A genome-wide map of diversity in Plasmodium falciparum

Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (pi = 1.16 x 10(-3)) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite.     

The NCBI dbGaP database of genotypes and phenotypes

The National Center for Biotechnology Information has created the dbGaP public repository for individual-level phenotype, exposure, genotype and sequence data and the associations between them. dbGaP assigns stable, unique identifiers to studies and subsets of information from those studies, including documents, individual phenotypic variables, tables of trait data, sets of genotype data, computed phenotype-genotype associations, and groups of study subjects who have given similar consents for use of their data.     

Conservation status of threatened fishes in Warner Basin, Oregon

Two federally listed fishes, the Foskett speckled dace and Warner sucker, are endemic to Warner Basin in south central Oregon. The Foskett speckled dace is native only to a single spring in Coleman Valley. A nearby spring was stocked with dace in 1979 and 1980, and now provides a second population. The present numbers of dace probably are at their highest levels since settlement of the region. The Warner sucker historically occurred throughout much of the Warner Valley, but its distribution and abundance have been reduced by construction of reservoirs and irrigation dams and the introduction of predatory game fishes. Lentic habitats have become dominated by introduced fishes, particularly white crappie, black crappie, and brown bullhead. The largest remaining population of Warner suckers occurs in Hart Lake, where successful reproduction was documented but there is no evidence of recruitment to the adult population.     

Overwinter survival of ring-necked pheasants in Utah

The influence of winter weather on the survival of Utah's ring-necked pheasants was evaluated using correlation analysis. This method used published Utah State Division of Wildlife Resources population data and a calculated winter warmth index. Results show four different patterns of survival occurring in the 14 counties analyzed.     

Vegetation zones and soil characteristics in vernal pools in the Channeled Scabland of eastern Washington

Vernal pools are seasonal pools occurring in Mediterranean-type climates within which grow concentric zones of vegetation. We studied two vernal pools that lie within an Artemisia tridentata/Festuca idahoensis shrub-steppe landscape in the Channeled Scabland of eastern Washington to determine the relationship between vegetation zonation and soil characteristics. Abundant plant species in the pools include Elymus cinereus, Poa scabrella, Lomatium grayi, Allium geyeri, Eleocharis palustris, Epilobium minutum, Myosurus aristatis, Deschampsia danthonioides, and Psilocarphus oregonus . We surveyed topography, measured plant species frequency and cover to describe the vegetation zones, and used Sorenson's index of percent to similarity to verify our designation of plant zones as communities. In one pool we described soil profiles and sampled soils throughout the growing season according to plant communities. We analyzed soils for pH; electrical conductivity; sodium, calcium, and magnesium ions; sodium absorption ratio; particle size; organic carbon; and water matric potential. ANOVA tests of soil characteristics and topography among plant communities showed that only differences in topography are statistically significant. There are, however, trends in particle size, some soil chemical parameters, and soil moisture potential among plant communities along the topographic gradient. Electrical conductivity decreased with increasing dryness of the soil through spring and summer. Seasonal changes in soil moisture potential showed that shallower soils in the centers of pools were wetter during the wet season and drier during the dry season than are deeper soils. These changes in moisture may be the most important influence on vegetation distribution within the vernal pools.     

GPR39: a Zn<Superscript>2+</Superscript>-activated G protein-coupled receptor that regulates pancreatic,gastrointestinal and neuronal functions

GPR39 is a vertebrate G protein-coupled receptor related to the ghrelin/neurotensin receptor subfamily. The receptor is expressed in a range of tissues including the pancreas, gut/gastrointestinal tract, liver, kidney and in some regions of the brain. GPR39 was initially thought to be the cognitive receptor for the peptide hormone, obestatin. However, subsequent in vitro studies have failed to demonstrate binding of this peptide to the receptor. Zn²⁺ has been shown to be a potent stimulator of GPR39 activity via the Gα_q, Gα_12/13 and Gα_s pathways. The potency and specificity of Zn²⁺ in activating GPR39 suggest it to be a physiologically important agonist. GPR39 is now emerging as an important transducer of autocrine and paracrine Zn²⁺ signals, impacting upon cellular processes such as insulin secretion, gastric emptying, neurotransmission and epithelial repair. This review focuses on the molecular, structural and biological properties of GPR39 and its various physiological functions.     

DMP1 mutations in autosomal recessive hypophosphatemia implicate a bone matrix protein in the regulation of phosphate homeostasis

Hypophosphatemia is a genetically heterogeneous disease. Here, we mapped an autosomal recessive form (designated ARHP) to chromosome 4q21 and identified homozygous mutations in DMP1 (dentin matrix protein 1), which encodes a non-collagenous bone matrix protein expressed in osteoblasts and osteocytes. Intact plasma levels of the phosphaturic protein FGF23 were clearly elevated in two of four affected individuals, providing a possible explanation for the phosphaturia and inappropriately normal 1,25(OH)2D levels and suggesting that DMP1 may regulate FGF23 expression.