The green June beetle (Cotinis nitida) (Coleoptera: Scarabaeidae): local variation in the beetle’s major avian predators and in the competition for mates

The green June beetle (Cotinis nitida) was observed in northern Virginia for a second and third flight season. The study yielded some results that were consistent with earlier findings, namely that mate-locating beetles were vulnerable to attack by avian predators and matings occurred primarily early in the flight season. Novel findings included the following: (1) blue jays (Cyanocitta cristata) were the major predators, not common grackles (Quiscalus quiscala), (2) some jays appeared to selectively prey on female beetles, (3) competition for mates among male beetles could be so intense that some males attempted to copulate with already mated (unreceptive) females, and (4) the sex ratio of the beetle population feeding on wild blackberries remained near equality late in the flight season despite the fact that the sex ratio of the population of beetles at the emergence site became highly female-biased over time.     

Swimming and bipedal bottom-running in the pig-nosed turtle Carettochelys insculpta Ramsay, 1886

The pig-nosed freshwater turtle Carettochelys insculpta Ramsay, 1886 has paddle-shaped foreflippers that resemble those of sea turtles. These turtles exhibit a wide range of swimming capabilities. As well as swimming by the action of synchronized foreflippers alone, they sometimes used alternate hindlimb action at the same time. They could swim by ipsilaterally synchronized action of all four limbs, or by hindlimb action alone (combined with stabilizer/lift function of the foreflippers). The turtles also showed flexibility in bottom-walking. Besides the ipsilaterally synchronized quadrupedal action characteristic of other freshwater turtles, they exhibited a bipedal walking mechanism never previously described. Propelled by alternate action of the hindlimbs, the animals held the head and plastron above the substratum, with the large foreflippers acting to provide anterior lift and stability against roll and yaw. Because both hindlimbs were sometimes off the substratum simultaneously during bipedal locomotion, their duty factors were < 0.5, implying a bipedal run.     

Exome sequencing of liver fluke-associated cholangiocarcinoma

Opisthorchis viverrini-related cholangiocarcinoma (CCA), a fatal bile duct cancer, is a major public health concern in areas endemic for this parasite. We report here whole-exome sequencing of eight O. viverrini-related tumors and matched normal tissue. We identified and validated 206 somatic mutations in 187 genes using Sanger sequencing and selected 15 genes for mutation prevalence screening in an additional 46 individuals with CCA (cases). In addition to the known cancer-related genes TP53 (mutated in 44.4% of cases), KRAS (16.7%) and SMAD4 (16.7%), we identified somatic mutations in 10 newly implicated genes in 14.8-3.7% of cases. These included inactivating mutations in MLL3 (in 14.8% of cases), ROBO2 (9.3%), RNF43 (9.3%) and PEG3 (5.6%), and activating mutations in the GNAS oncogene (9.3%). These genes have functions that can be broadly grouped into three biological classes: (i) deactivation of histone modifiers, (ii) activation of G protein signaling and (iii) loss of genome stability. This study provides insight into the mutational landscape contributing to O. viverrini-related CCA.     

A model-based approach for analysis of spatial structure in genetic data

Characterizing genetic diversity within and between populations has broad applications in studies of human disease and evolution. We propose a new approach, spatial ancestry analysis, for the modeling of genotypes in two- or three-dimensional space. In spatial ancestry analysis (SPA), we explicitly model the spatial distribution of each SNP by assigning an allele frequency as a continuous function in geographic space. We show that the explicit modeling of the allele frequency allows individuals to be localized on the map on the basis of their genetic information alone. We apply our SPA method to a European and a worldwide population genetic variation data set and identify SNPs showing large gradients in allele frequency, and we suggest these as candidate regions under selection. These regions include SNPs in the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B.     

Mutations in the PCNA-binding domain of CDKN1C cause IMAGe syndrome

IMAGe syndrome (intrauterine growth restriction, metaphyseal dysplasia, adrenal hypoplasia congenita and genital anomalies) is an undergrowth developmental disorder with life-threatening consequences. An identity-by-descent analysis in a family with IMAGe syndrome identified a 17.2-Mb locus on chromosome 11p15 that segregated in the affected family members. Targeted exon array capture of the disease locus, followed by high-throughput genomic sequencing and validation by dideoxy sequencing, identified missense mutations in the imprinted gene CDKN1C (also known as P57KIP2) in two familial and four unrelated patients. A familial analysis showed an imprinted mode of inheritance in which only maternal transmission of the mutation resulted in IMAGe syndrome. CDKN1C inhibits cell-cycle progression, and we found that targeted expression of IMAGe-associated CDKN1C mutations in Drosophila caused severe eye growth defects compared to wild-type CDKN1C, suggesting a gain-of-function mechanism. All IMAGe-associated mutations clustered in the PCNA-binding domain of CDKN1C and resulted in loss of PCNA binding, distinguishing them from the mutations of CDKN1C that cause Beckwith-Wiedemann syndrome, an overgrowth syndrome.     

Maize HapMap2 identifies extant variation from a genome in flux

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize.     

An eicosanoid-centric view of atherothrombotic risk factors

Cardiovascular disease is the foremost cause of morbidity and mortality in the Western world. Atherosclerosis followed by thrombosis (atherothrombosis) is the pathological process underlying most myocardial, cerebral, and peripheral vascular events. Atherothrombosis is a complex and heterogeneous inflammatory process that involves interactions between many cell types (including vascular smooth muscle cells, endothelial cells, macrophages, and platelets) and processes (including migration, proliferation, and activation). Despite a wealth of knowledge from many recent studies using knockout mouse and human genetic studies (GWAS and candidate approach) identifying genes and proteins directly involved in these processes, traditional cardiovascular risk factors (hyperlipidemia, hypertension, smoking, diabetes mellitus, sex, and age) remain the most useful predictor of disease. Eicosanoids (20 carbon polyunsaturated fatty acid derivatives of arachidonic acid and other essential fatty acids) are emerging as important regulators of cardiovascular disease processes. Drugs indirectly modulating these signals, including COX-1/COX-2 inhibitors, have proven to play major roles in the atherothrombotic process. However, the complexity of their roles and regulation by opposing eicosanoid signaling, have contributed to the lack of therapies directed at the eicosanoid receptors themselves. This is likely to change, as our understanding of the structure, signaling, and function of the eicosanoid receptors improves. Indeed, a major advance is emerging from the characterization of dysfunctional naturally occurring mutations of the eicosanoid receptors. In light of the proven and continuing importance of risk factors, we have elected to focus on the relationship between eicosanoids and cardiovascular risk factors.     

Fall diet of blue grouse in Oregon

The early fall diet of Oregon blue grouse ( Dendragapus obscurus pallidus ) from Wallowa County, Oregon, was determined from 145 crops obtained during 1981 and 1982. Of more than 50 plant and animal foods in the diet, short-horned grasshoppers ( Acrididae ), prickly lettuce ( Lactuca serriola ), yellow salsify ( Tragopogon dubius ), wild buck-wheat ( Eriogonum spp.), and snowberry ( Symphoricarpos albus ) occurred in 30% or more of the crops and collectively amounted to 68% of the diet by weight. Seven of the 12 most common foods were consumed differentially by the four sex and age classes of birds. Results indicated that blue grouse foraged in forest and grassland habitats.     

Nutritional condition of elk in Rocky Mountain National Park

We tested the hypothesis that elk in Rocky Mountain National Park (RMNP) were at ecological carrying capacity by determining herd-specific levels of nutritional condition and fecundity. Ingesta-free body fat levels in adult cows that were lactating were 10.6% ( s = 1.7; range = 6.2-15.4) and 7.7% ( s = 0.5; range = 5.9-10.1) in November 2001 for the Horseshoe and Moraine Park herds, respectively. Cows that were not lactating were able to accrue significantly more body fat: 14.0% ( s = 1.1; range = 7.7-19.3) and 11.5% ( s = 0.8; range = 8.6-15.1) for the Horseshoe and Moraine Park herds, respectively. Cow elk lost most of their body fat over winter (April 2002 levels were 3.9% [ s = 0.4] and 2.9% [ s = 0.4] for the Horseshoe and Moraine Park herds, respectively). Nutritional condition indicated that both Horseshoe Park and Moraine Park elk were well below condition levels elk can achieve on very good-excellent nutrition (i.e., > 15% body fat; Cook et al. 2004) and were comparable to other free-ranging elk populations. However, condition levels were higher than those expected at a ""food-limited"" carrying capacity, and a proportion of elk in each herd were able to achieve condition levels indicative of very good-excellent nutrition. Elk in RMNP are likely regulated and/or limited by a complex combination of density-independent (including significant heterogeneity in forage conditions across RMNP's landscape) and density-dependent processes, as condition levels contradict a simple density-dependent model of a population at ecological carrying capacity.