Water vole (Arvicola amphibius) abundance in grassland habitats of Glasgow

Water vole (Arvicola amphibius) populations have undergone a serious decline throughout the UK, and yet a stronghold of these small mammals is found in the greater Easterhouse area of Glasgow. The water voles in this location are mostly fossorial, living a largely subterranean existence in grasslands, rather than the more typical semi-aquatic lifestyle in riparian habitats. In this study, we carried out capture-mark-recapture surveys on water voles at two sites: Cranhill Park and Tillycairn Drive. We made a total of 62 captures including retraps, and the resulting population estimates were 78 individuals (95% confidence interval 41-197) for Cranhill Park and 42 individuals (20-141) for Tillycairn Drive. From these figures we estimated a population density of water voles, which appeared to be higher than other reports from the UK. Despite the difficulties of sampling in urban environments that resulted in relatively low capture rates, our data suggest that the greater Easterhouse area of Glasgow holds water voles at relatively high population densities. These results will inform future conservation in the City of Glasgow and surrounding areas, as well as raise awareness of important water vole populations in urban environments

Pastoral systems research in sub-Saharan Africa

Presents a collection of conference papers defining pastoral systems research; the survey and diagnostic phase of pastoral systems research; ILCA's experience in remote sensing techniques and aerial surveys; survey of vegetation resources; livestock productivity and animal nutrition; pastoral production strategies, wealth effects, household studies, and labour data collection as well as livestock marketing studies. Includes papers on possibilities for improvement in pastoral production; procedures relevant to pastoral systems research, and findings of case studies from Nigeria and Niger highlighting the experimental and testing procedures relevant to pastoral systems research

Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

Understanding the genesis of the block haplotype structure of the genome is a major challenge. With the completion of the sequencing of the Human Genome and the initiation of the HapMap project the concept that the chromosomes of the mammalian genome are a mosaic, or patchwork, of conserved extended block haplotype sequences is now accepted by the mainstream genomics research community. Ancestral Haplotypes (AHs) can be viewed as a recombined string of smaller Polymorphic Frozen Blocks (PFBs). How have such variant extended DNA sequence tracts emerged in evolution? Here the relevant literature on the problem is reviewed from various fields of molecular and cell biology particularly molecular immunology and comparative and functional genomics. Based on our synthesis we then advance a testable molecular and cellular model. A critical part of the analysis concerns the origin of the strand biased mutation signatures in the transcribed regions of the human and higher primate genome, A-to-G versus T-to-C (ratio ~1.5 fold) and C-to-T versus G-to-A (≥1.5 fold). A comparison and evaluation of the current state of the fields of immunoglobulin Somatic Hypermutation (SHM) and Transcription-Coupled DNA Repair focused on how mutations in newly synthesized RNA might be copied back to DNA thus accounting for some of the genome-wide strand biases (e.g., the A-to-G vs T-to-C component of the strand biased spectrum). We hypothesize that the genesis of PFBs and extended AHs occurs during mutagenic episodes in evolution (e.g., retroviral infections) and that many of the critical DNA sequence diversifying events occur first at the RNA level, e.g., recombination between RNA strings resulting in tandem and dispersed RNA duplications (retroduplications), RNA mutations via adenosine-to-inosine pre-mRNA editing events as well as error prone RNA synthesis. These are then copied back into DNA by a cellular reverse transcription process (also likely to be error-prone) that we have called "reverse transcription-mediated long DNA conversion." Finally we suggest that all these activities and others can be envisaged as being brought physically under the umbrella of special sites in the nucleus involved in transcription known as "transcription factories."

The geochemistry of sea-bed sediments of the United Kingdom Continental Shelf : the North Sea, Hebrides and West Shetland shelves, and the Malin-Hebrides sea area

The sea area around the United Kingdom is used for a wide range of human activities all of which have a significant impact on the marine environment. The naturally-occurring concentrations of chemical elements in sea-bed sediments may be enhanced by contaminants introduced by input from rivers and the atmosphere and by more localised sources arising from shipping operations, exploitation of oil and gas, and by direct discharges from drainage systems, sewage outfalls, effluents from industry and waste' disposal at sea. It is therefore important to identify components of sea-floor sediments which are due to the rocks or older sediments from which they are derived, and those which are introduced into the environment. This report presents regional geochemical data for a variety of sediment types occurring in a wide range of environments. Samples have been collected offshore of the eastern coast of the UK where major river systems which drain heavily populated and industrialised catchment areas, such as the Thames, Humber and Tyne, flow into the North Sea, and on the shelf west of Scotland where man's activities have had much less impact. The data presented here provide a baseline for chemical element concentrations in sea-bed sediments against which future work may be assessed. It should therefore be of significance to a diverse range of interests including pollution control, fishing, natural resources, nature conservation, shipping, tourism, recreation, and waste disposal management. In addition the information will be of use to geologists in identifying the source of sea-bed sediments and the underlying glacial deposits

Phytoplankton dynamics from the Cambrian Explosion to the onset of the Great Ordovician Biodiversification Event: a review of Cambrian acritarch diversity

Most early Palaeozoic acritarchs are thought to represent a part of the marine phytoplankton and so constituted a significant element at the base of the marine trophic chain during the ‘Cambrian Explosion’ and the subsequent ‘Great Ordovician Biodiversification Event.’ Cambrian acritarch occurrences have been recorded in a great number of studies. In this paper, published data on Cambrian acritarchs are assembled in order to reconstruct taxonomic diversity trends that can be compared with the biodiversity of marine invertebrates. We compile a database and calculate various diversity indices at global and regional (i.e. Gondwana or Baltica) scales. The stratigraphic bins applied are at the level of the ten Cambrian stages, or of fourteen commonly used biozones in a somewhat higher resolved scheme. Our results show marked differences between palaeogeographical regions. They also indicate limitations of the data and a potential sampling bias, as the taxonomic diversity indices of species are significantly correlated with the number of studies per stratigraphic bin. The total and normalized diversities of genera are not affected in the same way. The normalized genus diversity curves show a slow but irregular rise over the course of the Cambrian. These also are the least biased. A radiation of species and to a lesser extent of genera in the ‘lower’ Cambrian Series 2 appears to mirror the ‘Cambrian Explosion’ of metazoans. This radiation, not evident on Gondwana, is followed by a prominent low in species diversity in the upper Series 3 and lower Furongian. Highest diversities are reached globally, and on both Baltica and Gondwana, in the uppermost Cambrian Stage 10, more precisely in the Peltura trilobite Zone, preceding a substantial phase of acritarch species extinction below and at the Cambrian/Ordovician boundary. Nearly all the genera present in Stage 10 survived into the Ordovician. The forms that emerged during the Cambrian therefore became the foundation for the more rapid radiation of acritarchs during the ‘Great Ordovician Biodiversification Event’

Searching for Signatures of Cosmic Superstrings in the CMB

Because cosmic superstrings generically form junctions and gauge theoretic strings typically do not, junctions may provide a signature to distinguish between cosmic superstrings and gauge theoretic cosmic strings. In cosmic microwave background anisotropy maps, cosmic strings lead to distinctive line discontinuities. String junctions lead to junctions in these line discontinuities. In turn, edge detection algorithms such as the Canny algorithm can be used to search for signatures of strings in anisotropy maps. We apply the Canny algorithm to simulated maps which contain the effects of cosmic strings with and without string junctions. The Canny algorithm produces edge maps. To distinguish between edge maps from string simulations with and without junctions, we examine the density distribution of edges and pixels crossed by edges. We find that in string simulations without Gaussian noise (such as produced by the dominant inflationary fluctuations) our analysis of the output data from the Canny algorithm can clearly distinguish between simulations with and without string junctions. In the presence of Gaussian noise at the level expected from the current bounds on the contribution of cosmic strings to the total power spectrum of density fluctuations, the distinction between models with and without junctions is more difficult. However, by carefully analyzing the data the models can still be differentiated.Comment: 15 page

The 21 cm Signature of Shock Heated and Diffuse Cosmic String Wakes

The analysis of the 21 cm signature of cosmic string wakes is extended in several ways. First we consider the constraints on $G\mu$ from the absorption signal of shock heated wakes laid down much later than matter radiation equality. Secondly we analyze the signal of diffuse wake, that is those wakes in which there is a baryon overdensity but which have not shock heated. Finally we compare the size of these signals compared to the expected thermal noise per pixel which dominates over the background cosmic gas brightness temperature and find that the cosmic string signal will exceed the thermal noise of an individual pixel in the Square Kilometre Array for string tensions $G\mu > 2.5 \times 10^{-8}$.Comment: 10 pages, 4 figures, Appendix added, version published in JCA

Magnetic ordering of Mn sublattice, dense Kondo lattice behavior of Ce in (RPd3)8Mn (R = La, Ce)

We have synthesized two new interstitial compounds (RPd3)8Mn (R = La and Ce). The Mn ions present in "dilute" concentration of just 3 molar percent form a sublattice with an unusually large Mn-Mn near neighbor distance of ~ 85 nm. While the existence of (RPd3)8M (where M is a p-block element) is already documented in the literature, the present work reports for the first time the formation of this phase with M being a 3d element. In (LaPd3)8Mn, the Mn sub-lattice orders antiferromagnetically as inferred from the peaks in low-field magnetization at 48 K and 23 K. The latter peak progressively shifts towards lower temperatures in increasing magnetic field and disappears below 1.8 K in a field of ~ 8 kOe. On the other hand in (CePd3)8Mn the Mn sublattice undergoes a ferromagnetic transition around 35 K. The Ce ions form a dense Kondo-lattice and are in a paramagnetic state at least down to 1.5 K. A strongly correlated electronic ground state arising from Kondo effect is inferred from the large extrapolated value of C/T = 275 mJ/Ce-mol K^2 at T = 0 K. In contrast, the interstitial alloys RPd3Mnx (x = 0.03 and 0.06), also synthesized for the first time, have a spin glass ground state due to the random distribution of the Mn ions over the available "1b" sites in the parent RPd3 crystal lattice.Comment: 18 figures and 20 pages of text documen

Gammaherpesvirus infection modulates the temporal and spatial expression of SCGB1A1 (CCSP) and BPIFA1 (SPLUNC1) in the respiratory tract

Murine γ-herpesvirus 68 (MHV-68) infection of Mus musculus-derived strains of mice is an established model of γ-herpesvirus infection. We have previously developed an alternative system using a natural host, the wood mouse (Apodemus sylvaticus), and shown that the MHV-68 M3 chemokine-binding protein contributes significantly to MHV-68 pathogenesis. Here we demonstrate in A. sylvaticus using high-density micro-arrays that M3 influences the expression of genes involved in the host response including Scgb1a1 and Bpifa1 that encode potential innate defense proteins secreted into the respiratory tract. Further analysis of MHV-68-infected animals showed that the levels of both protein and RNA for SCGB1A1 and BPIFA1 were decreased at day 7 post infection (p.i.) but increased at day 14 p.i. as compared with M3-deficient and mock-infected animals. The modulation of expression was most pronounced in bronchioles but was also present in the bronchi and trachea. Double staining using RNA in situ hybridization and immunohistology demonstrated that much of the BPIFA1 expression occurs in club cells along with SCGB1A1 and that BPIFA1 is stored within granules in these cells. The increase in SCGB1A1 and BPIFA1 expression at day 14 p.i. was associated with the differentiation of club cells into mucus-secreting cells. Our data highlight the role of club cells and the potential of SCGB1A1 and BPIFA1 as innate defense mediators during respiratory virus infection