Conservation agriculture practices have changed habitat use by rodent pests: implications for management of feral house mice

Journal of Pest Science - The advent of ‘conservation agriculture’ (CA) farming using zero- or no-tillage practices and an accompanying change in crop rotations in the last...     

Tailor made plasmin substrates as potential diagnostic tool to test for mastitis

Plasmin is a protease in milk, which concentration is increased during mastitis. The aim of the study was design and characterize short, tailor made fluorogenic substrates for plasmin to see differences in plasmin activity in healthy milk compared to mastitic milk. According to the specificity matrix of plasmin, containing 125 currently known plasmin substrates, six novel plasmin specific substrates were designed and characterized. Eight other substrates were insensitive for plasmin, which was in line with our expectations. The plasmin-sensitive substrates showed no cross-reactivity with proteases from mastitogenic bacteria in vitro. A proof of concept to distinguish healthy milk from mastitic milk is described. Potentially, these substrates present a rapid alternative to the currently established methodologies to detect mastitis in milk.     

Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.     

Island biology and ecosystem functioning in epiphytic soil communities

Although island attributes such as size and accessibility to colonizing organisms can influence community structure, the consequences of these for ecosystem functioning are little understood. A study of the suspended soils of spatially discrete epiphytes or treetop "islands" in the canopies of New Zealand rainforest trees revealed that different components of the decomposer community responded either positively or negatively to island size, as well as to the tree species that the islands occurred in. This in turn led to important differences between islands in the rates of ecosystem processes driven by the decomposer biota. This system serves as a model for better understanding how attributes of both real and habitat islands may affect key ecosystem functions through determining the community structure of organisms that drive these functions.     

Long-range topological order in metallic glass

Glass lacks the long-range periodic order that characterizes a crystal. In the Ce(75)Al(25) metallic glass (MG), however, we discovered a long-range topological order corresponding to a single crystal of indefinite length. Structural examinations confirm that the MG is truly amorphous, isotropic, and unstrained, yet under 25 gigapascals hydrostatic pressures, every segment of a centimeter-length MG ribbon devitrifies independently into a face-centered cubic (fcc) crystal with the identical orientation. By using molecular dynamics simulations and synchrotron x-ray techniques, we elucidate that the mismatch between the large Ce and small Al atoms frustrates the crystallization and causes amorphization, but a long-range fcc topological order still exists. Pressure induces electronic transition in Ce, which eliminates the mismatch and manifests the topological order by the formation of a single crystal.     

Integrating what and when across the primate medial temporal lobe

Episodic memory or memory for the detailed events in our lives is critically dependent on structures of the medial temporal lobe (MTL). A fundamental component of episodic memory is memory for the temporal order of items within an episode. To understand the contribution of individual MTL structures to temporal-order memory, we recorded single-unit activity and local field potential from three MTL areas (hippocampus and entorhinal and perirhinal cortex) and visual area TE as monkeys performed a temporal-order memory task. Hippocampus provided incremental timing signals from one item presentation to the next, whereas perirhinal cortex signaled the conjunction of items and their relative temporal order. Thus, perirhinal cortex appeared to integrate timing information from hippocampus with item information from visual sensory area TE.