Notes on significant collections and additions to the flora of Glen Canyon National Recreation Area, Utah and Arizona, between 1992 and 2004

Symphyotrichum expansum (Puepp ex Spreng.) Nesom is reported new to Utah from the Escalante River drainage. A major range extension is reported for Aralia racemosa L. in the Escalante drainage, and additional populations are reported of the rare species Imperata brevifolia Vasey in Utah, including the 1st record for the Grand Staircase--Escalante National Monument. Heterotheca grandiflora Nutt. is reported new to north central Arizona. New locations and notes on an additional 22 rare species in Glen Canyon National Recreation Area are listed.     

Common variants at TRAF3IP2 are associated with susceptibility to psoriatic arthritis and psoriasis

Psoriatic arthritis (PsA) is an inflammatory joint disease that is distinct from other chronic arthritides and which is frequently accompanied by psoriasis vulgaris (PsV) and seronegativity for rheumatoid factor. We conducted a genome-wide association study in 609 German individuals with PsA (cases) and 990 controls with replication in 6 European cohorts including a total of 5,488 individuals. We replicated PsA associations at HLA-C and IL12B and identified a new association at TRAF3IP2 (rs13190932, P = 8.56 × 10?1?). TRAF3IP2 was also associated with PsV in a German cohort including 2,040 individuals (rs13190932, P = 1.95 × 10?3). Sequencing of the exons of TRAF3IP2 identified a coding variant (p.Asp10Asn, rs33980500) as the most significantly associated SNP (P = 1.13 × 10?2?, odds ratio = 1.95). Functional assays showed reduced binding of this TRAF3IP2 variant to TRAF6, suggesting altered modulation of immunoregulatory signals through altered TRAF interactions as a new and shared pathway for PsA and PsV.     

Influence of precipitation and temperature on ring, annual branch increment, and needle growth of White Fir and Douglas-fir in central Utah

The study evaluates growth variations in mixed stands of Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) and White Fir ( Abies concolor Hoopes) from the Bighorn Ranch in northern Sanpete County, Utah. The study area lies 26 km southwest of Thistle, Utah. Tree-ring width, annual branch growth and needle length for the period 1970–1976 were obtained from Douglas-Fir and White Fir individuals distributed along an altitudinal and moisture gradient. Elevation ranged from 2257 m to 2500 m above sea level. Temperature and precipitation are shown to exert a significant influence on needle and annual branch growth and width of the annual rings. It was found that multiple correlation coefficients were always larger than the simple correlation coefficients. This suggests that the trees are responding to both temperature and precipitation. Annual branch growth is shown to be positively correlated with ring width and needle length. The influence of precipitation on growth is synchronized with 1 October–1 June precipitation. Best growth occurs in cool, moist years and at lower elevations.     

Comparison of two roadside survey procedures for dwarf mistletoes on the Sawtooth National Forest, Idaho

Two roadside surveys were conducted for dwarf mistletoes parasitizing lodgepole pine and Douglas-fir on the Sawtooth National Forest, Idaho. One survey used variable-radius plots located less than 150 m from roads. The 2nd survey used variable-radius plots established at 200-m intervals along 1600-m transects run perpendicular to the same roads. Estimates of the incidence (percentage of trees infected and percentage of plots infested) and severity (average dwarf mistletoe rating) for both lodgepole pine and Douglas-fir dwarf mistletoes were not significantly different for the 2 survey methods. These findings are further evidence that roadside-plot surveys and transect-plot surveys conducted away from roads provide similar estimates of the incidence of dwarf mistletoes for large forested areas.     

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.     

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.     

Temporal and spatial patterns of small mammal density and species composition on a radioactive waste disposal area: the role of edge habitat

Small mammal populations inhabiting radioactive waste disposal areas could be important vectors of contaminant redistribution, given sufficiently high numbers. Earlier studies conducted at the Subsurface Disposal Area (SDA) in southeastern Idaho found small mammal densities equaling or exceeding densities in native habitat. Our live-trapping study was conducted in 1988 and 1989 to assess the role of edge habitat (where SDA crested wheatgrass [ Agropyron cristatum ] plantings and native sagebrush habitat are separated by an earthen dike) in facilitating use of this highly modified site by small mammals. Small mammals had a significantly greater density in SDA edge habitat than in the interior. Total density of small mammals and immediately around the SDA appeared to be less variable over time than density in native sagebrush habitat for years when data were available. This phenomenon was largely attributable to steady or increasing SDA population densities of the most common species, Peromyscus maniculatus and Perognathus parvus , during 1988-89, when most small mammal species had below-average densities in surrounding areas. The variety of foraging options in edge habitat may have allowed these relatively opportunistic species to avoid widespread population declines associated with drought years in 1988-89. Movements by P. manicualtus across the boundary were common, suggesting that this species did indeed utilize both habitat types. Preferences for edge habitat could potentially be used to formulate strategies that reduce use of waste site by small mammals.