Early Warning with Calibrated and Sharper Probabilistic Forecasts

Given a nonlinear model, a probabilistic forecast may be obtained by Monte Carlo simulations. At a given forecast horizon, Monte Carlo simulations yield sets of discrete forecasts, which can be converted to density forecasts. The resulting density forecasts will inevitably be downgraded by model misspecification. In order to enhance the quality of the density forecasts, one can mix them with the unconditional density. This paper examines the value of combining conditional density forecasts with the unconditional density. The findings have positive implications for issuing early warnings in different disciplines including economics and meteorology, but UK inflation forecasts are considered as an example. Copyright © 2012 John Wiley & Sons, Ltd.     

Structural basis of bacterial defense against g-type lysozyme-based innate immunity

Gram-negative bacteria can produce specific proteinaceous inhibitors to defend themselves against the lytic action of host lysozymes. So far, four different lysozyme inhibitor families have been identified. Here, we report the crystal structure of the Escherichia coli periplasmic lysozyme inhibitor of g-type lysozyme (PliG-Ec) in complex with Atlantic salmon g-type lysozyme (SalG) at a resolution of 0.95 Å, which is exceptionally high for a complex of two proteins. The structure reveals for the first time the mechanism of g-type lysozyme inhibition by the PliG family. The latter contains two specific conserved regions that are essential for its inhibitory activity. The inhibitory complex formation is based on a double ‘key-lock’ mechanism. The first key-lock element is formed by the insertion of two conserved PliG regions into the active site of the lysozyme. The second element is defined by a distinct pocket of PliG accommodating a lysozyme loop. Computational analysis indicates that this pocket represents a suitable site for small molecule binding, which opens an avenue for the development of novel antibacterial agents that suppress the inhibitory activity of PliG.     

Surface display of a single-domain antibody library on Gram-positive bacteria

Combinatorial protein engineering for selection of proteins with novel functions, such as enzymes and affinity reagents, is an important tool in biotechnology, drug discovery, and other biochemical fields. Bacterial display is an emerging technology for isolation of new affinity proteins from such combinatorial libraries. Cells have certain properties that are attractive for directed evolution purposes, in particular the option to use quantitative flow-cytometric cell sorting for selection of binders. Here, an immune library of around 10⁷ camelid single-domain antibody fragments (Nanobodies) was displayed on both the Gram-positive bacterium Staphylococcus carnosus and on phage. As demonstrated for the first time, the antibody repertoire was found to be well expressed on the bacterial surface and flow-cytometric sorting yielded a number of Nanobodies with subnanomolar affinity for the target protein, green fluorescent protein (GFP). Interestingly, the staphylococcal output repertoire and the binders from the phage display selection contained two slightly different sets of clones, containing both unique as well as several similar variants. All of the Nanobodies from the staphylococcal selection were also shown to enhance the fluorescence of GFP upon binding, potentially due to the fluorescence-based sorting principle. Our study highlights the impact of the chosen display technology on the variety of selected binders and thus the value of having alternative methods available, and demonstrates in addition that the staphylococcal system is suitable for generation of high-affinity antibody fragments.     

The unique features of follicular T cell subsets

The germinal center (GC) reaction is critical for humoral immunity, but also contributes adversely to a variety of autoimmune diseases. While the major protective function of GCs is mediated by plasma cells and memory B cells, follicular helper T (TFH) cells represent a specialized T cell subset that provides essential help to the antigen-specific B cells in the form of membrane-bound ligands and secreted factors such as IL-21. Recent studies have revealed that TFH cells are capable of considerable functional diversity as well as possessing the ability to form memory cells. The molecular basis of this plasticity and heterogeneity is only now emerging. It has also become apparent that several other populations of follicular T cells exist, including natural killer T cells and regulatory T cells. In this review we will discuss the function of follicular T cells and interaction of these populations within the GC response.     

Nesting phenology and productivity of birds in the White and Inyo Mountains, California, as assessed with nest-boxes

Nest-boxes were monitored from 1988 to 1992 on 5 grids in the pinyon-juniper ( Pinus-Juniperus ) woodlands of the White and Inyo Mountains, California, to determine breeding phenology and productivity of cavity-nesting birds, and characteristics of used and non-used nest-boxes. We found a total of 112 nests of 6 species. Bewicks Wrens ( Thryomanes bewicki i; 64 nests), Mountain Chickadees ( Poecile gambeli ; 18), Ash-throated Flycatchers ( Myiarchus cinerascens ; 12), and Juniper Titmice ( Baeolophus ridgwayi ; 11) were the most common species utilizing the boxes. Nest phenology and numbers of young were similar to values reported elsewhere in the literature for the species, although nesting success for Mountain Chickadees appeared lower in our study. Chickadees were associated with relatively dense, mature vegetation on southern slopes. Juniper Titmice used areas with tall juniper shrubs and generally sparse vegetation. Bewicks Wrens used areas with short trees, sparse vegetation, and many stumps. Nest-boxes were underutilized (< 15% use) by most species relative to their availability and relative to detected abundances of the species. We suggest that nest-boxes can provide valuable breeding biology information and can potentially increase the productivity of rare and cavity-limited species.     

Aquatic Oligochaeta (Annelida: Lumbriculidae, Haplotaxidae, Naididae, Tubificidae) of Utah

Thirty-six species of aquatic Oligochaeta (Lumbriculidae, Haplotaxidae, Naididae, Tubificidae) are now known form Utah. Aquatic habitats in 27 counties were sampled, with 32 oligochaete species identified. An additional 4 species were added from other published investigations. The majority of species are cosmopolitan and occur in other areas of North America. Nais barbata, N. alpina, and N. pardalis are reported from the western United States for the first time. Ilyodrilus frantzi was found to be a major component of the oliogochaete fauna in the Great Basin lentic environment. The North American distribution of Telmatodrilus vejdovskyi is extended significantly eastward. Tow undetermined species of Tubificidae are discussed.     

Prey selection and food habits of Burrowing Owls in Colorado

Food habits of Burrowing Owls ( Speotyto cunicularia ) were studied during the breeding seasons of 1990 and 1991 in central Colorado. Concurrent insect availability studies were conducted to determine selection for specific insect families. Analysis of 1445 castings indicated use of only one insect family, the carrion beetles (Silphidae), at a rate greater than expected based on availability in one year. Castings and prey remains showed different dietary components. Prey remains showed greater use of small mammals, moths, amphibians, and passerines, and castings indicated greater use of mice and beetles. Methodology in raptor food habits studies may therefore bias results.     

Differential responses to nitrogen form and concentration for Oryzopsis hymenoides and Elymus lanceolatus

In a greenhouse experiment, effects of nitrogen form and concentration on productivity and dry matter allocation differed between two species native to semiarid ecosystems of the Great Basin. Aboveground production of green surface area and of dry matter were consistently enhanced by increased nitrogen for the rhizomatous grass Elymus lanceolatus , but not for the bunchgrass Oryzopsis hymenoides . These differences were likely due to inherently low growth rates of O. hymenoides . Aboveground dry matter allocation also differed between the two species. O. hymenoides had more leaves per tiller with increased nitrogen, whereas leaf size but not number increased for E. lanceolatus . Furthermore, increases in tiller density with increased nitrogen for E. lanceolatus were almost three times greater than those for O. hymenoides . E. lanceolatus , but not O. hymenoides , was sensitive to the form of nitrogen supplied to the plants. When NH 4 -N was the only form of nitrogen supplied, high concentrations of NH 4 -N inhibited aboveground production of E. lanceolatus .