Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event

Streptococcus pneumoniae ('pneumococcus') causes an estimated 14.5 million cases of serious disease and 826,000 deaths annually in children under 5 years of age(1). The highly effective introduction of the PCV7 pneumococcal vaccine in 2000 in the United States(2,3) provided an unprecedented opportunity to investigate the response of an important pathogen to widespread, vaccine-induced selective pressure. Here, we use array-based sequencing of 62 isolates from a US national monitoring program to study five independent instances of vaccine escape recombination(4), showing the simultaneous transfer of multiple and often large (up to at least 44 kb) DNA fragments. We show that one such new strain quickly became established, spreading from east to west across the United States. These observations clarify the roles of recombination and selection in the population genomics of pneumococcus and provide proof of principle of the considerable value of combining genomic and epidemiological information in the surveillance and enhanced understanding of infectious diseases.     

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

To identify somatic mutations in pediatric diffuse intrinsic pontine glioma (DIPG), we performed whole-genome sequencing of DNA from seven DIPGs and matched germline tissue and targeted sequencing of an additional 43 DIPGs and 36 non-brainstem pediatric glioblastomas (non-BS-PGs). We found that 78% of DIPGs and 22% of non-BS-PGs contained a mutation in H3F3A, encoding histone H3.3, or in the related HIST1H3B, encoding histone H3.1, that caused a p.Lys27Met amino acid substitution in each protein. An additional 14% of non-BS-PGs had somatic mutations in H3F3A causing a p.Gly34Arg alteration.     

Trafficking and stability of voltage-gated calcium channels

Voltage-gated calcium channels are important mediators of calcium influx into electrically excitable cells. The amount of calcium entering through this family of channel proteins is not only determined by the functional properties of channels embedded in the plasma membrane but also by the numbers of channels that are expressed at the cell surface. The trafficking of channels is controlled by numerous processes, including co-assembly with ancillary calcium channel subunits, ubiquitin ligases, and interactions with other membrane proteins such as G protein coupled receptors. Here we provide an overview about the current state of knowledge of calcium channel trafficking to the cell membrane, and of the mechanisms regulating the stability and internalization of this important ion channel family.     

Habitat and nesting biology of Mountain Plovers in Wyoming

Although previous research has considered habitat associations and breeding biology of Mountain Plovers in Wyoming at discrete sites, no study has considered these attributes at a statewide scale. We located 55 Mountain Plover nests in 6 counties across Wyoming during 2002 and 2003. Nests occurred in 2 general habitat types: grassland and desert-shrub. Mean estimated hatch date was 26 June ( n = 31) in 2002 and 21 June ( n = 24) in 2003. Mean hatch date was not related to latitude or elevation. Hatch success of nests was inferred in 2003 by the presence of eggshell fragments in the nest scrape. Eggs in 14 of 22 (64%) known-fate nests hatched. All grassland sites and 90% of desert sites were host to ungulate grazers, although prairie dogs were absent at 64% of nest sites. Nest plots had less grass coverage and reduced grass height compared with random plots. More than 50% of nests occurred on elevated plateaus. The Mountain Plover's tendency to nest on arid, elevated plateaus further substantiates claims that the bird is also a disturbed- prairie species.     

Distribution of Brechmorhoga clubskimmers (Odonata: Libellulidae) in the Grand Canyon region, southwestern USA

We examined the distribution of Brechmorhoga mendax and B. pertinax (Libellulidae) in northern Arizona and southern Nevada. Brechmorhoga mendax occurs widely throughout the Southwest and in Arizona up to the Mogollon Rim, and up the Colorado River from the west to at least River Mile 132 (downstream from Lees Ferry, Arizona) at elevations of 110-1460 m. In Grand Canyon it occurs along small to large tributaries and on the mainstream at elevations below 650 m. The only previously reported locality for B. pertinax in the United States is in southeastern Arizona, where it was presumed to be accidental. We report B. pertinax along 5 small, perennial tributaries emanating from Redwall Formation aquifer springs on the south side of central Grand Canyon. Those springs habitats may be threatened by regional groundwater depletion. Brechmorhoga pertinax appears to be somewhat more stenotolerant in its habitat requirements than B. mendax , a finding in keeping with these differences in range. The presence of isolated populations of B. pertinax in Grand Canyon is an example of a Neotropical influence on the fauna and indicates biogeographic corridor and refuge functions of this large, deep canyon.     

Biogeographic and taxonomic relationships among the mountain snails (Gastropoda: Oreohelicidae) of the central Great Basin

Described here are 4 species of mountain snails, Oreohelix , isolated on mountains in the central Great Basin of Nevada and Utah since the end of the Pleistocene. Forty-three mountains were searched during an 18-year period, resulting in 24 mountains found with no oreohelicids present. One population, Oreohelix loisae (19 mm to 23 mm in shell diameter), is described here as a new species related to, but geographically isolated from, the species Oreohelix nevadensis (17 mm to 22 mm diameter). Oreohelix loisae is present only in the Goshute Mountains while O. nevadensis is represented in 3 geographically adjacent ranges in the central Great Basin. These 2 species are possibly related to the Oreohelix haydeni group from the northern Wasatch Range. The subspecies Oreohelix strigosa depressa (15 mm to 21 mm diameter) is present on 11 ranges from western Utah west to east central Nevada. This subspecies is closely related to populations found today in the northern Wasatch Mountains of Utah. The smallest species in diameter (8 mm to 14 mm), Oreohelix hemphilli , is centered in the central Great Basin and found on 16 ranges often in sympatry with 1 or 2 of the larger conspecifics. Both qualitative and quantitative information on shell characters and soft anatomy is provided here for these 4 species. Shell characters, soft anatomy, geographical isolation, and statistical analysis suggest that 4 distinct species inhabit the central Great Basin today. Xeric and calciphilic species include O. hemphilli and O. loisae , while O. strigosa and O. nevadensis typically are associated with permanent water and both metamorphic and limestone mountains.     

Recurrence of Mexican long-tongued bats ( Choeronycteris mexicana ) at historical sites in Arizona and New Mexico

The Mexican long-tongued bat ( Choeronycteris mexicana ) is a nectar-eating species that seasonally inhabits the southwestern United States. Since 1906, fewer than 1500 individuals of C. mexicana have been documented throughout the range of the species. We conducted a field survey in Arizona and New Mexico during summer 1999 to check historically occupied areas for recurrence of C. mexicana . We observed C. mexicana occupying a majority (75%, n = 18) of visited sites. Multiple individuals were observed at many sites, including young-of-year. Choeronycteris mexicana roosted in lighted areas close to entrances within mine adits, abandoned buildings, wide rock crevices, and caves. All occupied sites in Madrean evergreen woodlands or semidesert grasslands where species of Agave were present. Most sites were located near a water source and, with the exception of a single site, near areas of riparian vegetation. Sites at which we did not encounter C. mexicana were frequently disturbed, difficult to search, or historically occupied by single individuals. Based on the relatively high rate of bat recurrence, we do not believe that populations of C. mexicana in the region have declined dramatically over the past several decades.     

Early brood-rearing habitat use and productivity of Greater Sage-Grouse in Wyoming

Populations of Greater Sage-Grouse ( Centrocercus urophasianus ) have been declining throughout their range since the 1960s. Productivity, which includes production and survival of young, is often cited as a factor in these declines. We monitored radio-equipped Greater Sage-Grouse at 3 sites in western Wyoming to assess early brood-rearing habitat use (through 14 days post-hatch) and productivity. Logistic and linear regression analyses with Akaike's Information Criterion were used to evaluate early brooding habitat use and to examine relationships between productivity and vegetation, insect size and abundance, and weather parameters. Females with broods were found in areas with greater sagebrush canopy and grass cover, and fewer invertebrates compared to random areas. The number of juveniles per female (estimated from wing barrel collections during fall harvest) was positively related to the abundance of medium-length Hymenoptera and grass cover, and the proportion of females with confirmed chicks 14 days post-hatch was positively related to abundance of medium-length Coleoptera and total herbaceous cover. Although the specific parameters varied slightly, Greater Sage-Grouse productivity in Wyoming appeared to be associated with a combination of insect and herbaceous cover elements. Managing for abundant and diverse insect communities within dense protective sagebrush stands should help ensure high-quality early brood-rearing habitat and increased Greater Sage-Grouse productivity.     

Arthropod and plant communities as indicators of land rehabilitation effectiveness in a semiarid shrubsteppe

We describe a case study evaluating the ecological impact of Bromus tectorum L. (cheatgrass) invasion following fire disturbance and the effectiveness of revegetation as a means of rehabilitation in a degraded semiarid shrubsteppe system. The effectiveness of rehabilitation efforts was assessed relative to arthropod richness, vegetation and arthropod community composition, and ground-cover characteristics in 3 habitats: undisturbed, burned and weed infested ( B. tectorum ), and burned then rehabilitated with native and nonnative vegetation. Arthropods were collected in each habitat using pitfall traps. Differences in arthropod richness were compared using rarefaction curves. Nonmetric multidimensional scaling and nonparametric multivariate statistical procedures, including analysis of similarity and similarity percentage routines, were used to compare arthropod and vegetation community composition and ground-cover characteristics between habitats. Arthropod communities in the rehabilitated habitat were distinct from those observed in the undisturbed and weed-infested habitats. Rehabilitation in this study resulted in a shift toward conditions observed in an undisturbed habitat and perhaps is an intermediate step to complete restoration. Arthropod richness, arthropod and vegetation community composition, and ground-cover characteristics were all useful indicators but returned slightly different results. Assessing multiple variables yielded the most complete understanding of the habitats studied.     

A relocation technique for black-tailed prairie dogs

Relocations of black-tailed prairie dogs have occurred both to save individual prairie dogs from urban development and to reestablish populations that have been extirpated. Unfortunately, however, many past relocation efforts rarely exceeded 40% retention. Many factors have contributed to very low retention rates in past relocation efforts including lack of (1) suitable habitat, (2) proper artificial burrow systems, (3) aboveground acclimation cages or pens, and (4) skilled people conducting the relocations. In an attempt to increase prairie dog relocation success, we developed techniques that are easy to implement, promote high retention, and effectively conserve labor, financial resources, and prairie dog populations. We conducted 3 relocations along the Front Range of Colorado in 2001 and 2002. Relocation techniques we developed resulted in at least 46%-92% retention. Our results suggest that a large percentage of prairie dogs can be retained by (1) ensuring that habitat is suitable, (2) using underground nest chambers modeled after natural nest chambers, (3) acclimating prairie dogs to the release site in large retention pens rather than in retention caps or other small acclimation cages (i.e., rabbit hutch), and (4) providing supplemental feed and water ad libitum to the prairie dogs.