Life in a dark biosphere: a review of circadian physiology in "arrhythmic" environments

Most of the life with which humans interact is exposed to highly rhythmic and extremely predictable changes in illumination that occur with the daily events of sunrise and sunset. However, while the influence of the sun feels omnipotent to surface dwellers such as ourselves, life on earth is dominated, in terms of biomass, by organisms isolated from the direct effects of the sun. A limited understanding of what life is like away from the sun can be inferred from our knowledge of physiology and ecology in the light biosphere, but a full understanding can only be gained by studying animals from the dark biosphere, both in the laboratory and in their natural habitats. One of the least understood aspects of life in the dark biosphere is the rhythmicity of physiology and what it means to live in an environment of low or no rhythmicity. Here we describe methods that may be used to understand rhythmic physiology in the dark and summarise some of the studies of rhythmic physiology in “arrhythmic” environments, such as the poles, deep sea and caves. We review what can be understood about the adaptive value of rhythmic physiology on the Earth’s surface from studies of animals from arrhythmic environments and what role a circadian clock may play in the dark

Development of the Astyanax mexicanus circadian clock and non-visual light responses

Most animals and plants live on the planet exposed to periods of rhythmic light and dark. As such, they have evolved endogenous circadian clocks to regulate their physiology rhythmically, and non-visual light detection mechanisms to set the clock to the environmental light-dark cycle. In the case of fish, circadian pacemakers are not only present in the majority of tissues and cells, but these tissues are themselves directly light-sensitive, expressing a wide range of opsin photopigments. This broad non-visual light sensitivity exists to set the clock, but also impacts a wide range of fundamental cell biological processes, such as DNA repair regulation. In this context, Astyanax mexicanus is a very intriguing model system with which to explore non-visual light detection and circadian clock function. Previous work has shown that surface fish possess the same directly light entrainable circadian clocks, described above. The same is true for cave strains of Astyanax in the laboratory, though no daily rhythms have been observed under natural dark conditions in Mexico. There are, however, clear alterations in the cave strain light response and changes to the circadian clock, with a difference in phase of peak gene expression and a reduction in amplitude. In this study, we expand these early observations by exploring the development of non-visual light sensitivity and clock function between surface and cave populations. When does the circadian pacemaker begin to oscillate during development, and are there differences between the various strains? Is the difference in acute light sensitivity, seen in adults, apparent from the earliest stages of development? Our results show that both cave and surface populations must experience daily light exposure to establish a larval gene expression rhythm. These oscillations begin early, around the third day of development in all strains, but gene expression rhythms show a significantly higher amplitude in surface fish larvae. In addition, the light induction of clock genes is developmentally delayed in cave populations. Zebrafish embryonic light sensitivity has been shown to be critical not only for clock entrainment, but also for transcriptional activation of DNA repair processes. Similar downstream transcriptional responses to light also occur in Astyanax. Interestingly, the establishment of the adult timing profile of clock gene expression takes several days to become apparent. This fact may provide mechanistic insight into the key differences between the cave and surface fish clock mechanisms

Local impacts of climate change on winter wheat in Great Britain

Under future CMIP5 climate change scenarios for 2050, an increase in wheat yield of about 10% is predicted in Great Britain (GB) as a result of the combined effect of CO2 fertilization and a shift in phenology. Compared to the present day, crops escape increases in the climate impacts of drought and heat stresses on grain yield by developing before these stresses can occur. In the future, yield losses from water stress over a growing season will remain about the same across Great Britain with losses reaching around 20% of potential yield, while losses from drought around flowering will decrease and account for about 9% of water limited yield. Yield losses from heat stress around flowering will remain negligible in the future. These conclusions are drawn from a modelling study based on the response of the Sirius wheat simulation model to local-scale 2050-climate scenarios derived from 19 Global Climate Models from the CMIP5 ensemble at 25 locations representing current or potential wheat-growing areas in GB. However, depending on susceptibility to water stress, substantial interannual yield variation between locations is predicted, in some cases suggesting low wheat yield stability. For this reason, local-scale studies should be performed to evaluate uncertainties in yield prediction related to future weather patterns

PCDDB: new developments at the Protein Circular Dichroism Data Bank

The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. It also includes links for each entry to bioinformatics databases. The data are freely available to accessors either as single files or as complete data bank downloads. The PCDDB has found broad usage by the structural biology, bioinformatics, analytical and pharmaceutical communities, and has formed the basis for new software and methods developments

Communicating the uncertainty in estimated greenhouse gas emissions from agriculture

In an effort to mitigate anthropogenic effects on the global climate system, industrialised countries are required to quantify and report, for various economic sectors, the annual emissions of greenhouse gases from their several sources and the absorption of the same in different sinks. These estimates are uncertain, and this uncertainty must be communicated effectively, if government bodies, research scientists or members of the public are to draw sound conclusions. Our interest is in communicating the uncertainty in estimates of greenhouse gas emissions from agriculture to those who might directly use the results from the inventory. We tested six methods of communication. These were: a verbal scale using the IPCC calibrated phrases such as ‘likely’ and ‘very unlikely’; probabilities that emissions are within a defined range of values; confidence intervals for the expected value; histograms; box plots; and shaded arrays that depict the probability density of the uncertain quantity. In a formal trial we used these methods to communicate uncertainty about four specific inferences about greenhouse gas emissions in the UK. Sixty four individuals who use results from the greenhouse gas inventory professionally participated in the trial, and we tested how effectively the uncertainty about these inferences was communicated by means of a questionnaire. Our results showed differences in the efficacy of the methods of communication, and interactions with the nature of the target audience. We found that, although the verbal scale was thought to be a good method of communication it did not convey enough information and was open to misinterpretation. Shaded arrays were similarly criticised for being open to misinterpretation, but proved to give the best impression of uncertainty when participants were asked to interpret results from the greenhouse gas inventory. Box plots were most favoured by our participants largely because they were particularly favoured by those who worked in research or had a stronger mathematical background. We propose a combination of methods should be used to convey uncertainty in emissions and that this combination should be tailored to the professional grou

Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data

Abstract The effects of spectral magnitude on the calculated secondary structures derived from circular dichroism (CD) spectra were examined for a number of the most commonly used algorithms and reference databases. Proteins with different secondary structures, ranging from mostly helical to mostly ␤-sheet, but which were not components of existing reference databases, were used as test systems. These proteins had known crystal structures, so it was possible to ascertain the effects of magnitude on both the accuracy of determining the secondary structure and the goodness-of-fit of the calculated structures to the experimental data. It was found that most algorithms are highly sensitive to spectral magnitude, and that the goodness-of-fit parameter may be a useful tool in assessing the correct scaling of the data. This means that parameters that affect magnitude, including calibration of the instrument, the spectral cell pathlength, and the protein concentration, must be accurately determined to obtain correct secondary structural analyses of proteins from CD data using empirical methods. Keywords: circular dichroism (CD) spectroscopy; calibration; secondary structure analyses; synchrotron radiation circular dichroism (SRCD) Circular dichroism (CD) spectroscopy can be a valuable method for determining the secondary structures of proteins. However, an accurate analysis relies on (among other things) having the correct magnitude for the spectrum. The determination of the magnitude of a circular dichroism spectrum can be adversely affected by a number of factors including errors in instrument calibration, cell pathlength, and protein concentration. Often these factors are not carefully considered when spectra are reported in the literature or analyzed by empirical secondary structure calculation methods. A number of years ago we examined the effects of magnitude on constrained, unconstrained, and normalized leastsquares methods of analyses of protein secondary structures from CD data (Wallace and Teeters 1987). We demonstrated that all except the normalized methods were highly influenced by the magnitudes of the spectra. Since that time, much more sophisticated algorithms have been developed for such empirical analyses, including variable selection, neural network, and principal component methods Abbreviations: CD, circular dichroism; cCD, conventional circular dichroism; CSA, camphor sulfonic acid; NRMSD, normalized root-meansquare deviation; QAA, quantitative amino acid analysis; SRCD, synchrotron radiation circular dichroism. Article and publication are at http://www.proteinscience.org/cg

Facilitating the elicitation of beliefs for use in Bayesian Belief modelling

Expert opinion is increasingly being used to inform Bayesian Belief Networks, in particular to define the conditional dependencies modelled by the graphical structure. The elicitation of such expert opinion remains a major challenge due to both the quantity of information required and the ability of experts to quantify subjective beliefs effectively. In this work, we introduce a method designed to initialise conditional probability tables based on a small number of simple questions that capture the overall shape of a conditional probability distribution before enabling the expert to refine their results in an efficient way. These methods have been incorporated into a software Application for Conditional probability Elicitation (ACE), freely available at https://github.com/KirstyLHassall/ACE Hassall (2019

Stabilisation of Na,K-ATPase structure by the cardiotonic steroid ouabain

Cardiotonic steroids such as ouabain bind with high affinity to the membrane-bound cation-transporting P-type Na,K-ATPase, leading to complete inhibition of the enzyme. Using synchrotron radiation circular dichroism we show that the enzyme-ouabain complex is less susceptible to thermal denaturation (unfolding) than the ouabain-free enzyme, and this protection is observed with Na,K-ATPase purified from pig kidney as well as from shark rectal glands. It is also shown that detergent-solubilised preparations of Na,K-ATPase are stabilised by ouabain, which could account for the successful crystallisation of Na,K-ATPase in the ouabain-bound form. The secondary structure is not significantly affected by the binding of ouabain. Ouabain appears however, to induce a reorganization of the tertiary structure towards a more compact protein structure which is less prone to unfolding; recent crystal structures of the two enzymes are consistent with this interpretation. These circular dichroism spectroscopic studies in solution therefore provide complementary information to that provided by crystallography

Obtaining more benefits from crop residues as soil amendments by application as chemically heterogeneous mixtures

Crop residues are valuable soil amendments in terms of the carbon and other nutrients they contain, but incorporation of residues does not always translate into increases in nutrient availability, soil organic matter (SOM), soil structure, and overall soil fertility. Studies have demonstrated accelerated decomposition rates of chemically heterogeneous litter mixtures, compared to the decomposition of individual litters, in forest and grassland systems. Mixing high C:N ratio with low C:N ratio amendments may result in greater carbon use efficiency and non-additive benefits in soil properties. We hypothesised that non-additive benefits would accrue from mixtures of low-quality (straw or woodchips) and high-quality (vegetable-waste compost) residues applied before lettuce planting in a full-factorial field experiment. Properties indicative of soil structure and nutrient cycling were used to assess benefits from residue mixtures, including soil respiration, aggregate stability, bulk density, SOM, available and potentially mineralisable N, available P, K and Mg, and crop yield. Soil organic matter and mineral nitrogen levels were significantly and non-additively greater in the straw-compost mixture compared to individual residues, which mitigated the N immobilisation occurring with straw-only applications. Addition of compost significantly increased soil available N, K and Mg levels. Together, these observations suggest that greater nutrient availability improved the ability of decomposer organisms to degrade straw in the straw-compost mixture. We demonstrate that mixtures of crop residues can influence soil properties non-additively. Thus, greater benefits may be achieved by removing, mixing, and re-applying crop residues, than by simply returning them to the soils in situ

Analysis of uncertainties in the estimates of nitrous oxide and methane emissions in the UK’s greenhouse gas inventory for agriculture

The UK’s greenhouse gas inventory for agriculture uses a model based on the IPCC Tier 1 and Tier 2 26 methods to estimate the emissions of methane and nitrous oxide from agriculture. The inventory 27 calculations are disaggregated at country level (England, Wales, Scotland and Northern Ireland). 28 Before now, no detailed assessment of the uncertainties in the estimates of emissions had been 29 done. We used Monte Carlo simulation to do such an analysis. We collated information on the 30 uncertainties of each of the model inputs. The uncertainties propagate through the model and result 31 in uncertainties in the estimated emissions. Using a sensitivity analysis, we found that in England and 32 Scotland the uncertainty in the emission factor for emissions from N inputs (EF1) affected 33 uncertainty the most, but that in Wales and Northern Ireland, the emission factor for N leaching and 34 runoff (EF5) had greater influence. We showed that if the uncertainty in any one of these emission 35 factors is reduced by 50%, the uncertainty in emissions of nitrous oxide reduces by 10%. The 36 uncertainty in the estimate for the emissions of methane emission factors for enteric fermentation 37 in cows and sheep most affected the uncertainty in methane emissions. When inventories are 38 disaggregated (as that for the UK is) correlation between separate instances of each emission factor 39 will affect the uncertainty in emissions. As more countries move towards inventory models with 40 disaggregation, it is important that the IPCC give firm guidance on this topic