MYH9 is associated with nondiabetic end-stage renal disease in African Americans

As end-stage renal disease (ESRD) has a four times higher incidence in African Americans compared to European Americans, we hypothesized that susceptibility alleles for ESRD have a higher frequency in the West African than the European gene pool. We carried out a genome-wide admixture scan in 1,372 ESRD cases and 806 controls and found a highly significant association between excess African ancestry and nondiabetic ESRD (lod score = 5.70) but not diabetic ESRD (lod = 0.47) on chromosome 22q12. Each copy of the European ancestral allele conferred a relative risk of 0.50 (95% CI = 0.39-0.63) compared to African ancestry. Multiple common SNPs (allele frequencies ranging from 0.2 to 0.6) in the gene encoding nonmuscle myosin heavy chain type II isoform A (MYH9) were associated with two to four times greater risk of nondiabetic ESRD and accounted for a large proportion of the excess risk of ESRD observed in African compared to European Americans.     

Differential effects of oncogenic K-Ras and N-Ras on proliferation, differentiation and tumor progression in the colon

Kras is commonly mutated in colon cancers, but mutations in Nras are rare. We have used genetically engineered mice to determine whether and how these related oncogenes regulate homeostasis and tumorigenesis in the colon. Expression of K-Ras(G12D) in the colonic epithelium stimulated hyperproliferation in a Mek-dependent manner. N-Ras(G12D) did not alter the growth properties of the epithelium, but was able to confer resistance to apoptosis. In the context of an Apc-mutant colonic tumor, activation of K-Ras led to defects in terminal differentiation and expansion of putative stem cells within the tumor epithelium. This K-Ras tumor phenotype was associated with attenuated signaling through the MAPK pathway, and human colon cancer cells expressing mutant K-Ras were hypersensitive to inhibition of Raf, but not Mek. These studies demonstrate clear phenotypic differences between mutant Kras and Nras, and suggest that the oncogenic phenotype of mutant K-Ras might be mediated by noncanonical signaling through Ras effector pathways.     

Arthropod community dynamics in undisturbed and intensively managed mountain brush habitats

The population dynamics and decomposition activities of litter arthropods in an unmanaged sagehrush/bitterbrush habitat in southeastern Wyoming were assessed in 1986. The effects of sagebrush/bitterbrush management practices on litter arthropod communities and the role of these communities in decomposition were also assessed. Insecticide applications were used to selectively exclude arthropods in order to determine the ecological impact of these detritivores. Application of a herbicide, 2,4-D, was associated with increased arthropod populations for 30 days following treatment. Mowing increased arthropod densities at two different times, 10-30 days and 50 days post treatment, perhaps as a result of functional and numerical responses by litter arthropods. Elimination of arthropods from otherwise undisturbed shrub habitats by the use of broad-spectrum insecticides reduced the rate of litter decomposition during the growing season, indicating that these organisms play an important role in decomposition and nutrient cycling.     

Effects of rangefire on soil algal crusts in semiarid shrub-steppe of the Lower Columbia Basin and their subsequent recovery

Effects of rangefire on soil algae in sagebrush steppe in the Lower Columbia Basin were studied. Dynamics of recovery of the soil algal community in the first two years following the fire were also documented. The study site was on the Arid Lands Ecology Reserve managed by Battelle Pacific Northwest Laboratory. Fire decreased the numbers of algae by more than an order of magnitude. Species composition in burned plots was similar to that in unburned plots, although some cyanophyte algae, particularly Nostoc commune , were decimated by the fire. Algal recovery took place in the winter months of the second year. Ninety taxa of algae were identified during the course of the study, over half of which were chlorophytes. Seasonal changes in the algal flora were also noted.     

Microbial spatial heterogeneity in microbiotic crusts in Colorado National Monument. I. Algae

Spatial heterogeneity in visually similar sites under Utah juniper canopy in Colorado National Monument was examined. Sample sites were arranged in a transect 24 m long, such that distances between samples were 0.013 m, 0.03 m, 1.0 m, 12 m, and 24 m. Twenty-five taxa of algae were observed, mostly belonging to Cyanophyta. Algal density varied by more than an order of magnitude within the 46 samples examined. The coefficients of variation for each distance class were very similar, demonstrating that algal patchiness can be as significant on a scale less than 0.013 m as it is on a scale of 24 m. Goodall's random pairing analysis of spatial pattern supported this conclusion by indicating that the minimal area for sampling soil algal crust populations at this site was equal to or less than 0.013 m. Because of the microscale heterogeneity in algal communities in this study, we recommend that future researchers take composite samples if they wish to quantify algae of microbiotic crusts.     

Composition of forest stands used by White-headed Woodpeckers for nesting in Washington

In this study, I examined the composition of managed ponderosa pine ( Pinus ponderosa ) forests used by nesting White-headed Woodpeckers ( Picoides albolarvatus ) along the eastern slope of the Cascade Range in Washington. I sampled trees and snags using the point-centered quarter method to assess species composition, tree and snag density, and stand basal area in 16 forest stands containing White-headed Woodpecker nests. All stands had a history of timber management and 2 had been burned and salvage-logged. Mean live-tree density (≥10.16 cm dbh) was 182.3 trees · ha –1 (SE = 13.52), mean snag density (≥10.16 cm dbh) was 11.5 snags · ha –1 (SE = 1.92), and mean stand basal area was 17.2 m 2 · ha –1 (SE = 1.58). Ponderosa pine had the highest importance value (mean = 220.9, SE = 17.25) of any tree species in all but 2 stands. Mean dbh of ponderosa pines was 33.0 cm (SE = 0.26) and ranged from 26.1 to 50.2 cm within stands. Mean density of ponderosa pine was greatest in the 20.3–30.5 cm dbh size class and lowest in the 50.8–61.0 cm and >61.0 cm dbh size classes. Tree density was up to 5.3 times greater than densities believed to be typical of ponderosa pine forests prior to fire suppression. Snag densities were within the range estimated for historical dry forests of the eastern Cascades, yet only 50% of all snags sampled had a dbh >25.4 cm. Although White-headed Woodpeckers are considered strongly associated with old-growth ponderosa pine, my results suggest that they may be more adaptable to using forests dominated by smaller diameter trees. En este estudio, examiné la composición de los bosques manejados de pino ponderosa ( Pinus ponderosa ), utilizados para anidamiento por el pájaro carpintero cabeciblanco ( Picoides albolarvatus ), a lo largo de la vertiente oriental de la cordillera Cascade del Estado de Washington. Muestreé árboles vivos y muertos usando el método de cuadrantes al punto central en 16 rodales con nidos del pájaro carpintero cabeciblanco para evaluar la composición de especies, la densidad de árboles vivos y muertos y el área basal del rodal. Todas las áreas tenían una historia de manejo maderable y 2 habían sido quemadas y taladas para recuperar madera. La densidad promedio de árboles vivos (≥10.16 cm DAP) fue 182.3 árboles · ha –1 (DE = 13.52), la densidad promedio de árboles muertos (≥10.16 cm DAP) fue 11.5 árboles muertos · ha –1 (DE = 1.92) y el área basal promedio de los rodales fue 17.2 m 2 · ha –1 (DE = 1.58). El pino ponderosa tuvo el valor de importancia más alto (promedio = 220.9, DE = 17.25) de las especies de árboles en todos, menos 2 rodales. El DAP promedio de los pinos ponderosa fue 33.0 cm (DE = 0.26) y variaba de 26.1 a 50.2 cm dentro de rodales. La densidad promedio del pino ponderosa fue la mayor en la clase de 20.3–30.5 cm DAP y menor de las clases de 50.8–61.0 cm y >61.0 cm DAP. La densidad de árboles fue hasta 5.3 veces mayor que las consideradas típicas para bosques de pino ponderosa antes de la intervención para prevenir incendios. Las densidades de árboles muertos estuvo dentro del rango estimado para los bosques secos históricos del oriente de la cordillera Cascade, no obstante sólo 50% de los árboles muertos muestreados tuvieron un DAP >25.4 cm. Aunque se considera que los pájaros carpinteros cabeciblancos están estrechamente asociados con bosques primarios de pino ponderosa, mis resultados sugieren que podrían ser más adaptados a usar bosques donde predominan árboles de diámetro menor.     

Lichens of soil crust communities in the Intermountain Area of the western United States

Lichens are common components of microbiotic soil crusts. A total of 34 species from 17 genera are reported from soil crust communities throughout the Intermountain Area. Distribution of terricolous lichens is determined by various physical and biological factors: physical and chemical characteristics of the soil, moisture regimes, temperature, insolation, and development and composition of the vascular plant community. Some species demonstrate a broad ecological amplitude while others have a more restricted distribution. All growth forms are represented; however, the vast majority of soil crust lichens are squamulose (minutely foliose). Fruticose species are least abundant. In exposed, middle-elevation sites vagrant (detached) species are common. This paper describes and discusses terricolous lichen communities of desert habitats of the intermountain western United States. Effects of various human-related activities including grazing, wildfire, air pollution, and recreation vehicles on soil crust lichens are discussed. Gypsoplaca macrophylla (Zahlbr.) Timdal, a rare squamulose lichen which occurs on gypsifersous soils, was recently collected in Emery County, Utah, and is reported as new to the state.     

The genome of the extremophile crucifer Thellungiella parvula

Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance.     

Loss of the SKI proto-oncogene in individuals affected with 1p36 deletion syndrome is predicted by strain-dependent defects in Ski-/- mice.

Experiments involving overexpression of Ski have suggested that this gene is involved in neural tube development and muscle differentiation. In agreement with these findings, Ski-/- mice display a cranial neural tube defect that results in exencephaly and a marked reduction in skeletal muscle mass. Here we show that the penetrance and expressivity of the phenotype changes when the null mutation is backcrossed into the C57BL6/J background, with the principal change involving a switch from a neural tube defect to midline facial clefting. Other defects, including depressed nasal bridge, eye abnormalities, skeletal muscle defects and digit abnormalities, show increased penetrance in the C57BL6/J background. These phenotypes are interesting because they resemble some of the features observed in individuals diagnosed with 1p36 deletion syndrome, a disorder caused by monosomy of the short arm of human chromosome 1p (refs. 6-9). These similarities prompted us to re-examine the chromosomal location of human SKI and to determine whether SKI is included in the deletions of 1p36. We found that human SKI is located at distal 1p36.3 and is deleted in all of the individuals tested so far who have this syndrome. Thus, SKI may contribute to some of the phenotypes common in 1p36 deletion syndrome, and particularly to facial clefting.