Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration

Age-related macular degeneration (AMD) is a common, late-onset disease with seemingly typical complexity: recurrence ratios for siblings of an affected individual are three- to sixfold higher than in the general population, and family-based analysis has resulted in only modestly significant evidence for linkage. In a case-control study drawn from a US-based population of European descent, we have identified a previously unrecognized common, noncoding variant in CFH, the gene encoding complement factor H, that substantially increases the influence of this locus on AMD, and we have strongly replicated the associations of four other previously reported common alleles in three genes (P values ranging from 10(-6) to 10(-70)). Despite excellent power to detect epistasis, we observed purely additive accumulation of risk from alleles at these genes. We found no differences in association of these loci with major phenotypic categories of advanced AMD. Genotypes at these five common SNPs define a broad spectrum of interindividual disease risk and explain about half of the classical sibling risk of AMD in our study population.     

Early life history of the sheepnose (Plethobasus cyphyus) (Mollusca: Bivalvia: Unionoida)

Managing a rare species can be improved with knowledge of its natural history. The sheepnose (Plethobasus cyphyus) is a freshwater mussel recently listed by the US as federally endangered. We used standard methods to study P. cyphyus brooding behaviour, host fishes in the laboratory and under natural conditions, and glochidial morphology. We monitored a population of P. cyphyus in the Chippewa River, WI during spring and summer 2007–2009 and 2011 and found brooding animals between mid-May and early August. Gravid individuals ranged between 5 and 27 yr (mean age ± 1 s.d. = 13 ± 4 yr). Plethobasus cyphyus brooded glochidia in outer gills, which varied in colour from red, orange, pink, cream, or white. We observed mature glochidia more commonly in individuals with cream or white gills and these glochidia were released in a clear, adhesive, mucus matrix. In laboratory trials we found several minnow and topminnow species (29 spp.) served as productive suitable native hosts. The mean number of juvenile mussels released per cyprinid per day was significantly higher for trials conducted at 22–25°C compared with those at 18–20°C, and 83% of trials conducted at 18–20°C using suitable host species produced no juveniles. Glochidia had a unique outline and shell morphometrics that distinguished P. cyphyus from seven other Chippewa River mussel species that produce similar sized glochidia. Using morphometrics we determined that mimic shiners (Notropis volucellus) were natural hosts for P. cyphyus, round pigtoe (Pleurobema sintoxia), and Wabash pigtoe (Fusconaia flava). Releasing mucus-bound glochidia has evolved in a variety of mussel species and may be more common than is currently realized. Our data show that P. cyphyus is a cyprinid host specialist, and propagation efforts for this species can be strengthened through improved access to mature glochidia by using females with cream-coloured gills and increased juvenile production through warmer fish holding temperatures.     

Riparian vegetation along the middle Snake River, Idaho: zonation, geographical trends, and historical changes

A baseline study was conducted on an 83-km free-flowing reach of the Snake River between Swan Falls Dam and the Idaho-Oregon border. The research had 2 components: (1) field characterization and inventory of existing riparian flora, vegetation, and environment (soils, topography, streamflow), and (2) determination and mapping, using a geographic information system, of historic changes in riparian vegetation based on a time series (1938-39, 1957, 1969, 1987) of aerial photographs. The flora was diverse, with 185 species of vascular plants identified, 63 of which were exotics. Vegetation was structured vertically along the riverbank gradient into lifeform-defined habitat types: emergent, riparian shrub-forb, tree, transitional grass-shrub, and upland. Riverbank seepage, probably of agricultural origin, blurred zonation patterns on some sites and added species to the overall flora. Upstream-downstream differences existed in the physical characteristics and vegetation of river subreaches. Coverage of riparian woodland, island riparian and total riparian vegetation, and area of islands increased since the 1930s, with the greatest changes in the 1969-1987 interval. Possible contributing facts were (1) significant declines in annual minimum flows since the 1950s, (2) decreases in peak flows following the completion of Swan Falls Dam and some upstream dams since the 1920s, (3) introduction and spread of exotic tree species ( Elaeagnus angustifolia and Tamarix spp.) and (4) possible effects of intensive agriculture on river sediment load and soil nutrients. The introduction and proliferation of purple loosestrife ( Lythrum salicaria ) could have considerable future effects on vegetation-channel dynamics in the middle Snake River.     

Habitat use of leatherside chub ( Gila copei ) in the presence of predatory brown trout ( Salmo trutta )

The objectives of this study were to (1) examine distribution and habitat use of leatherside chub ( Gila copei ) in a creek with high densities of predatory brown trout ( Salmo trutta ), and (2) compare study results with published accounts of leatherside chub habitat use in streams with few or no brown trout. A 14-km section of Diamond Fork Creek, Utah, was point-shocked to determine macrohabitat (main channel and lateral habitat) and microhabitat (current, depth, substrate, and cover) use of leatherside chug. At the macrohabitat level, leatherside chub were most common in lower reaches of Diamond Fork Creek where the channel was braided and lateral habitats (cutoff pools and backwaters) were abundant. Only a single leatherside chub was found in the main channel of Diamond Fork. Investigations in other systems lacking brown trout indicated that leatherside chub occupy main channel habitats. At the microhabitat level, we found significant positive associations between presence of leatherside chub and both habitat depth and silt. In addition, we found a significant negative association between presence of leatherside chub and number of brown trout. Our results suggest predation by brown trout may limit leatherside chub to lateral habitats that could provide refugia against predation. The introduction of brown trout to systems with little lateral habitat could have serious effects on persistence of resident leatherside chub populations.     

Presence of hepcidin-25 in biological fluids: Bile,ascitic and pleural fluids

AIM: To examine body fluids such as ascitic fluid (AF),saliva,bile and pleural effusions for the presence of hepcidin using a novel radioimmunoassay (RIA).METHODS: Serum samples were collected from 25 healthy volunteers (mean age: 36 ± 11.9 years,11 males,14 females).In addition bile was obtained from 12 patients undergoing endoscopic retrograde cholangiopancreatography (mean age: 66.9 ± 16.7 years,M:F = 5:7).Saliva was collected from 17 healthy volunteers (mean age: 35 ± 9.9 years,M:F = 8:9).Pleural and AF...     

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14

The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7-2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors-including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes-may cause the number of malaria cases to double over the next two decades. To stimulate basic research and facilitate the development of new drugs and vaccines, the genome of Plasmodium falciparum clone 3D7 has been sequenced using a chromosome-by-chromosome shotgun strategy. We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence. These chromosomes represent about 35% of the 23-megabase P. falciparum genome.     

Distance Models for Three-Way Tables and Three-Way Association

p similarity function, the L _p -transform and the Minkowski-p distance. For triadic distance models defined by the L _p -transform we will prove that they do not model three-way association. Moreover, triadic distance models defined by the L _p -transform are restricted multiple dyadic distances, where each dyadic distance is defined for a two-way margin of the three-way table. Distance models for three-way two-mode data, called three-way distance models, do succeed in modeling three-way association.