Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed

Small Stem Total Hip Arthroplasty in Hypoplasia of the Femur

Total hip arthroplasty in hypoplastic femurs is technically difficult and the incidence of complications and aseptic loosening is relatively high. Cemented, uncemented, off-the-shelf, and custom-made stems all have been advocated in these cases. From 1978 to 1997, we performed 86 total hip arthroplasties in 77 patients with a hypoplastic femur using a cemented, off-the-shelf, small, curved, cobalt-chromium stem. We hypothesized results equaled those of the identical but larger-sized stems in normal-sized femora which were used as comparisons. Clinical and radiographic evaluations were performed. Minimum followup was 4.2 years (mean, 12 years; range, 4.2–20.3 years); mean Harris hip score was 88, and mean hip flexion was 104°. Six stems were revised: four because of aseptic loosening, one after a femoral fracture, and one because of malpositioning. Complications included one perforation and one fracture of the femur, one fracture, one nonunion of the greater trochanter, and one deep infection. Implant survivorship for all hips at 15 years with aseptic revision of the stem as the end point was 90% (confidence interval, 82–99) which equaled results of the larger stems. The small off-the-shelf cemented Weber stem has a high long-term survival and a low complication rate. Survival compares favorably with other small-sized total hip systems

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms. •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137Keywords: recombination., allele frequency gradients, linkage disequilibrium (LD), population structure, black cottonwood (Populus trichocarpa), genome resequencin

Human rotavirus-specific IgM memory B cells have differential cloning efficiencies and switch capacities and play a role in antiviral immunity in vivo

Q1Q110829-10840Protective immunity to rotavirus (RV) is primarily mediated by antibodies produced by RV-specific memory B cells (RV-mBc). Of note, most of these cells express IgM, but the function of this subset is poorly understood. Here, using limiting dilution assays of highly sort-purified human IgM mBc, we found that 62% and 21% of total (non-antigen-specific) IgM and RV-IgM mBc, respectively, switched in vitro to IgG production after polyclonal stimulation. Moreover, in these assays, the median cloning efficiencies of total IgM (17%) and RV-IgM (7%) mBc were lower than those of the corresponding switched (IgG IgA) total (34%) and RV-mBc (17%), leading to an underestimate of their actual frequency. In order to evaluate the in vivo role of IgM RV mBc in antiviral immunity, NOD/Shi-scid interleukin-2 receptor-deficient (IL-2Rnull) immunodeficient mice were adoptively transferred highly purified human IgM mBc and infected with virulent murine rotavirus. These mice developed high titers of serum human RV-IgM and IgG and had significantly lower levels than control mice of both antigenemia and viremia. Finally, we determined that human RV-IgM mBc are phenotypically diverse and significantly enriched in the IgMhi IgDlow subset. Thus, RV IgM mBc are heterogeneous, occur more frequently than estimated by traditional limiting dilution analysis, have the capacity to switch Ig class in vitro as well as in vivo, and can mediate systemic antiviral immunity