Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments

The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, similar to 70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHe(corr)-0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala's ability to maintain gene flow and adapt across divergent environments as long as the required food source is available

Endogenous Murine BST-2/Tetherin Is Not a Major Restriction Factor of Influenza A Virus Infection.

BST-2 (tetherin, CD317, HM1.24) restricts virus growth by tethering enveloped viruses to the cell surface. The role of BST-2 during influenza A virus infection (IAV) is controversial. Here, we assessed the capacity of endogenous BST-2 to restrict IAV in primary murine cells. IAV infection increased BST-2 surface expression by primary macrophages, but not alveolar epithelial cells (AEC). BST-2-deficient AEC and macrophages displayed no difference in susceptibility to IAV infection relative to wild type cells. Furthermore, BST-2 played little role in infectious IAV release from either AEC or macrophages. To examine BST-2 during IAV infection in vivo, we infected BST-2-deficient mice. No difference in weight loss or in viral loads in the lungs and/or nasal tissues were detected between BST-2-deficient and wild type animals. This study rules out a major role for endogenous BST-2 in modulating IAV in the mouse model of infection

Lack of BST-2 does not alter the susceptibility of mice to IAV infection or the ability of IAV to replicate in the airways.

<p>(A) Peripheral blood from wild type and BST-2^-/- mice was screened by the Advia2120 automated hematology analyzer. Each symbol represents an individual mouse and the bar indicates the mean. n.s. = no significant difference, <i>p</i> = > 0.05, two way ANOVA followed by Bonferroni analysis. (B) Wild type and BST-2^-/- mice were infected with either 10² PFU or 10⁴ PFU of HKx31 via the intranasal route. Mice were weighed daily and the results expressed as the mean percentage weight change per group (± 1 SEM) relative to original body weight. (C) Virus titres were determined in clarified homogenates prepared from lungs and nasal tissues using a standard plaque assay on MDCK cells. Symbols show titres from individual animals and horizontal bars represent the mean virus titre. n.s. = no significant difference, <i>p</i> = > 0.05, Student’s <i>t</i>-test; two-tailed.</p

BST-2 expression does not modulate IAV susceptibility of murine epithelial cells and macrophages to IAV infection.

<p>(A) Primary AEC or (B) macrophages isolated from BST-2 wild type (WT) and BST-2-deficient (BST-2^-/-) mice were incubated with the indicated MOI and strain of IAV for 1 hour at 37°C, washed to remove excess virus and cultured as indicated. Monolayers were fixed at 8 hours post-infection before staining by immunofluorescence to detect newly synthesized viral NP. Data show the mean (± 1 SD) pooled from 3 independent experiments. n.s. = no significant difference, <i>p</i> = > 0.05, two-way ANOVA followed by Bonferroni analysis.</p

BST-2 expression does not modulate IAV release from murine epithelial cells and macrophages following IAV infection.

<p>(A) Primary AEC or (B) macrophages isolated from BST-2 wild type (WT) and BST-2-deficient (BST-2^-/-) mice were incubated with the indicated strain of IAV for 1 hour at 37°C, washed to remove excess virus and cultured. AEC were infected at a MOI of 1 of HKx31, Brazil/78 and Sol Is/06 and macrophages infected at a MOI 5 for HKx31 and a MOI of 50 for Brazil/78. Culture supernatants were removed at 2 hours, or at 8, 24 or 48 hours as indicated, clarified by centrifugation and titres of infectious virus were determined by plaque assay on MDCK cells. Data is displayed as viral titer (log₁₀PFU/ml) and represent the mean (± 1 SD) from triplicate samples. Data is representative of 2 independent experiments. n.s. = no significant difference, *** <i>p</i> < 0.001, two-way ANOVA followed by Bonferroni analysis.</p

BST-2 expression is upregulated on murine macrophages but not alveolar epithelial cells in response to influenza A virus.

<p>Monolayers of (A) the LA-4 AEC line and primary AEC, or (B) RAW264.7 macrophages and primary macrophages were incubated (i) with a MOI of 5 (HKx31) for 1 hour at 37°C and washed to remove excess virus (IAV infection, solid black line), (ii) in 1000 IU/ml recombinant mouse IFNα (dashed line) or (iii) in media alone (no infection, grey histogram). Cells were then incubated at 37°C for a total of 4 or 24 hours and levels of cell-surface BST-2 determined by flow cytometry. For each cell type, the isotype control (solid black histograms) is shown for ‘no infection’ cells only but is representative of profiles obtained using IAV-infected and IFNα-treated cells. Data are representative of 3 independent experiments.</p

Genome-wide association study of homocysteine levels in Filipinos provides evidence for CPS1 in women and a stronger MTHFR effect in young adults

Plasma homocysteine (Hcy) level is associated with cardiovascular disease and may play an etiologic role in vascular damage, a precursor for atherosclerosis. We performed a genome-wide association study for Hcy in 1786 unrelated Filipino women from the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The most strongly associated single-nucleotide polymorphism (SNP) (rs7422339, P = 4.7 × 10−13) encodes Thr1405Asn in the gene CPS1 and explained 3.0% of variation in the Hcy level. The widely studied MTHFR C677T SNP (rs1801133) was also highly significant (P = 8.7 × 10−10) and explained 1.6% of the trait variation. We also genotyped these two SNPs in 1679 CLHNS young adult offspring. The MTHFR C677T SNP was strongly associated with Hcy (P = 1.9 × 10−26) and explained ∼5.1% of the variation in the offspring. In contrast, the CPS1 variant was significant only in females (P = 0.11 in all; P = 0.0087 in females). Combined analysis of all samples confirmed that the MTHFR variant was more strongly associated with Hcy in the offspring (interaction P = 1.2 × 10−5). Furthermore, although there was evidence for a positive synergistic effect between the CPS1 and MTHFR SNPs in the offspring (interaction P = 0.0046), there was no significant evidence for an interaction in the mothers (P = 0.55). These data confirm a recent finding that CPS1 is a locus influencing Hcy levels in women and suggest that genetic effects on Hcy may differ across developmental stages