Effect of Animal Stocking Density and Habitat Enrichment on Survival and Vitality of Wild Green Shore Crabs, Carcinus maenas, Maintained in the Laboratory.

The wide geographic distribution, large size and ease of capture has led to decapod crustaceans being used extensively in laboratory experiments. Recently in the United Kingdom decapod crustaceans were listed as sentient beings, resulting in their inclusion in animal care protocols. Ironically, little is known about how captive conditions affect the survival and general condition of wild decapod crustaceans. We used the green shore crab, Carcinus maenas, to investigate the effects of stocking density and shelter on survival and vitality indices during a 6 month period in the laboratory. Neither stocking density nor the presence of shelter affected survival. Stocking density also had no effect on the vitality indices (limb loss, claw strength, BRIX, righting time, leg flare and retraction). The presence of shelter did affect the number of limbs lost and the leg retraction response, but had no effect on the other vitality indices. All vitality indices changed, and mortality increased over time, independent of treatment: this became most apparent after 8 to 11 weeks storage in the laboratory. This decline in condition may have been due to repeated handling of the crabs, rather than the stocking conditions. In support of this, untracked, non-handled (control) individuals sustained a 4% mortality rate compared with 67% mortality in experimental crabs during the 6 month period. Although simple experimental monitoring of crabs with biweekly vitality tests only produced transient short-term stress events, the repeated handling over time apparently led to a cumulative stress and a deterioration in animal health. Bringing wild crustaceans into the laboratory and holding them, even with modest experimental manipulation, may result in high mortality rates. Researchers and animal care committees need to be aware that wild captive invertebrates will respond very differently to laboratory-bred vertebrates, and plan experiments accordingly

The Lothian Birth Cohort 1936: a study to examine influences on cognitive ageing from age 11 to age 70 and beyond

BACKGROUND: Cognitive ageing is a major burden for society and a major influence in lowering people's independence and quality of life. It is the most feared aspect of ageing. There are large individual differences in age-related cognitive changes. Seeking the determinants of cognitive ageing is a research priority. A limitation of many studies is the lack of a sufficiently long period between cognitive assessments to examine determinants. Here, the aim is to examine influences on cognitive ageing between childhood and old age. METHODS/DESIGN: The study is designed as a follow-up cohort study. The participants comprise surviving members of the Scottish Mental Survey of 1947 (SMS1947; N = 70,805) who reside in the Edinburgh area (Lothian) of Scotland. The SMS1947 applied a valid test of general intelligence to all children born in 1936 and attending Scottish schools in June 1947. A total of 1091 participants make up the Lothian Birth Cohort 1936. They undertook: a medical interview and examination; physical fitness testing; extensive cognitive testing (reasoning, memory, speed of information processing, and executive function); personality, quality of life and other psycho-social questionnaires; and a food frequency questionnaire. They have taken the same mental ability test (the Moray House Test No. 12) at age 11 and age 70. They provided blood samples for DNA extraction and testing and other biomarker analyses. Here we describe the background and aims of the study, the recruitment procedures and details of numbers tested, and the details of all examinations. DISCUSSION: The principal strength of this cohort is the rarely captured phenotype of lifetime cognitive change. There is additional rich information to examine the determinants of individual differences in this lifetime cognitive change. This protocol report is important in alerting other researchers to the data available in the cohort

Effects of handling during experimental procedures on stress indices in the green shore crab, Carcinus maenas (L)

Stress due to handling is often an unavoidable feature of experimental investigations. In some cases, appropriate settling times are not considered, and as such, physiological responses caused by handling may become additive with those of experimental treatments. This study investigated the effect of different handling procedures on the acute physiological responses of green shore crab (Carcinus maenas). Handling, such as would occur during transport around a research facility or transfer during experimental procedure, was designated as light (10 min emersion) or severe (10 min emersion with shaking). Oxygen consumption (MO2) and haemolymph glucose and haemolymph L-lactate concentrations were elevated post-handling, the magnitude of the change related to the severity of handling stress. Glucose and L-lactate concentrations peaked within 1 h and returned to basal levels within 6 h, but MO2 remained elevated for 10 h, reflecting the additional energy required to oxidize L-lactate and replenish energy reserves. Differences between light and severe handling treatments showed that vibration (shaking) was a major contributor to the stress response, rather than the experimental emersion. This was confirmed in a second experiment where crabs were handled without emersion, and MO2 remained elevated for 14 h. In this experiment, the most pronounced increase in MO2 and metabolic parameters occurred in crabs that were physically touched and moved rapidly from the holding to experimental tanks. Here the touch, as well as vibration and visual stimuli, provoked a fight-flight response in the crabs. Stress responses were also evident in crabs gently transferred by containers. The fact that transferring crabs with no physical touching and minimal visual and vibrational stimuli still evoked a stress response, albeit less pronounced, supports a recommendation that crustaceans should be left to settle in the apparatus for at least 12 h after handling before experimental procedures are initiated

Exploitation of symmetry in periodic Self-Consistent-Field ab initio calculations: application to large three-dimensional compounds

Symmetry can dramatically reduce the computational cost (running time and memory allocation) of Self-Consistent-Field ab initio calculations for crystalline systems. Crucial for running time is use of symmetry in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the SACO (Symmetry Adapted Crystalline Orbital) basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. We here illustrate the effectiveness of this scheme, following recent advancements in the CRYSTAL code, concerning memory allocation and direct basis set transformation. Quantitative examples are given for large unit cell systems, such as zeolites (all-silica faujasite and silicalite MFI) and garnets (pyrope). It is shown that the full SCF of 3D systems containing up to 576 atoms and 11136 Atomic Orbitals in the cell can be run with a hybrid functional on a single core PC with 500 MB RAM in about 8 h. © 2014 Science China Press and Springer-Verlag Berlin Heidelberg

Predicting badger visits to farm yards and making predictions available to farmers

This is the final version. Available on open access from Public Library of Science via the DOI in this recordData Availability: All relevant data are within the manuscript and its Supporting Information files.The use of agricultural resources or environments by wildlife may result in opportunities for transmission of infections amongst wild animals, livestock and humans. Targeted use of biosecurity measures may therefore reduce disease risks, although this requires practical knowledge of where such measures would be most effective, and effective means of communicating risks so that stakeholders can make informed decisions about such investment. In parts of Europe, the European badger Meles meles may act as a wildlife reservoir for Mycobacterium bovis, the causative agent of bovine tuberculosis, and badger visits to farmyards may provide potential opportunities for transmission of M. bovis to cattle. Biosecurity measures are effective in reducing badger activity in farmyards, although it is unclear which farms should be targeted with such measures. We used cameras to monitor badger activity in 155 farmyards in south west England and Wales, and related variations in the presence and frequency of badger visits to farm characteristics. Badgers were recorded on camera in 40% of farmyards monitored. However, the frequency of visits was highly variable, with badgers recorded on >50% of nights in only 10% of farms. The presence of badgers in farmyards was positively associated with the density of badger setts, the number of feed stores and the number of cattle sheds, and negatively associated with the distance to the nearest active badger sett, the presence of a house/dwelling and the number of cattle housed on the farm. The frequency of visits was negatively associated with the distance to the nearest active badger sett and the number of cattle housed. Models predicted the presence/absence of badgers in farmyards with 73% accuracy (62% sensitivity, 81% specificity, using a cut off value of 0.265). Models could not distinguish between farms with low/high frequency of visits, although farms predicted as having badgers present typically had a higher frequency of visits than those that were not. We developed and present an interactive web based application: the Badger Farm Assessment Tool (BFAT), to allow users to enter the characteristics of a farm and generate a relative risk score describing the likelihood of badger visits.DEFR

A Worldwide Phylogeography for the Human X Chromosome

BACKGROUND: We reasoned that by identifying genetic markers on human X chromosome regions where recombination is rare or absent, we should be able to construct X chromosome genealogies analogous to those based on Y chromosome and mitochondrial DNA polymorphisms, with the advantage of providing information about both male and female components of the population. METHODOLOGY/PRINCIPAL FINDINGS: We identified a 47 Kb interval containing an Alu insertion polymorphism (DXS225) and four microsatellites in complete linkage disequilibrium in a low recombination rate region of the long arm of the human X chromosome. This haplotype block was studied in 667 males from the HGDP-CEPH Human Genome Diversity Panel. The haplotypic diversity was highest in Africa (0.992+/-0.0025) and lowest in the Americas (0.839+/-0.0378), where no insertion alleles of DXS225 were observed. Africa shared few haplotypes with other geographical areas, while those exhibited significant sharing among themselves. Median joining networks revealed that the African haplotypes were numerous, occupied the periphery of the graph and had low frequency, whereas those from the other continents were few, central and had high frequency. Altogether, our data support a single origin of modern man in Africa and migration to occupy the other continents by serial founder effects. Coalescent analysis permitted estimation of the time of the most recent common ancestor as 182,000 years (56,700-479,000) and the estimated time of the DXS225 Alu insertion of 94,400 years (24,300-310,000). These dates are fully compatible with the current widely accepted scenario of the origin of modern mankind in Africa within the last 195,000 years and migration out-of-Africa circa 55,000-65,000 years ago. CONCLUSIONS/SIGNIFICANCE: A haplotypic block combining an Alu insertion polymorphism and four microsatellite markers on the human X chromosome is a useful marker to evaluate genetic diversity of human populations and provides a highly informative tool for evolutionary studies

Bacterial microevolution and the Pangenome

The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history

Challenging fear: Chemical alarm signals are not causing morphology changes in crucian carp (Carassius carassius)

Crucian carp develops a deep body in the presence of chemical cues from predators, which makes the fish less vulnerable to gape-limited predators. The active components originate in conspecifics eaten by predators, and are found in the filtrate of homogenised conspecific skin. Chemical alarm signals, causing fright reactions, have been the suspected inducers of such morphological changes. We improved the extraction procedure of alarm signals by collecting the supernatant after centrifugation of skin homogenates. This removes the minute particles that normally make a filtered sample get turbid. Supernatants were subsequently diluted and frozen into ice-cubes. Presence of alarm signals was confirmed by presenting thawed ice-cubes to crucian carp in behaviour tests at start of laboratory growth experiments. Frozen extracts were added further on three times a week. Altogether, we tested potential body-depth-promoting properties of alarm signals twice in the laboratory and once in the field. Each experiment lasted for a minimum of 50 days. Despite growth of crucian carp in all experiments, no morphology changes were obtained. Accordingly, we conclude that the classical alarm signals that are releasing instant fright reactions are not inducing morphological changes in this species. The chemical signals inducing a body-depth increase are suspected to be present in the particles removed during centrifugation (i.e., in the precipitate). Tissue particles may be metabolized by bacteria in the intestine of predators, resulting in water-soluble cues. Such latent chemical signals have been found in other aquatic organisms, but hitherto not reported in fishe