Are textbook references to Darwin close to extinction?

The textbooks used to teach GCE A-level biology 30 years ago tended to concentrate on traditional zoology and botany, with just a passing reference to evolution. As biology established itself as a new discipline, books (and syllabuses) began to take an integrated approach, and evolution became an important theme that helped students to appreciate the interrelationships between plants and animals, cells and molecules, biochemistry and physiology, systematics and genetics, and ecology and behaviour. With the modularisation of modern specifications this theme has all but disappeared from textbooks and a detailed discussion of Darwin and the evidence for evolution has been replaced by perfunctory references to variation and selection and, in some cases, politically correct acknowledgements of creationism

Lithium Intercalation into the Excitonic Insulator Candidate Ta2NiSe5

A new reduced phase derived from the excitonic insulator candidate Ta2NiSe5 has been synthesized via the intercalation of lithium. LiTa2NiSe5 crystallizes in the orthorhombic space group Pmnb (no. 62) with lattice parameters a = 3.50247(3) Å, b = 13.4053(4) Å, c = 15.7396(2) Å, and Z = 4, with an increase of the unit cell volume by 5.44(1)% compared with Ta2NiSe5. Significant rearrangement of the Ta-Ni-Se layers is observed, in particular a very significant relative displacement of the layers compared to the parent phase, similar to that which occurs under hydrostatic pressure. Neutron powder diffraction experiments and computational analysis confirm that Li occupies a distorted triangular prismatic site formed by Se atoms of adjacent Ta2NiSe5 layers with an average Li-Se bond length of 2.724(2) Å. Li-NMR experiments show a single Li environment at ambient temperature. Intercalation suppresses the distortion to monoclinic symmetry that occurs in Ta2NiSe5 at 328 K and that is believed to be driven by the formation of an excitonic insulating state. Magnetometry data show that the reduced phase has a smaller net diamagnetic susceptibility than Ta2NiSe5 due to the enhancement of the temperature-independent Pauli paramagnetism caused by the increased density of states at the Fermi level evident also from the calculations, consistent with the injection of electrons during intercalation and formation of a metallic phase

Calculating association indices in captive animals : controlling for enclosure size and shape

Indices of association are used to quantify and evaluate social affiliation among animals living in groups. Association models assume that physical proximity is an indication of social affiliation; however, individuals seen associating might simply be together by chance. This problem is particularly pronounced in studies of captive animals, whose movements are sometimes severely spatially restricted relative to the wild. Few attempts have been made to estimate – and thus control for – chance encounters based on enclosure size and shape. Using geometric probability and Geographic Information Systems, we investigated the likely effect of chance encounters on association indices within dyads (pairs of animals), when different distance criteria for defining associations are used in shapes of a given area. We developed a simple R script, which can be used to provide a robust estimate of the probability of a chance encounter in a square of any area. We used Monte Carlo methods to determine that this provided acceptable estimates of the probability of chance encounters in rectangular shapes and the shapes of six actual zoo enclosures, and we present an example of its use to correct observed indices of association. Applying this correction controls for differences in enclosure size and shape, and allows association indices between dyads housed in different enclosures to be compared

A Tale of Two Current Sheets

I outline a new model of particle acceleration in the current sheet separating the closed from the open field lines in the force-free model of pulsar magnetospheres, based on reconnection at the light cylinder and "auroral" acceleration occurring in the return current channel that connects the light cylinder to the neutron star surface. I discuss recent studies of Pulsar Wind Nebulae, which find that pair outflow rates in excess of those predicted by existing theories of pair creation occur, and use those results to point out that dissipation of the magnetic field in a pulsar's wind upstream of the termination shock is restored to life as a viable model for the solution of the "$\sigma$" problem as a consequence of the lower wind 4-velocity implied by the larger mass loading.Comment: 17 pages, 6 figures, Invited Review, Proceedings of the "ICREA Workshop on The High-Energy Emission from Pulsars and their Systems", Sant Cugat, Spain, April 12-16, 201

Cytosine-to-Uracil Deamination by SssI DNA Methyltransferase

The prokaryotic DNA(cytosine-5)methyltransferase M.SssI shares the specificity of eukaryotic DNA methyltransferases (CG) and is an important model and experimental tool in the study of eukaryotic DNA methylation. Previously, M.SssI was shown to be able to catalyze deamination of the target cytosine to uracil if the methyl donor S-adenosyl-methionine (SAM) was missing from the reaction. To test whether this side-activity of the enzyme can be used to distinguish between unmethylated and C5-methylated cytosines in CG dinucleotides, we re-investigated, using a sensitive genetic reversion assay, the cytosine deaminase activity of M.SssI. Confirming previous results we showed that M.SssI can deaminate cytosine to uracil in a slow reaction in the absence of SAM and that the rate of this reaction can be increased by the SAM analogue 5’-amino-5’-deoxyadenosine. We could not detect M.SssI-catalyzed deamination of C5-methylcytosine (m5C). We found conditions where the rate of M.SssI mediated C-to-U deamination was at least 100-fold higher than the rate of m5C-to-T conversion. Although this difference in reactivities suggests that the enzyme could be used to identify C5-methylated cytosines in the epigenetically important CG dinucleotides, the rate of M.SssI mediated cytosine deamination is too low to become an enzymatic alternative to the bisulfite reaction. Amino acid replacements in the presumed SAM binding pocket of M.SssI (F17S and G19D) resulted in greatly reduced methyltransferase activity. The G19D variant showed cytosine deaminase activity in E. coli, at physiological SAM concentrations. Interestingly, the C-to-U deaminase activity was also detectable in an E. coli ung+ host proficient in uracil excision repair

Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function.

This is the author accepted manuscript. The final version is available from Oxford University Press via the DOI in this record Data Availability: Transcriptomic data from RNA sequencing is available from the Gene Expression Omnibus (GEO) with identifier GSE199428. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (80) partner repository with the dataset identifier PXD032742.Large-scale genomic studies of schizophrenia implicate genes involved in the epigenetic regulation of transcription by histone methylation and genes encoding components of the synapse. However, the interactions between these pathways in conferring risk to psychiatric illness are unknown. Loss-of-function (LoF) mutations in the gene encoding histone methyltransferase, SETD1A, confer substantial risk to schizophrenia. Among several roles, SETD1A is thought to be involved in the development and function of neuronal circuits. Here, we employed a multi-omics approach to study the effects of heterozygous Setd1a LoF on gene expression and synaptic composition in mouse cortex across five developmental timepoints from embryonic day 14 to postnatal day 70. Using RNA sequencing, we observed that Setd1a LoF resulted in the consistent downregulation of genes enriched for mitochondrial pathways. This effect extended to the synaptosome, in which we found age-specific disruption to both mitochondrial and synaptic proteins. Using large-scale patient genomics data, we observed no enrichment for genetic association with schizophrenia within differentially expressed transcripts or proteins, suggesting they derive from a distinct mechanism of risk from that implicated by genomic studies. This study highlights biological pathways through which SETD1A loss-of-function may confer risk to schizophrenia. Further work is required to determine whether the effects observed in this model reflect human pathology.Medical Research CouncilWellcome Trus

The UK medical education database (UKMED) what is it?:Why and how might you use it?

The development of UKMED has not been directly funded by but has received support from the General Medical Council and Medical Schools Council as well as staff time from all participating organisations.Peer reviewedPublisher PD

An Investigation into the Determining Factors of Zoo Visitor Attendances in UK Zoos

The debate as to which animals are most beneficial to keep in zoos in terms of financial and conservative value is readily disputed; however, demographic factors have also been shown to relate to visitor numbers on an international level. The main aims of this research were: (1) To observe the distribution and location of zoos across the UK, (2) to develop a way of calculating zoo popularity in terms of the species kept within a collection and (3) to investigate the factors related to visitor numbers regarding admission costs, popularity of the collection in terms of the species kept and local demographic factors. Zoo visitor numbers were positively correlated with generated popularity ratings for zoos based on the species kept within a collection and admission prices (Pearson correlation: n = 34, r = 0.268, P = 0.126 and n = 34, r = −0.430, P = 0.011). Animal collections are aggregated around large cities and tourist regions, particularly coastal areas. No relationship between demographic variables and visitor numbers was found (Pearson correlation: n = 34, r = 0.268, P = 0.126), which suggests that the popularity of a zoo's collection relative to the types and numbers of species kept is more indicative of a collection's visitor numbers than its surrounding demographic figures. Zoos should incorporate generating high popularity scores as part of their collection planning strategies, to ensure that they thrive in the future, not only as tourist attractions but also as major conservation organizations

Behind the scenes: a cross-country study into third-party website referencing and the online advertising ecosystem

The ubiquitous nature of the Internet provides an ideal platform for human communication, trade, information sharing and learning. Websites play a central role in these activities as they often act as a key point of interaction for individuals in navigating through cyberspace. In this article, we look beyond the visual interface of websites to consider exactly what occurs when a webpage is visited. In particular, we focus on the various web scripts that are often programmatically executed, to explore the extent to which third-party sites are referenced. Our aim is to study these references and the ecosystem that they create. To gain maximal impact while also allowing for a cross-country comparison, our study is scoped to an assessment of the top 250 sites in the UK, USA, Germany, Russia and Japan. From our analysis, there are various novel contributions of note. These include the empirical identification of a vast ecosystem of third-party information processing sites, especially advertisement networks, and the evidential discovery of a few significant players irrespective of country and locale. Through a user study, we also find that while individuals do have some knowledge of the prevalence of advertisements in websites, their understanding of the variety of activities that occur upon visiting websites, is not widely known. Going forward, we therefore advocate for increased transparency in such activities and the wider online advertisement ecosystem

A new hammer to crack an old nut : interspecific competitive resource capture by plants is regulated by nutrient supply, not climate

Peer reviewedPublisher PD