scholarly journals Balance equations can buffer noisy and sustained environmental perturbations of circadian clocks

2010 ◽  
Vol 1 (1) ◽  
pp. 177-186 ◽  
Author(s):  
Mirela Domijan ◽  
David A. Rand
Keyword(s):  
Temperature Compensation ◽  
Regulatory Networks ◽  
Circadian Clocks ◽  
Balance Equations ◽  
New Approach ◽  
Environmental Perturbations ◽  
Environmental Fluctuations ◽  
Free Running ◽  
Temperature Levels

We present a new approach to understanding how regulatory networks such as circadian clocks might evolve robustness to environmental fluctuations. The approach is in terms of new balance equations that we derive. We use it to describe how an entrained clock can buffer the effects of daily fluctuations in light and temperature levels. We also use it to study a different approach to temperature compensation where instead of considering a free-running clock, we study temperature buffering of the phases in a light-entrained clock, which we believe is a more physiological setting.

scholarly journals A circadian clock in a nonphotosynthetic prokaryote

2021 ◽  
Vol 7 (2) ◽  
pp. eabe2086
Author(s):  
Zheng Eelderink-Chen ◽  
Jasper Bosman ◽  
Francesca Sartor ◽  
Antony N. Dodd ◽  
Ákos T. Kovács ◽  
...  
Keyword(s):  
Temperature Compensation ◽  
Temporal Structure ◽  
Bacterial Biofilm ◽  
Circadian Clocks ◽  
Industrial Processes ◽  
Free Living ◽  
Considerable Potential ◽  
Free Running ◽  
Free Running Period ◽  
Constant Dark

Circadian clocks create a 24-hour temporal structure, which allows organisms to occupy a niche formed by time rather than space. They are pervasive throughout nature, yet they remain unexpectedly unexplored and uncharacterized in nonphotosynthetic bacteria. Here, we identify in Bacillus subtilis circadian rhythms sharing the canonical properties of circadian clocks: free-running period, entrainment, and temperature compensation. We show that gene expression in B. subtilis can be synchronized in 24-hour light or temperature cycles and exhibit phase-specific characteristics of entrainment. Upon release to constant dark and temperature conditions, bacterial biofilm populations have temperature-compensated free-running oscillations with a period close to 24 hours. Our work opens the field of circadian clocks in the free-living, nonphotosynthetic prokaryotes, bringing considerable potential for impact upon biomedicine, ecology, and industrial processes.

A New Approach to Bioprocess Control by the Analysis of Regulatory Networks

1997 ◽  
Vol 30 (5) ◽  
pp. 197-202
Author(s):  
Karl Bayer ◽  
Monika Cserjan ◽  
Eberhard Dürrschmid
Keyword(s):  
Regulatory Networks ◽  
New Approach ◽  
Bioprocess Control

scholarly journals Genetic interactions between clock mutations in Neurospora crassa : can they help us to understand complexity?

2001 ◽  
Vol 356 (1415) ◽  
pp. 1717-1724 ◽  
Author(s):  
Louis W. Morgan ◽  
Jerry F. Feldman ◽  
Deborah Bell-Pedersen
Keyword(s):  
Coupled Oscillators ◽  
Temperature Compensation ◽  
White Collar ◽  
Circadian System ◽  
Genetic Interactions ◽  
Circadian Clocks ◽  
Metabolic Effects ◽  
Clock Model ◽  
Number Of Genes ◽  
Single Oscillator

Recent work on circadian clocks in Neurospora has primarily focused on the frequency ( frq ) and white–collar ( wc ) loci. However, a number of other genes are known that affect either the period or temperature compensation of the rhythm. These include the period (no relationship to the period gene of Drosophila ) genes and a number of genes that affect cellular metabolism. How these other loci fit into the circadian system is not known, and metabolic effects on the clock are typically not considered in single–oscillator models. Recent evidence has pointed to multiple oscillators in Neurospora , at least one of which is predicted to incorporate metabolic processes. Here, the Neurospora clock–affecting mutations will be reviewed and their genetic interactions discussed in the context of a more complex clock model involving two coupled oscillators: a FRQ/WC–based oscillator and a ‘ frq –less’ oscillator that may involve metabolic components.

scholarly journals A circadian clock in Saccharomyces cerevisiae

2010 ◽  
Vol 107 (5) ◽  
pp. 2043-2047 ◽  
Author(s):  
Zheng Eelderink-Chen ◽  
Gabriella Mazzotta ◽  
Marcel Sturre ◽  
Jasper Bosman ◽  
Till Roenneberg ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Model ◽  
Circadian Clocks ◽  
Model Systems ◽  
Model Organisms ◽  
Biological Clocks ◽  
Experimental Systems ◽  
Fundamental Biological Process ◽  
Free Running ◽  
And Behavior

Circadian timing is a fundamental biological process, underlying cellular physiology in animals, plants, fungi, and cyanobacteria. Circadian clocks organize gene expression, metabolism, and behavior such that they occur at specific times of day. The biological clocks that orchestrate these daily changes confer a survival advantage and dominate daily behavior, for example, waking us in the morning and helping us to sleep at night. The molecular mechanism of circadian clocks has been sketched out in genetic model systems from prokaryotes to humans, revealing a combination of transcriptional and posttranscriptional pathways, but the clock mechanism is far from solved. Although Saccharomyces cerevisiae is among the most powerful genetic experimental systems and, as such, could greatly contribute to our understanding of cellular timing, it still remains absent from the repertoire of circadian model organisms. Here, we use continuous cultures of yeast, establishing conditions that reveal characteristic clock properties similar to those described in other species. Our results show that metabolism in yeast shows systematic circadian entrainment, responding to cycle length and zeitgeber (stimulus) strength, and a (heavily damped) free running rhythm. Furthermore, the clock is obvious in a standard, haploid, auxotrophic strain, opening the door for rapid progress into cellular clock mechanisms.

scholarly journals Genetic variation and phenotypic plasticity in circadian rhythms in an armed beetle, Gnatocerus cornutus (Tenebrionidae)

2020 ◽  
Vol 130 (1) ◽  
pp. 34-40 ◽  
Author(s):  
Kentarou Matsumura ◽  
Masato S Abe ◽  
Manmohan D Sharma ◽  
David J Hosken ◽  
Taishi Yoshii ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Phenotypic Plasticity ◽  
Circadian Rhythms ◽  
Temperature Effects ◽  
Temperature Compensation ◽  
Biological Rhythms ◽  
Total Activity ◽  
Biological Clocks ◽  
Isofemale Lines ◽  
Free Running

Abstract Circadian rhythms, their free-running periods and the power of the rhythms are often used as indicators of biological clocks, and there is evidence that the free-running periods of circadian rhythms are not affected by environmental factors, such as temperature. However, there are few studies of environmental effects on the power of the rhythms, and it is not clear whether temperature compensation is universal. Additionally, genetic variation and phenotypic plasticity in biological clocks are important for understanding the evolution of biological rhythms, but genetic and plastic effects are rarely investigated. Here, we used 18 isofemale lines (genotypes) of Gnatocerus cornutus to assess rhythms of locomotor activity, while also testing for temperature effects. We found that total activity and the power of the circadian rhythm were affected by interactions between sex and genotype or between sex, genotype and temperature. The males tended to be more active and showed greater increases in activity, but this effect varied across both genotypes and temperatures. The period of activity varied only by genotype and was thus independent of temperature. The complicated genotype–sex–environment interactions we recorded stress the importance of investigating circadian activity in more integrated ways.

scholarly journals Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco

DNA Research ◽  
2020 ◽  
Vol 27 (2) ◽  
Author(s):  
Pingping Liu ◽  
Jie Luo ◽  
Qingxia Zheng ◽  
Qiansi Chen ◽  
Niu Zhai ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Developmental Process ◽  
Pearson Correlation ◽  
Molecular Networks ◽  
Environmental Perturbations ◽  
Carotenoid Metabolism ◽  
Gene Modules

Abstract Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene–metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.

scholarly journals timrit Lengthens Circadian Period in a Temperature-Dependent Manner through Suppression of PERIOD Protein Cycling and Nuclear Localization

1999 ◽  
Vol 19 (6) ◽  
pp. 4343-4354 ◽  
Author(s):  
Akira Matsumoto ◽  
Kenji Tomioka ◽  
Yoshihiko Chiba ◽  
Teiichi Tanimura
Keyword(s):  
Nuclear Localization ◽  
Temperature Compensation ◽  
Feedback Loop ◽  
Gene Dosage ◽  
Dependent Manner ◽  
Temperature Dependent ◽  
Protein Levels ◽  
Free Running ◽  
Free Running Period ◽  
Posttranscriptional Level

ABSTRACT A fundamental feature of circadian clocks is temperature compensation of period. The free-running period of ritsu(timrit ) (a novel allele oftimeless [tim]) mutants is drastically lengthened in a temperature-dependent manner. PER and TIM protein levels become lower in timrit mutants as temperature becomes higher. This mutation reduces per mRNA but not tim mRNA abundance. PER constitutively driven by the rhodopsin1 promoter is lowered in ritmutants, indicating that timrit mainly affects the per feedback loop at a posttranscriptional level. An excess of per + gene dosage can ameliorate allrit phenotypes, including the weak nuclear localization of PER, suggesting that timrit affects circadian rhythms by reducing PER abundance and its subsequent transportation into nuclei as temperature increases.

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