Invasion of host cells by JC virus identifies a novel role for caveolae in endosomal sorting of noncaveolar ligands

Invasion of glial cells by the human polyomavirus, JC virus (JCV), leads to a rapidly progressing and uniformly fatal demyelinating disease known as progressive multifocal leukoencephalopathy. The endocytic trafficking steps used by JCV to invade cells and initiate infection are not known. We demonstrated that JCV infection was inhibited by dominant defective and constitutively active Rab5-GTPase mutants that acted at distinct steps in endosomal sorting. We also found that labeled JCV colocalized with labeled cholera toxin B and with caveolin-1 (cav-1) on early endosomes following internalization by clathrin-dependent endocytosis. JCV entry and infection were both inhibited by dominant defective mutants of eps15 and Rab5-GTPase. Expression of a dominant-negative scaffolding mutant of cav-1 did not inhibit entry or infection by JCV. A single-cell knockdown experiment using cav-1 shRNA did not inhibit JCV entry but interfered with a downstream trafficking event important for infection. These data show that JCV enters cells by clathrin-dependent endocytosis, is transported immediately to early endosomes, and is then sorted to a caveolin-1-positive endosomal compartment. This latter step is dependent on Rab5-GTPase, cholesterol, caveolin-1, and pH. This is the first example of a ligand that enters cells by clathrin-dependent endocytosis and is then sorted from early endosomes to caveosomes, indicating that caveolae-derived vesicles play a more important role than previously realized in sorting cargo from early endosomes.     

Tools for glycoproteomic analysis: size exclusion chromatography facilitates identification of tryptic glycopeptides with N-linked glycosylation sites

Proteomic techniques, such as HPLC coupled to tandem mass spectrometry (LC-MS/MS), have proved useful for the identification of specific glycosylation sites on glycoproteins (glycoproteomics). Glycosylation sites on glycopeptides produced by trypsinization of complex glycoprotein mixtures, however, are particularly difficult to identify both because a repertoire of glycans may be expressed at a particular glycosylation site, and because glycopeptides are usually present in relatively low abundance (2% to 5%) in peptide mixtures compared to nonglycosylated peptides. Previously reported methods to facilitate glycopeptide identification require either several pre-enrichment steps, involve complex derivatization procedures, or are restricted to a subset of all the glycan structures that are present in a glycoprotein mixture. Because the N-linked glycans expressed on tryptic glycopeptides contribute substantially to their mass, we demonstrate that size exclusion chromatography (SEC) provided a significant enrichment of N-linked glycopeptides relative to nonglycosylated peptides. The glycosylated peptides were then identified by LC-MS/MS after treatment with PNGase-F by the monoisotopic mass increase of 0.984 Da caused by the deglycosylation of the peptide. Analyses performed on human serum showed that this SEC glycopeptide isolation procedure results in at least a 3-fold increase in the total number of glycopeptides identified by LC-MS/MS, demonstrating that this simple, nonselective, rapid method is an effective tool to facilitate the identification of peptides with N-linked glycosylation sites.     

Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif

The human JC polyomavirus (JCV) causes a fatal demyelinating disease, progressive multifocal leukoencephalopathy (PML), in immunocompromised individuals. Current treatment options for PML are inadequate. Sialylated oligosaccharides and the serotonin receptor are known to be necessary for JCV entry, but the molecular interactions underlying JCV attachment remain unknown. Using glycan array screening and viral infectivity assays, we identify?a linear sialylated pentasaccharide with the sequence NeuNAc-α2,6-Gal-β1,4-GlcNAc-β1,3-Gal-β1,4-Glc (LSTc) present on host glycoproteins and glycolipids as a specific JCV recognition motif. The crystal structure of the JCV capsid protein VP1 was solved alone and in complex with LSTc. It reveals extensive interactions with the terminal sialic acid of the LSTc motif and specific recognition of an extended conformation of LSTc. Mutations in the JCV oligosaccharide-binding sites abolish cell attachment, viral spread, and infectivity, further validating the importance of this interaction. Our findings provide a powerful platform for the development of antiviral compounds.     

Fatty acid‐based diet estimates suggest ringed seal remain the main prey of southern Beaufort Sea polar bears despite recent use of onshore food resources

Polar bears (Ursus maritimus) from the southern Beaufort Sea (SB) subpopulation have traditionally fed predominantly upon ice‐seals; however, as the proportion of the subpopulation using onshore habitat has recently increased, foraging on land‐based resources, including remains of subsistence‐harvested bowhead whales (Balaena mysticetus) and colonial nesting seabirds has been observed. Adipose tissue samples were collected from this subpopulation during the springs of 2013–2016 and analyzed for fatty acid signatures. Diet estimates were generated for the proportional consumption of ringed seal (Pusa hispida), bearded seal (Erignathus barbatus), and beluga whale (Delphinapterus leucas), relative to onshore foods, including bowhead whale remains and seabird, as represented by black guillemot (Cepphus grylle mandtii) nestlings and eggs. Quantitative fatty acid signature analysis (QFASA) estimated that the ice‐obligate prey, ringed seal, remained the predominant prey species of SB polar bears (46.4 ± 1.8%), with much lower consumption of bearded seal (19.6 ± 2.0%), seabird (17.0 ± 1.2%), bowhead whale (15.0 ± 1.4%), and hardly any beluga whale (2.0 ± 0.5%). Adult and subadult females appeared to depend more on the traditional ringed seal prey than adult and subadult males. Diet estimates of SB polar bears showed significant interannual variability for all prey (F_{12, 456} = 3.17, p < .001). Longer‐term estimates suggested that both types of onshore prey, bowhead whale remains and seabird, have represented a moderate proportion of the food resources used by SB polar bears since at least the start of the 21st Century.     

Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height

Height is a classic complex trait with common variants in a growing list of genes known to contribute to the phenotype. Using a genecentric genotyping array targeted toward cardiovascular-related loci, comprising 49,320 SNPs across approximately 2000 loci, we evaluated the association of common and uncommon SNPs with adult height in 114,223 individuals from 47 studies and six ethnicities. A total of 64 loci contained a SNP associated with height at array-wide significance (p < 2.4 × 10⁻⁶), with 42 loci surpassing the conventional genome-wide significance threshold (p < 5 × 10⁻⁸). Common variants with minor allele frequencies greater than 5% were observed to be associated with height in 37 previously reported loci. In individuals of European ancestry, uncommon SNPs in IL11 and SMAD3, which would not be genotyped with the use of standard genome-wide genotyping arrays, were strongly associated with height (p < 3 × 10⁻¹¹). Conditional analysis within associated regions revealed five additional variants associated with height independent of lead SNPs within the locus, suggesting allelic heterogeneity. Although underpowered to replicate findings from individuals of European ancestry, the direction of effect of associated variants was largely consistent in African American, South Asian, and Hispanic populations. Overall, we show that dense coverage of genes for uncommon SNPs, coupled with large-scale meta-analysis, can successfully identify additional variants associated with a common complex trait.     

Millennial Medical Anthropology: From There to Here and Beyond,or the Problem of Global Health

While much of Medical Anthropology was and is what we can call “Normal” (following Kuhn) Medical Anthropology, I coined the term Millennial Medical Anthropology for that branch of the discipline that, in the 1990s, was departing from the Normal research paradigms and was deserving of a distinct sobriquet. This paper considers the Strong Program in Medical Anthropology’s Millennial Medical Anthropology and its key subdivisions, the Cultural Studies of Science and Cultural Bioethics. Specifically it considers Medical Anthropology’s movement from the past into an ethical future wherein Normal Biomedicine, Bioethics and Global Health are problematized. This provides the basis for the construction of a truly anthropological global health (i.e., Global, Global Health or Global Health 2.0).     

Island biogeography extends to small-scale habitats: low competitor density and richness on islands may drive trait variation in nonnative plants

Previous island biogeography studies have quantified species richness on the scale of entire islands rather than smaller scales relevant to plant-to-plant competitive interactions. Further, they have not accounted for density compensation. Using mainland and island sites along the New England coast, we asked two questions. First, are both richness and density lower in small-scale habitats within islands than in similar mainland habitats? Second, do differences in competitor richness and density drive post-establishment trait variation in nonnative plant species? We used field surveys and individual-based rarefaction to estimate richness and density in 100-m² plots and demonstrated that island sites have significantly fewer species and individuals per unit area than mainland sites. We then conducted a field study in which we removed competing neighbors from nonnative plant individuals and found that when competitors were removed, individuals in low-competition environments demonstrated a lesser increase in vegetative growth but a greater increase in reproductive effort and herbivore tolerance relative to mainland individuals whose neighbors were also removed. We found that the central concept of island biogeography, i.e., that islands host fewer species than comparable mainland habitats, can be extended to smaller-scale habitats and that this difference in competitive pressure between mainland and island habitats can act as a driver of trait variation in nonnative plants.