Quantification and propagation of errors when converting vertebrate biomineral oxygen isotope data to temperature for palaeoclimate reconstruction

Oxygen isotope analysis of bioapatite in vertebrate remains (bones and teeth) is commonly used to address questions on palaeoclimate from the Eocene to the recent past. Researchers currently use a range of methods to calibrate their data, enabling the isotopic composition of precipitation and the air temperature to be estimated. In some situations the regression method used can significantly affect the resulting palaeoclimatic interpretations. Furthermore, to understand the uncertainties in the results, it is necessary to quantify the errors involved in calibration. Studies in which isotopic data are converted rarely address these points, and a better understanding of the calibration process is needed. This paper compares regression methods employed in recent publications to calibrate isotopic data for palaeoclimatic interpretation and determines that least-squares regression inverted to x=(y-b)/a is the most appropriate method to use for calibrating causal isotopic relationships. We also identify the main sources of error introduced at each conversion stage, and investigate ways to minimise this error. We demonstrate that larger sample sizes substantially reduce the uncertainties inherent within the calibration process: typical uncertainty in temperature inferred from a single sample is at least ±4°C, which multiple samples can reduce to ±1-2°C. Moreover, the gain even from one to four samples is greater than the gain from any further increases. We also show that when converting δ18Oprecipitation to temperature, use of annually averaged data can give significantly less uncertainty in inferred temperatures than use of monthly rainfall data. Equations and an online spreadsheet for the quantification of errors are provided for general use, and could be extended to contexts beyond the specific application of this paper.Palaeotemperature estimation from isotopic data can be highly informative for our understanding of past climates and their impact on humans and animals. However, for such estimates to be useful, there must be confidence in their accuracy, and this includes an assessment of calibration error. We give a series of recommendations for assessing uncertainty when making calibrations of δ18Obioapatite-δ18Oprecipitation-Temperature. Use of these guidelines will provide a more solid foundation for palaeoclimate inferences made from vertebrate isotopic data.We are grateful to the University of Cambridge (AJEP) and the Royal Society (RES) for financial support

Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes-organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem. © 2012 Author(s)

On fractionality of the path packing problem

In this paper, we study fractional multiflows in undirected graphs. A fractional multiflow in a graph G with a node subset T, called terminals, is a collection of weighted paths with ends in T such that the total weights of paths traversing each edge does not exceed 1. Well-known fractional path packing problem consists of maximizing the total weight of paths with ends in a subset S of TxT over all fractional multiflows. Together, G,T and S form a network. A network is an Eulerian network if all nodes in N\T have even degrees. A term "fractionality" was defined for the fractional path packing problem by A. Karzanov as the smallest natural number D so that there exists a solution to the problem that becomes integer-valued when multiplied by D. A. Karzanov has defined the class of Eulerian networks in terms of T and S, outside which D is infinite and proved that whithin this class D can be 1,2 or 4. He conjectured that D should be 1 or 2 for this class of networks. In this paper we prove this conjecture.Comment: 18 pages, 5 figures in .eps format, 2 latex files, main file is kc13.tex Resubmission due to incorrectly specified CS type of the article; no changes to the context have been mad

Partitioning of fungal assemblages across different marine habitats

© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd. Fungi are a highly diverse group of microbes that fundamentally influence the biogeochemistry of the biosphere, but we currently know little about the diversity and distribution of fungi in aquatic habitats. Here we describe shifts in marine fungal community composition across different marine habitats, using targeted pyrosequencing of the fungal Internal Transcribed Spacer (ITS) region. Our results demonstrate strong partitioning of fungal community composition between estuarine, coastal and oceanic samples, with each habitat hosting discrete communities that are controlled by patterns in salinity, temperature, oxygen and nutrients. Whereas estuarine habitats comprised a significant proportion of fungal groups often found in terrestrial habitats, the open ocean sites were dominated by previously unidentified groups. The patterns observed here indicate that fungi are potentially a significant, although largely overlooked, feature of the ocean's microbiota, but greater efforts to characterize marine species are required before the full ecological and biogeochemical importance of marine fungi can be ascertained

Strong but opposing effects of associational resistance and susceptibility on defense phenotype in an African savanna plant

The susceptibility of plants to herbivores can be strongly influenced by the identity, morphology and palatability of neighboring plants. While the defensive traits of neighbors often determine the mechanism and strength of associational resistance and susceptibility, the effect of neighbors on plant defense phenotype remains poorly understood. We used field surveys and a prickle-removal experiment in a semi-arid Kenyan savanna to evaluate the efficacy of physical defenses against large mammalian herbivores in a common understory plant, Solanum campylacanthum. We then quantified the respective effects of spinescent Acacia trees and short-statured grasses on browsing damage and prickle density in S. campylacanthum. We paired measurements of prickle density beneath and outside tree canopies with long-term herbivore-exclusion experiments to evaluate whether associational resistance reduced defense investment by decreasing browsing damage. Likewise, we compared defense phenotype within and outside pre-existing and experimentally created clearings to determine whether grass neighbors increased defense investment via associational susceptibility. Removing prickles increased the frequency of browsing by ~25%, and surveys of herbivory damage on defended leaves suggested that herbivores tended to avoid prickles. As predicted, associational resistance and susceptibility had opposing effects on plant phenotype: individuals growing beneath Acacia canopies (or, analogously, within large-herbivore exclosures) had a significantly lower proportion of their leaves browsed and produced ~ 70–80% fewer prickles than those outside refuges, whereas plants in grass-dominated clearings were more heavily browsed and produced nearly twice as many prickles as plants outside clearings. Our results demonstrate that associational resistance and susceptibility have strong, but opposing, effects on plant defense phenotype, and that variable herbivore damage is a major source of intraspecific variation in defense phenotype in this system

Making sense of information about HPV in cervical screening: a qualitative study

Introducing human papillomavirus (HPV) testing into cervical cancer screening has the potential to change the way that women understand cervical cancer, the psychological impact of abnormal screening results and the likelihood of future participation in screening. The study used in-depth interviews to examine how women make sense of information about HPV in the context of cervical cancer screening. A total of 74 women were recruited following participation in HPV testing. Women varied widely in their beliefs about the aetiology of cervical cancer and its relationship with sexual activity, as well as in their understanding of the sexually transmitted nature of HPV. While some women who understood that HPV is sexually transmitted were able to integrate this into their existing model of cervical cancer, others were shocked by the link between cervical cancer and sex, of which they had been previously unaware. Women were generally reassured to know that HPV is common, has no symptoms, can lie dormant for many years, can clear up on its own and need not raise concerns about transmission to sexual partners. Women's understanding of HPV varied considerably, even after participation in testing. The way in which information is presented to women will be crucial in minimising the negative psychological impact of testing positive and ensuring that participation in screening remains high

Hybrid Rules with Well-Founded Semantics

A general framework is proposed for integration of rules and external first order theories. It is based on the well-founded semantics of normal logic programs and inspired by ideas of Constraint Logic Programming (CLP) and constructive negation for logic programs. Hybrid rules are normal clauses extended with constraints in the bodies; constraints are certain formulae in the language of the external theory. A hybrid program is a pair of a set of hybrid rules and an external theory. Instances of the framework are obtained by specifying the class of external theories, and the class of constraints. An example instance is integration of (non-disjunctive) Datalog with ontologies formalized as description logics. The paper defines a declarative semantics of hybrid programs and a goal-driven formal operational semantics. The latter can be seen as a generalization of SLS-resolution. It provides a basis for hybrid implementations combining Prolog with constraint solvers. Soundness of the operational semantics is proven. Sufficient conditions for decidability of the declarative semantics, and for completeness of the operational semantics are given

Photochemical Spin Dynamics of the Vitamin B12 Derivative, Methylcobalamin

Derivatives of vitamin B12 are six-coordinate cobalt corrinoids found in humans, other animals and micro-organisms. By acting as enzymatic cofactors and photoreceptor chromophores they serve vital metabolic and photoprotective functions. Depending on the context, the chemical mechanisms of the biologically-active derivatives of B12 – methylcobalamin (MeCbl) and 5’-deoxyadenosylcobalamin (AdoCbl) – can be very different from one another. The extent to which this chemistry is tuned by the upper axial ligand, however, is not yet clear. Here, we have used a combination of time-resolved FT-EPR, magnetic field effect experiments and spin dynamic simulations to reveal that the upper axial ligand alone only results in relatively minor changes to the photochemical spin dynamics of B12. By studying the photolysis of MeCbl, we find that, much like for AdoCbl, the initial (or ‘geminate’) radical pairs are born predominantly in the singlet spin-state and thus originate from singlet excited-state precursors. This is in contrast to the triplet radical pairs and precursors proposed previously. Unlike AdoCbl, the extent of geminate recombination is limited following MeCbl photolysis, resulting in significant distortions to the FT-EPR signal caused by polarization from spin-correlated methyl-methyl radical ‘f-pairs’ formed following rapid diffusion. Despite the photophysical mechanism that precedes photolysis of MeCbl showing a wavelength-dependence, the subsequent spin dynamics appear to be largely independent of excitation wavelength, again much like for AdoCbl. Our data finally provide clarity to what in the literature to date has been a confused and contradictory picture. We conclude that, although the upper axial position of MeCbl and AdoCbl does impact their reactivity to some extent, the remarkable biochemical diversity of these fascinating molecules is most likely a result of tuning by their protein environment

RNA-Seq of Huntington's disease patient myeloid cells reveals innate transcriptional dysregulation associated with proinflammatory pathway activation

Innate immune activation beyond the central nervous system is emerging as a vital component of the pathogenesis of neurodegeneration. Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene. The systemic innate immune system is thought to act as a modifier of disease progression; however, the molecular mechanisms remain only partially understood. Here we use RNA-sequencing to perform whole transcriptome analysis of primary monocytes from thirty manifest HD patients and thirty-three control subjects, cultured with and without a proinflammatory stimulus. In contrast with previous studies that have required stimulation to elicit phenotypic abnormalities, we demonstrate significant transcriptional differences in HD monocytes in their basal, unstimulated state. This includes previously undetected increased resting expression of genes encoding numerous proinflammatory cytokines, such as IL6 Further pathway analysis revealed widespread resting enrichment of proinflammatory functional gene sets, while upstream regulator analysis coupled with Western blotting suggests that abnormal basal activation of the NFĸB pathway plays a key role in mediating these transcriptional changes. That HD myeloid cells have a proinflammatory phenotype in the absence of stimulation is consistent with a priming effect of mutant huntingtin, whereby basal dysfunction leads to an exaggerated inflammatory response once a stimulus is encountered. These data advance our understanding of mutant huntingtin pathogenesis, establish resting myeloid cells as a key source of HD immune dysfunction, and further demonstrate the importance of systemic immunity in the potential treatment of HD and the wider study of neurodegeneration