Computing inbreeding coefficients and the inverse numerator relationship matrix in large populations of honey bees

The inbreeding coefficients are considered in breeding decisions, and the inverse numerator relationship matrix A ^?1 is a prerequisite for breeding value estimation. Polyandry and haploid males are among the specifics of relationships between honey bees. Brascamp and Bijma (2014) averaged out the manifold possible relationships among honey bees that appear to have the same parents in a pedigree and assigned a single entry in A to animals that behave as a unit, for example, the workers of a hive. Their methods of calculation connected full‐sibs in the variance matrix of the Mendelian sampling terms D , via nonzero off‐diagonal elements. This impedes the inversion of A and the closely connected calculation of inbreeding coefficients, because efficient algorithms for this task take D to be a diagonal matrix. Memory limitations necessitate their use for large data sets. We adapted the quickest of them to the block diagonal matrix D , that is postulated for the honey bee. To our knowledge, the presented algorithm is the first one that facilitates the method of Brascamp and Bijma (2014) on large data sets.     

Avian assemblages in eucalypt forests,plantations and pastures in northern NSW,Australia

Eucalypt plantations are expanding rapidly in Australia, and their value for native fauna requires investigation. The relative conservation value of young eucalypt plantations was investigated through assessment of avifauna richness, abundance and composition using transect surveys incorporating point counts in five broad habitat types—dryland forests, riparian forests, dryland plantations, riparian plantations, and riparian pastures (strips of riparian vegetation surrounded by pastures). A total of 73 species were recorded during formal surveys. Species richness and abundance were comparable among all habitat types except dryland plantations, which supported fewer species and in lower numbers. The avifauna assemblage differed according to broad habitat types. Forest habitats (dryland and riparian) harboured more forest- and woodland-dependent species, and a greater abundance of nectarivores and insectivores. Riparian plantations supported a similar number of forest- and woodland-dependent species to forest habitats, but also retained some open-country species. Riparian pastures had the highest cumulative species richness, reflecting a diverse mix of forest- and woodland-dependent birds and open-country species. It was the preferred habitat type for granivores and vertebrate eaters. Dryland plantations were dominated by common species and omnivores, and supported fewer forest- and woodland-dependent birds, insectivores and frugivores compared with other habitat types. The presence of riparian strips increased avifauna diversity and abundance in plantations and pastures to a greater extent than predicted by the proportional area of riparian habitat. The importance of riparian habitats needs to be recognised and incorporated into management policies if biodiversity conservation is to be an objective of plantation establishment.     

Camel Streptococcus agalactiae populations are associated with specific disease complexes and acquired the tetracycline resistance gene tetM via a Tn916-like element

Camels are the most valuable livestock species in the Horn of Africa and play a pivotal role in the nutritional sustainability for millions of people. Their health status is therefore of utmost importance for the people living in this region. Streptococcus agalactiae, a Group B Streptococcus (GBS), is an important camel pathogen. Here we present the first epidemiological study based on genetic and phenotypic data from African camel derived GBS. Ninety-two GBS were characterized using multilocus sequence typing (MLST), capsular polysaccharide typing and in vitro antimicrobial susceptibility testing. We analysed the GBS using Bayesian linkage, phylogenetic and minimum spanning tree analyses and compared them with human GBS from East Africa in order to investigate the level of genetic exchange between GBS populations in the region. Camel GBS sequence types (STs) were distinct from other STs reported so far. We mapped specific STs and capsular types to major disease complexes caused by GBS. Widespread resistance (34%) to tetracycline was associated with acquisition of the tetM gene that is carried on a Tn916-like element, and observed primarily among GBS isolated from mastitis. The presence of tetM within different MLST clades suggests acquisition on multiple occasions. Wound infections and mastitis in camels associated with GBS are widespread and should ideally be treated with antimicrobials other than tetracycline in East Africa.     

Assessment of the ultrasonographic characteristics of the podotrochlear apparatus in clinically normal horses and horses with navicular syndrome

OBJECTIVE: To characterize the normal ultrasonographic appearance of the podotrochlear apparatus in horses by use of standardized measurements and identify soft tissue changes associated with navicular syndrome. DESIGN: Prospective study. ANIMALS: 7 clinically normal horses and 28 horses with navicular syndrome. PROCEDURE: The feasibility of identifying and measuring the soft tissue structures of the podotrochlear apparatus ultrasonographically via the transcuneal approach was assessed in 2 additional horses without navicular syndrome; both horses were euthanatized, and the structures identified ultrasonographically were confirmed at necropsy. Ultrasonographs were obtained in the study horses. Objective and subjective data were obtained to characterize ultrasonographic changes associated with navicular syndrome. RESULTS: Abnormalities of the flexor surface of the distal sesamoid (navicular) bone, the impar ligament, the distal digital annular ligament, deep digital flexor tendon (DDFT), and the podotrochlear (navicular) bursa were assessed via the transcuneal ultrasonographic approach. No significant differences were found between the measurements of the podotrochlear apparatus in normal horses and those with navicular syndrome; however, important subjective differences were detected ultrasonographically in horses with navicular syndrome. In horses with navicular syndrome, ultrasonographic findings were indicative of navicular bursitis, dystrophic mineralization of the DDFT and impar ligament, tendonitis and insertional tenopathy of the DDFT, desmitis of the impar ligament, and cortical changes in the flexor surface of the navicular bone. CONCLUSIONS AND CLINICAL RELEVANCE: Findings of ultrasonographic evaluation of the hoof appear to be useful in determining the cause of caudal heel pain and characterizing the components of navicular syndrome in horses.     

Do plant species encourage soil biota that specialise in the rapid decomposition of their litter?

Plants are often nutrient limited and soil organisms are important in mediating nutrient availability to plants. Thus, there may be a selective advantage to plants that alter the soil community in ways that enhance the decomposition of their litter and, hence, their ability to access nutrients. We incubated litter from three tree species (Fagus sylvatica, Acer pseudoplatanus and Picea sitchensis) in the presence of biota extracted from soil beneath a stand of each species to test the hypothesis that litter decomposes fastest in the presence of biota derived from soil where that species is locally abundant. We found that respiration rate, a measure of decomposer activity and carbon mineralisation, was affected by litter type and source of soil biota, whereas, mass loss was only affected by litter type. However, litter from each tree species did not decompose faster in the presence of indigenous soil biota. These findings, therefore, provide no support for the notion that woodland plants encourage the development of soil communities that rapidly decompose their litter.     

Farmers' attitudes towards techniques for improving oestrus detection in dairy herds in South West England

Unidentified heats contribute to declining fertility rates in English dairy herds. Several techniques have been advocated to improve heat detection rates. Despite demonstrable technical efficacy and cost-effectiveness, uptake is low. A study in South West England used the Theory of Reasoned Action (TORA) to explore dairy farmers' attitudes and beliefs towards heat detection techniques. Few farmers were convinced that following prescribed observation times, milk progesterone testing and using pedometers would fit their system or improve on their current heat detection practices. Perceived difficulty of using a technique was not a constraint on adoption. Without promotion that addresses identified barriers and drivers to adoption, little change in current practice can be expected.     

Counting low-copy number proteins in a single cell

We have designed a microfluidic device in which we can manipulate, lyse, label, separate, and quantify the protein contents of a single cell using single-molecule fluorescence counting. Generic labeling of proteins is achieved through fluorescent-antibody binding. The use of cylindrical optics enables high-efficiency (approximately 60%) counting of molecules in micrometer-sized channels. We used this microfluidic device to quantify beta2 adrenergic receptors expressed in insect cells (SF9). We also analyzed phycobiliprotein contents in individual cyanobacterial cells (Synechococcus sp. PCC 7942) and observed marked differences in the levels of specific complexes in cell populations that were grown under nitrogen-depleted conditions.     

A selective activity-dependent requirement for dynamin 1 in synaptic vesicle endocytosis

Dynamin 1 is a neuron-specific guanosine triphosphatase thought to be critically required for the fission reaction of synaptic vesicle endocytosis. Unexpectedly, mice lacking dynamin 1 were able to form functional synapses, even though their postnatal viability was limited. However, during spontaneous network activity, branched, tubular plasma membrane invaginations accumulated, capped by clathrin-coated pits, in synapses of dynamin 1-knockout mice. Synaptic vesicle endocytosis was severely impaired during strong exogenous stimulation but resumed efficiently when the stimulus was terminated. Thus, dynamin 1-independent mechanisms can support limited synaptic vesicle endocytosis, but dynamin 1 is needed during high levels of neuronal activity.     

Estimating the spatial scales of landscape effects on abundance

Context

Spatial variation in abundance is influenced by local- and landscape-level environmental variables, but modeling landscape effects is challenging because the spatial scales of the relationships are unknown. Current approaches involve buffering survey locations with polygons of various sizes and using model selection to identify the best scale. The buffering approach does not acknowledge that the influence of surrounding landscape features should diminish with distance, and it does not yield an estimate of the unknown scale parameters.

Objectives

The purpose of this paper is to present an approach that allows for statistical inference about the scales at which landscape variables affect abundance.

Methods

Our method uses smoothing kernels to average landscape variables around focal sites and uses maximum likelihood to estimate the scale parameters of the kernels and the effects of the smoothed variables on abundance. We assessed model performance using a simulation study and an avian point count dataset.

Results

The simulation study demonstrated that estimators are unbiased and produce correct confidence interval coverage except in the rare case in which there is little spatial autocorrelation in the landscape variable. Canada warbler abundance was more highly correlated with site-level measures of NDVI than landscape-level NDVI, but the reverse was true for elevation. Canada warbler abundance was highest when elevation in the surrounding landscape, defined by an estimated Gaussian kernel, was between 1300 and 1400 m.

Conclusions

Our method provides a rigorous way of formally estimating the scales at which landscape variables affect abundance, and it can be embedded within most classes of statistical models.