Genomic organization and evolution of the ULBP genes in cattle

BACKGROUND: The cattle UL16-binding protein 1 (ULBP1) and ULBP2 genes encode members of the MHC Class I superfamily that have homology to the human ULBP genes. Human ULBP1 and ULBP2 interact with the NKG2D receptor to activate effector cells in the immune system. The human cytomegalovirus UL16 protein is known to disrupt the ULBP-NKG2D interaction, thereby subverting natural killer cell-mediated responses. Previous Southern blotting experiments identified evidence of increased ULBP copy number within the genomes of ruminant artiodactyls. On the basis of these observations we hypothesized that the cattle ULBPs evolved by duplication and sequence divergence to produce a sufficient number and diversity of ULBP molecules to deliver an immune activation signal in the presence of immunogenic peptides. Given the importance of the ULBPs in antiviral immunity in other species, our goal was to determine the copy number and genomic organization of the ULBP genes in the cattle genome. RESULTS: Sequencing of cattle bacterial artificial chromosome genomic inserts resulted in the identification of 30 cattle ULBP loci existing in two gene clusters. Evidence of extensive segmental duplication and approximately 14 Kbp of novel repetitive sequences were identified within the major cluster. Ten ULBPs are predicted to be expressed at the cell surface. Substitution analysis revealed 11 outwardly directed residues in the predicted extracellular domains that show evidence of positive Darwinian selection. These positively selected residues have only one residue that overlaps with those proposed to interact with NKG2D, thus suggesting the interaction with molecules other than NKG2D. CONCLUSION: The ULBP loci in the cattle genome apparently arose by gene duplication and subsequent sequence divergence. Substitution analysis of the ULBP proteins provided convincing evidence for positive selection on extracellular residues that may interact with peptide ligands. These results support our hypothesis that the cattle ULBPs evolved under adaptive diversifying selection to avoid interaction with a UL16-like molecule whilst preserving the NKG2D binding site. The large number of ULBPs in cattle, their extensive diversification, and the high prevalence of bovine herpesvirus infections make this gene family a compelling target for studies of antiviral immunity

Monitoring temporal change in riparian vegetation of Great Basin National Park

Disturbance in riparian areas of semiarid ecosystems involves complex interactions of pulsed hydrologic flows, herbivory, fire, climatic effects, and anthropogenic influences. We resampled riparian vegetation within ten 10-m × 100-m plots that were initially sampled in 1992 in 4 watersheds of the Snake Range, east central Nevada. Our finding of significantly lower coverage of grasses, forbs, and shrubs within plots in 2001 compared with 1992 was not consistent with the management decision to remove livestock grazing from the watersheds in 1999. Change over time in cover of life-forms or bare ground was not predicted by scat counts within plots in 2001. Cover results were also not well explained by variability between the 2 sampling periods in either density of native herbivores or annual precipitation. In contrast, Engelmann spruce (Picea engelmannii) exhibited reduced abundance at all but the highest-elevation plot in which it occurred in 1992, and the magnitude of change in abundance was strongly predicted by plot elevation. Abundance of white fir (Abies concolor) individuals increased while aspen (Populus tremuloides) individuals decreased at 4 of 5 sites where they were sympatric, and changes in abundance in the 2 species were negatively correlated across those sites. Utility of monitoring data to detect change over time and contribute to adaptive management will vary with sample size, observer bias, use of repeatable or published methods, and precision of measurements, among other factors

Social–ecological mismatches create conservation challenges in introduced species management

This is the final version. Available from the Ecological Society of America via the DOI in this recordIntroduced species can have important effects on the component species and processes of native ecosystems. However, effective introduced species management can be complicated by technical and social challenges. We identify “social–ecological mismatches” (that is, differences between the scales and functioning of interacting social and ecological systems) as one such challenge. We present three case studies in which mismatches between the organization and functioning of key social and ecological systems have contributed to controversies and debates surrounding introduced species management and policy. We identify three common issues: social systems and cultures may adapt to a new species’ arrival at a different rate than ecosystems; ecological impacts can arise at one spatial scale while social impacts occur at another; and the effects of introduced species can spread widely, whereas management actions are constrained by organizational and/or political boundaries. We propose strategies for collaborative knowledge building and adaptive management that may help address these challenges

Prediction of milk protein concentration from elements of the metabolizable protein system

Elements of the metabolizable protein system in the United Kingdom were examined for their suitability as potential predictors of milk protein concentration. Models were based on data from 163 cows offered five forage mixtures for ad libitum intake plus concentrates at 3, 6, or 9 kg/d of dry matter. The models were then tested on a separate data set of 100 cows offered seven forage mixtures for ad libitum intake plus concentrates at 6 kg/d of dry matter. To minimize problems with collinearity, variables were arranged hierarchically; successive elements were components of variables at higher element levels. Variables from different element levels were not used in the same models. Models were constructed using ridge regression to minimize problems with collinearity. The fit and precision of prediction were generally poor because these models did not take into account animal variables. Models using undegradable dietary protein performed slightly better than did those using digestible undegraded protein. The use of slowly degradable protein and quickly degradable protein rather than rumen-degradable protein generally resulted in improvements in prediction. Models using neutral detergent fiber and quickly fermented carbohydrate were better than those using total carbohydrate. We concluded that there was little to be gained from using the elements of the metabolizable protein system considered here for the prediction of milk protein concentration

Creating Porcine Biomedical Models Through Recombineering

Recent advances in genomics provide genetic information from humans and other mammals (mouse, rat, dog and primates) traditionally used as models as well as new candidates (pigs and cattle). In addition, linked enabling technologies, such as transgenesis and animal cloning, provide innovative ways to design and perform experiments to dissect complex biological systems. Exploitation of genomic information overcomes the traditional need to choose naturally occurring models. Thus, investigators can utilize emerging genomic knowledge and tools to create relevant animal models. This approach is referred to as reverse genetics. In contrast to ‘forward genetics’, in which gene(s) responsible for a particular phenotype are identified by positional cloning (phenotype to genotype), the ‘reverse genetics’ approach determines the function of a gene and predicts the phenotype of a cell, tissue, or organism (genotype to phenotype). The convergence of classical and reverse genetics, along with genomics, provides a working definition of a ‘genetic model’ organism (3). The recent construction of phenotypic maps defining quantitative trait loci (QTL) in various domesticated species provides insights into how allelic variations contribute to phenotypic diversity. Targeted chromosomal regions are characterized by the construction of bacterial artificial chromosome (BAC) contigs to isolate and characterize genes contributing towards phenotypic variation. Recombineering provides a powerful methodology to harvest genetic information responsible for phenotype. Linking recombineering with gene-targeted homologous recombination, coupled with nuclear transfer (NT) technology can provide ‘clones’ of genetically modified animals

Characterization of the Prion Protein (PRP) Gene in Ten Breeds of Sheep

Transmissible Spongiform Encephalopathies (TSE\u27s) are neurodegenerative disorders characterized by a long generation time, spongy degeneration in the cerebral gray matter, neuronal loss and proliferation and hypertrophy of glial cells. An abnormal form of the prion protein (PrP) plays a major part in TSE pathogenesis and has been hypothesized to be the only component of the infectious agent. Some animals exposed to scrapie, the TSE affecting sheep and goats, seem to be resistant to development of the disease. Alleles encoding amino acid substitutions at codons 136 (A/V) and 171 (Q/R/H) have been associated with scrapie resistance. Other amino acid substitutions at codons 112 (M/T), 137 (M/T), 141 (L/F), 154 (R/H), and 211 (R/Q) have been reported but not associated with scrapie resistance. It may be possible to reduce the incidence of ovine scrapie by increasing the frequency of resistant genotypes (AA-136, RR-171, or QR-171). Thus, an important consideration is the frequency of these genotypes in different breeds of sheep. In this study, the genetic sequence for codons 104-175 was determined for at least ten animals of ten sheep breeds (n=207). Genotypes at codons 112, 136, 154, and 171 were determined. For codon 136, the frequency of the susceptible allele (V) was less than 0.20 in all breeds. In contrast, the frequency of the susceptible allele (Q) at codon 171 ranged from 0.27 (St. Croix) to 0.96 (Hampshire). In addition, a previously unreported substitution was found at codon 143 (H/R), with frequencies as high as 0.40

Splanchnic metabolism of nutrients and hormones in steers fed alfalfa under conditions of increased absorption of ammonia and L-arginine supply across the portal-drained viscera

Effects of increased ammonia and/or arginine absorption on net splanchnic (portal-drained viscera [PDV] plus liver) metabolism of nonnitrogenous nutrients and hormones in cattle were examined. Six Hereford × Angus steers (501 ± 1 kg BW) prepared with vascular catheters for measurements of net flux across the splanchnic bed were fed a 75% alfalfa:25% (as-fed basis) corn and soybean meal diet (0.523 MJ of ME/[kg BW0.75.d]) every 2 h without (27.0 g of N/kg of DM) and with 20 g of urea/kg of DM (35.7 g of N/kg of DM) in a split-plot design. Net flux measurements were made immediately before and after a 72-h mesenteric vein infusion of L-arginine (15 mmol/h). There were no treatment effects onPDVor hepaticO2 consumption. Dietary urea had no effect on splanchnic metabolism of glucose or L-lactate, but arginine infusion decreased net hepatic removal of L-lactate when urea was fed (P < 0.01). Net PDV appearance of n-butyrate was increased by arginine infusion (P < 0.07), and both dietary urea (P < 0.09) and arginine infusion (P < 0.05) increased net hepatic removal of n-butyrate. Dietary urea also increased total splanchnic acetate output (P < 0.06), tended to increase arterial glucagon concentration (P < 0.11), and decreased arterial ST concentration (P < 0.03). Arginine infusion increased arterial concentration (P < 0.07) and net PDV release (P < 0.10) and tended to increase hepatic removal (P < 0.11) of insulin, as well as arterial concentration (P < 0.01) and total splanchnic output (P < 0.01) of glucagon. Despite changes in splanchnic N metabolism, increased ammonia and arginine absorption had little measurable effect on splanchnic metabolism of glucose and other nonnitrogenous components of splanchnic energy metabolism

Effects of Water-Level Management on Nesting Success of Common Loons

Water-level management is widespread and illustrates how contemporary climate can interact directly and indirectly with numerous biological and abiotic factors to influence reproductive success of wildlife species. We studied common loons, an iconic waterbird sensitive to timing and magnitude of waterlevel changes during the breeding season, using a before-after-control-impact design on large lakes in Voyageurs National Park (Minnesota, USA), to assess the effect of anthropogenic changes in hydroregime on their nesting success and productivity. We examined multiple competing a priori hypotheses in an information-theoretic framework, and predicted that magnitude of changes in loon productivity would be greater in the Namakan Reservoir, where water-level management was altered to mimic a more natural hydroregime, than in Rainy Lake, where management remained relatively unchanged. We determined outcomes from 278 nests during 2004–2006 by performing boat-based visits every 3–5 days, and measuring hydrologic, vegetative, and microtopographic covariates. Relative to comparably collected data for 260 total loon pairs during 1983–1986, productivity (chicks hatched/territorial pair) increased 95% in the Namakan Reservoir between the 2 time periods. Nest success declined in both lakes over the 2 study periods but less so in the Namakan Reservoir than in Rainy Lake. Flooding was a primary cause of nest failures (though second nests were less likely to flood). Nest predation appears to have increased considerably between the 2 study periods. Top-ranked models suggested that timing of nest initiation, probability of nest flooding, probability of nest stranding, and probability of nest success were each related to 2–4 factors, including date of initiation, timing of initiation relative to peak water levels, changes in the elevation of the nest edge, maximum waterlevel change between initiation and peak water levels, and maximum water-level change between initiation and nest outcome. The top model for all variables except stranding each garnered \u3e82% of total model weight. Results demonstrate that water-level management can be altered to benefit productivity of common loons. However, nuanced interactions between land-use change, invasive species, human development, recreation, climate change, and recovery of top predators may often complicate both management decisions and interpretation of water-level impacts on wildlife

Ecological Consequences of Anomalies in Atmospheric Moisture and Snowpack

Although increased frequency of extreme‐weather events is one of the most secure predictions associated with contemporary climate change, effects of such events on distribution and abundance of climate‐sensitive species remain poorly understood. Montane ecosystems may be especially sensitive to extreme weather because of complex abiotic and biotic interactions that propagate from climate‐driven reductions in snowpack. Snowpack not only protects subnivean biotas from extreme cold, but also influences forage availability through timing of melt‐off and water availability. We related relative abundances of an alpine mammal, the American pika (Ochotona princeps), to measures of weather and snowpack dynamics over an 8‐yr period that included before and after a year of record‐low snowpack in Washington, USA. We sought to (1) quantify any change in pika abundance associated with the snowpack anomaly and (2) identify aspects of weather and snowpack that influenced abundance of pikas. Pikas showed a 1‐yr lag response to the snowpack anomaly and exhibited marked declines in abundance at elevations below 1,400 m simultaneous with increased abundances at higher elevations. Atmospheric moisture, indexed by vapor pressure deficit (VPD), was especially important, evidenced by strong support for the top‐ranked model that included the interaction of VPD with snowpack duration. Notably, our novel application of VPD from gridded climate data for analyses of animal abundances shows strong potential for improving species distribution models because VPD represents an important aspect of weather that influences the physiology and habitat of biota. Pikas were apparently affected by cold stress without snowpack at mid elevations, whereas changes to forage associated with snowpack and VPD were influential at high and low elevations. Our results reveal context dependency in pika responses to weather and illustrate how snow drought can lead to rapid change in the abundance of subnivean animals

Transcriptome profiling of the small intestinal epithelium in germfree versus conventional piglets

<p>Abstract</p> <p>Background</p> <p>To gain insight into host-microbe interactions in a piglet model, a functional genomics approach was used to address the working hypothesis that transcriptionally regulated genes associated with promoting epithelial barrier function are activated as a defensive response to the intestinal microbiota. Cesarean-derived germfree (GF) newborn piglets were colonized with adult swine feces, and villus and crypt epithelial cell transcriptomes from colonized and GF neonatal piglets were compared using laser-capture microdissection and high-density porcine oligonucleotide microarray technology.</p> <p>Results</p> <p>Consistent with our hypothesis, resident microbiota induced the expression of genes contributing to intestinal epithelial cell turnover, mucus biosynthesis, and priming of the immune system. Furthermore, differential expression of genes associated with antigen presentation (pan SLA class I, <it>B2M</it>, <it>TAP1 </it>and <it>TAPBP</it>) demonstrated that microbiota induced immune responses using a distinct regulatory mechanism common for these genes. Specifically, gene network analysis revealed that microbial colonization activated both type I (IFNAR) and type II (IFNGR) interferon receptor mediated signaling cascades leading to enhanced expression of signal transducer and activator of transcription 1 (STAT1), STAT2 and IFN regulatory factor 7 (IRF7) transcription factors and the induction of IFN-inducible genes as a reflection of intestinal epithelial inflammation. In addition, activated RNA expression of NF-kappa-B inhibitor alpha (<it>NFκBIA</it>; a.k.a I-kappa-B-alpha, IKBα) and toll interacting protein (<it>TOLLIP</it>), both inhibitors of inflammation, along with downregulated expression of the immunoregulatory transcription factor GATA binding protein-1 (<it>GATA1</it>) is consistent with the maintenance of intestinal homeostasis.</p> <p>Conclusion</p> <p>This study supports the concept that the intestinal epithelium has evolved to maintain a physiological state of inflammation with respect to continuous microbial exposure, which serves to sustain a tight intestinal barrier while preventing overt inflammatory responses that would compromise barrier function.</p