An independent microbial flora of the epithelium and its role in the ecomicrobiology of the rumen

IT has been suggested that the bacterial flora of the rumen should be considered as three distinct, interacting populations-the bacteria of rumen fluid (the population which has been studied most extensively), the bacteria associated with food particles, and the bacteria adhering to the epithelial wall of the organ(1). Until now, studies of the 'epithelial' population have been restricted to examination of postmortem samples of wall tissue and its attached bacterial flora(2-5). A recently developed technique(6) for feeding young sheep for long periods solely by infusion of protein and other essential nutrients into the abomasum, and of volatile fatty acids and bicarbonate buffer into the rumen, has provided us with an opportunity to study in isolation the role of the bacterial population of the wall in the ecomicrobiology of the rumen in the living animal. Our studies show that this population can exist independently of the other two populations, that it is primarily responsible for urea digestion in the rumen and that it initiates breakdown of dead epithelial tissue. Furthermore, our results point to an inverse relationship between ammonia concentration and ureolytic activity in rumen fluid, which may account for the control which ammonia exerts over flux of urea across the rumen wall(7-9).     

Interactions among squirrels, mycorrhizal fungi, and coniferous forests in Oregon

We examined the mycophagy (ingestion of fungi) of squirrels of five genera and eight species in the coniferous forests of Oregon. Data from 644 dietary samples demonstrated that squirrels of all eight species are mycophagous and eat the belowground fruiting bodies of at least 26 genera of mycorrhizal fungi. Four species are primarily arboreal and active throughout the year; the other four are primarily terrestrial and hibernate during winter. Of the squirrels examined, only the northern flying squirrel ( Glaucomys sabrinus [Shaw]) is nocturnal and almost exclusively a fungivore. The flying squirrel is used to illustrate the dynamics of all the squirrels in association with hypogeous mycorrhizal fungi, nitrogen-fixing bacteria, yeast, and coniferous trees in Oregon forests because we have studied it the most. Squirrels may prove to be vital links among different processes within temperate coniferous forests.     

Distribution of the Shoshone scuplin ( Cottus greenei: Cottidae) in the Hagerman Valley of south central Idaho

Cottus greenei, a potentially threatened species endemic to Idaho, was collected from 49 localities in 25 springs/streams in south central Idaho. Most localities were along the north bank of the Snake River in waters of the Thousand Springs formation, Gooding County. One population was found in a spring in the main Snake River. Another sculpin, Cottus bairdi, was collected with C. greenei at 23 locations in 16 springs/streams. Confusion concerning the type locality of Cottus greenei is discussed.        

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.     

Genome-wide detection and characterization of positive selection in human populations

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.     

A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21

We tested 310,605 SNPs for association in 778 individuals with celiac disease and 1,422 controls. Outside the HLA region, the most significant finding (rs13119723; P = 2.0 x 10(-7)) was in the KIAA1109-TENR-IL2-IL21 linkage disequilibrium block. We independently confirmed association in two further collections (strongest association at rs6822844, 24 kb 5' of IL21; meta-analysis P = 1.3 x 10(-14), odds ratio = 0.63), suggesting that genetic variation in this region predisposes to celiac disease.