The circadian clock provides essential timing information to ensure optimal growth to prevailing external environmental conditions. A major time-setting mechanism (zeitgeber) in clock synchronization is light. Differing light wavelengths, intensities, and photoperiodic duration are processed for the clock-setting mechanism. Many studies on light-input pathways to the clock have focused on Arabidopsis thaliana. Photoreceptors are specific chromic proteins that detect light signals and transmit this information to the central circadian oscillator through a number of different signalling mechanisms. The most well-characterized clock-mediating photoreceptors are cryptochromes and phytochromes, detecting blue, red, and far-red wavelengths of light. Ultraviolet and shaded light are also processed signals to the oscillator. Notably, the clock reciprocally generates rhythms of photoreceptor action leading to so-called gating of light responses. Intermediate proteins, such as Phytochrome interacting factors (PIFs), constitutive photomorphogenic 1 (COP1) and EARLY FLOWERING 3 (ELF3), have been established in signalling pathways downstream of photoreceptor activation. However, the precise details for these signalling mechanisms are not fully established. This review highlights both historical and recent efforts made to understand overall light input to the oscillator, first looking at how each wavelength of light is detected, this is then related to known input mechanisms and their interactions.
ArticleAbstract. Rhythmic processes are found at all biological and ecological scales, and are fun-5 damental to the efficient functioning of living systems in changing environments. The biochemical 6 mechanisms underpinning these rhythms are therefore of importance, especially in the context of 7 anthropogenic challenges such as pollution or changes in climate and land use. Here we develop and 8 test a new method for clustering rhythmic biological data with a focus on circadian oscillations. The 9 method combines locally stationary wavelet time series modelling with functional principal compo-10 nents analysis and thus extracts the time-scale patterns arising in a range of rhythmic data. We 11 demonstrate the advantages of our methodology over alternative approaches, by means of a simula-12 tion study and real data applications, using both a published circadian dataset and a newly generated 13 one. The new dataset records plant response to various levels of stress induced by a soil pollutant, a 14 biological system where existing methods which assume stationarity are shown to be inappropriate. 15Our method successfully clusters the circadian data in an interesting way, thereby facilitating wider 16 ranging analyses of the response of biological rhythms to environmental changes. 17Key words. evolutionary wavelet spectrum, nondecimated wavelet transform, nonstationary 18 processes, unsupervised learning, plant circadian clock 19
Rhythmic data are ubiquitous in the life sciences. Biologists need reliable statistical tests to identify whether a particular experimental treatment has caused a significant change in a rhythmic signal. When these signals display nonstationary behaviour, as is common in many biological systems, the established methodologies may be misleading. Therefore, there is a real need for new methodology that enables the formal comparison of nonstationary processes. As circadian behaviour is best understood in the spectral domain, here we develop novel hypothesis testing procedures in the (wavelet) spectral domain, embedding replicate information when available. The data are modelled as realisations of locally stationary wavelet processes, allowing us to define and rigorously estimate their evolutionary wavelet spectra. Motivated by three complementary applications in circadian biology, our new methodology allows the identification of three specific types of spectral difference. We demonstrate the advantages of our methodology over alternative approaches, by means of a comprehensive simulation study and real data applications, using both published and newly generated circadian datasets. In contrast to the current standard methodologies, our method successfully identifies differences within the motivating circadian datasets, and facilitates wider ranging analyses of rhythmic biological data in general.MSC 2010 subject classifications: Primary 62M10, 60G18; secondary 60-08.
Freezing stress affects all plants from temperate zones to the poles. Global climate change means such freezing events are becoming less predictable. This in turn reduces the ability of plants to predict the approaching low temperatures and cold acclimate. This has consequences for crop yields and distribution of wild plant species. C-repeat binding factors (CBFs) are transcription factors previously shown to play a vital role in the acclimation process of Arabidopsis thaliana, controlling the expression of hundreds of genes whose products are necessary for freezing tolerance. Work in other plant species cements CBFs as key determinants in the trait of freezing tolerance in higher plants. To test the function of CBFs from highly freezing tolerant plants species we cloned and sequenced CBF transcription factors from three Vaccinium species (Vaccinium myrtillus, Vaccinium uliginosum and Vaccinium vitis-idaea) which we collected in the Arctic. We tested the activity of CBF transcription factors from the three Vaccinium species by producing transgenic Arabidopsis lines overexpressing them. Only the Vaccinium myrtillus CBF was able to substantially activate COR (CBF-target) gene expression in the absence of cold. Correspondingly, only the lines expressing the Vaccinium myrtillus CBF were constitutively freezing tolerant. The basis for the differences in potency of the three Vaccinium CBFs was tested by observing cellular localisation and protein levels. All three CBFs were correctly targeted to the nucleus, but Vaccinium uliginosum CBF appeared to be relatively unstable. The reasons for lack of potency for Vaccinium vitis-idaea CBF were not due to stability or targeting, and we speculate that this was due to altered transcription factor function.
Research programme Research projects-Background On 31 December 2019, the National Health Commission of the People's Republic of China notified the World Health Organization (WHO) of a cluster of cases of pneumonia of unknown cause in Wuhan City, Hubei Province, China. Most early cases were associated with visiting Wuhan South China Seafood City market, which reportedly sold meat, poultry, seafood and live animals. probability has been provided, decisions should also be informed by the individual probabilities assigned to each section (Appendix 2) as necessary. Next steps This risk assessment has been used to inform our business guidance and consumer guidance on food and food packaging during the pandemic.
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