 AM ET on Saturday, July 12 due to maintenance. We apologize for the inconvenience.


Title: Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod
Diel rhythms are observed across taxa and are important for maintaining synchrony between the environment and organismal physiology. A striking example of this is the diel vertical migration undertaken by zooplankton, some of which, such as the 5 mm-long copepod Pleuromamma xiphias (P. xiphias), migrate hundreds of meters daily between the surface ocean and deeper waters. Some of the molecular pathways that underlie the expressed phenotype at different stages of this migration are entrained by environmental variables (e.g., day length and food availability), while others are regulated by internal clocks. We identified a series of proteomic biomarkers that vary across ocean DVM and applied them to copepods incubated in 24 h of darkness to assess circadian control. The dark-incubated copepods shared some proteomic similarities to the ocean-caught copepods (i.e., increased abundance of carbohydrate metabolism proteins at night). Shipboard-incubated copepods demonstrated a clearer distinction between night and day proteomic profiles, and more proteins were differentially abundant than in the in situ copepods, even in the absence of the photoperiod and other environmental cues. This pattern suggests that there is a canalization of rhythmic diel physiology in P. xiphias that reflects likely circadian clock control over diverse molecular pathways.  more » « less
Award ID(s):
1829318
PAR ID:
10507435
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
ACS publications
Date Published:
Journal Name:
Journal of Proteome Research
ISSN:
1535-3893
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Biological clocks are evolved time-keeping systems by which organisms rhythmically coordinate physiology within the body, and align it with rhythms in their environment. Clocks are highly sensitive to light and are at the interface of several major endocrine pathways. Worryingly, exposure to artificial-light-at-night (ALAN) is rapidly increasing in ever more extensive parts of the world, with likely impact on wild organisms mediated by endocrine–circadian pathways. In this overview, we first give a broad-brush introduction to biological rhythms. Then, we outline interactions between the avian clock, endocrine pathways, and environmental and internal modifiers. The main focus of this review is on the circadian hormone, melatonin. We summarize information from avian field and laboratory studies on melatonin and its relationships with behaviour and physiology, including often neglected developmental aspects. When exposed to ALAN, birds are highly vulnerable to disruption of behavioural rhythms and of physiological systems under rhythmic control. Several studies suggest that melatonin is likely a key mediator for a broad range of effects. We encourage further observational and experimental studies of ALAN impact on melatonin, across the full functional range of this versatile signalling molecule, as well as on other candidate compounds at the endocrine–circadian interface. This article is part of the theme issue ‘Endocrine responses to environmental variation: conceptual approaches and recent developments’. 
    more » « less
  2. Temporal ecological niche partitioning is an underappreciated driver of speciation. While insects have long been models for circadian biology, the genes and circuits that allow adaptive changes in diel-niches remain poorly understood. We compared gene expression in closely related day- and night-active non-model wild silk moths, with otherwise similar ecologies. Using an ortholog-based pipeline to compare RNA-Seq patterns across two moth species, we find over 25 pairs of gene orthologs showing differential expression. Notably, the genedisco,involved in circadian control, optic lobe and clock neuron development inDrosophila, shows robust adult circadian mRNA cycling in moth heads.Discois highly conserved in moths and has additional zinc-finger domains with specific nocturnal and diurnal mutations. We proposediscoas a candidate gene for the diversification of temporal diel-niche in moths. 
    more » « less
  3. Copepods, which play major roles in marine food webs and biogeochemical cycling, frequently undergo diel vertical migration (DVM), swimming downwards during the day to avoid visual predation and upwards at night to feed. Natural water columns that are stratified with chemical stressors at depth, such as hypoxia and acidification, are increasing with climate change. Understanding behavioral responses of copepods to these stresses—in particular, whether copepods alter their natural migration—is important to anticipating impacts of climate change on marine ecosystems. We conducted laboratory experiments using stratified water columns to measure the effects of bottom water hypoxia and pH on mortality, distribution, and swimming behaviors of the calanoid copepodCalanuspacificus. When exposed to hypoxic (0.65 mg O2l-1) bottom waters, the height ofC.pacificusfrom the bottom increased 20% within hypoxic columns, and swimming speed decreased 46% at the bottom of hypoxic columns and increased 12% above hypoxic waters. When exposed to low pH (7.48) bottom waters, swimming speeds decreased by 8 and 9% at the base of the tanks and above acidic waters, respectively. Additionally, we found a 118% increase in ‘moribund’ (immobile on the bottom) copepods when exposed to hypoxic, but not acidic, bottom waters. Some swimming statistics differed between copepods collected from sites with versus without historical hypoxia and acidity. Observed responses suggest potential mechanisms underlyinginsituchanges in copepod population distributions when exposed to chemical stressors at depth. 
    more » « less
  4. Abstract The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue‐specific clocks connected by mobile signals have previously been found to run at different speeds inArabidopsis thalianatissues. However, tissue variation in circadian clocks in crop species is unknown. In this study, leaf and tuber global gene expression in cultivated potato under cycling and constant environmental conditions was profiled. In addition, we used a circadian‐regulated luciferase reporter construct to study tuber gene expression rhythms. Diel and circadian expression patterns were present among 17.9% and 5.6% of the expressed genes in the tuber. Over 500 genes displayed differential tissue specific diel phases. Intriguingly, few core circadian clock genes had circadian expression patterns, while all such genes were circadian rhythmic in cultivated tomato leaves. Furthermore, robust diel and circadian transcriptional rhythms were observed among detached tubers. Our results suggest alternative regulatory mechanisms and/or clock composition is present in potato, as well as the presence of tissue‐specific independent circadian clocks. We have provided the first evidence of a functional circadian clock in below‐ground storage organs, holding important implications for other storage root and tuberous crops. 
    more » « less
  5. Dunlap, J (Ed.)
    Abstract Circadian rhythms broadly regulate physiological functions by tuning oscillations in the levels of mRNAs and proteins to the 24-h day/night cycle. Globally assessing which mRNAs and proteins are timed by the clock necessitates accurate recognition of oscillations in RNA and protein data, particularly in large omics data sets. Tools that employ fixed-amplitude models have previously been used to positive effect. However, the recognition of amplitude change in circadian oscillations required a new generation of analytical software to enhance the identification of these oscillations. To address this gap, we created the Pipeline for Amplitude Integration of Circadian Exploration suite. Here, we demonstrate the Pipeline for Amplitude Integration of Circadian Exploration suite’s increased utility to detect circadian trends through the joint modeling of the Mus musculus macrophage transcriptome and proteome. Our enhanced detection confirmed extensive circadian posttranscriptional regulation in macrophages but highlighted that some of the reported discrepancy between mRNA and protein oscillations was due to noise in data. We further applied the Pipeline for Amplitude Integration of Circadian Exploration suite to investigate the circadian timing of noncoding RNAs, documenting extensive circadian timing of long noncoding RNAs and small nuclear RNAs, which control the recognition of mRNA in the spliceosome complex. By tracking oscillating spliceosome complex proteins using the PAICE suite, we noted that the clock broadly regulates the spliceosome, particularly the major spliceosome complex. As most of the above-noted rhythms had damped amplitude changes in their oscillations, this work highlights the importance of the PAICE suite in the thorough enumeration of oscillations in omics-scale datasets. 
    more » « less