A microbial symbiosis factor prevents intestinal inflammatory disease

Humans are colonized by multitudes of commensal organisms representing members of five of the six kingdoms of life; however, our gastrointestinal tract provides residence to both beneficial and potentially pathogenic microorganisms. Imbalances in the composition of the bacterial microbiota, known as dysbiosis, are postulated to be a major factor in human disorders such as inflammatory bowel disease. We report here that the prominent human symbiont Bacteroides fragilis protects animals from experimental colitis induced by Helicobacter hepaticus, a commensal bacterium with pathogenic potential. This beneficial activity requires a single microbial molecule (polysaccharide A, PSA). In animals harbouring B. fragilis not expressing PSA, H. hepaticus colonization leads to disease and pro-inflammatory cytokine production in colonic tissues. Purified PSA administered to animals is required to suppress pro-inflammatory interleukin-17 production by intestinal immune cells and also inhibits in vitro reactions in cell cultures. Furthermore, PSA protects from inflammatory disease through a functional requirement for interleukin-10-producing CD4+ T cells. These results show that molecules of the bacterial microbiota can mediate the critical balance between health and disease. Harnessing the immunomodulatory capacity of symbiosis factors such as PSA might potentially provide therapeutics for human inflammatory disorders on the basis of entirely novel biological principles.     

Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses

We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks （Agaricomycetes/Agaricomycotina/Basidiomycota） along with the most recent treatments of taxonomic systems in these taxa. Establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized.     

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

Bacteria and Archaea have developed several defence strategies against foreign nucleic acids such as viral genomes and plasmids. Among them, clustered regularly interspaced short palindromic repeats (CRISPR) loci together with cas (CRISPR-associated) genes form the CRISPR/Cas immune system, which involves partially palindromic repeats separated by short stretches of DNA called spacers, acquired from extrachromosomal elements. It was recently demonstrated that these variable loci can incorporate spacers from infecting bacteriophages and then provide immunity against subsequent bacteriophage infections in a sequence-specific manner. Here we show that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading to plasmid loss. Acquired spacers that match antibiotic-resistance genes provide a novel means to naturally select bacteria that cannot uptake and disseminate such genes. We also provide in vivo evidence that the CRISPR1/Cas system specifically cleaves plasmid and bacteriophage double-stranded DNA within the proto-spacer, at specific sites. Our data show that the CRISPR/Cas immune system is remarkably adapted to cleave invading DNA rapidly and has the potential for exploitation to generate safer microbial strains.     

Phylogenetic divergence in a desert fish: differentiation of speckled dace within the Bonneville, Lahontan, and upper Snake river basins

Historical events have had a great impact on the biogeography of fishes of western North America. We examined the genetic variation of the speckled dace ( Rhinichthys osculus ) to determine the effects on this species of extensive hydrological changes during the last 10 million years in the Bonneville and Lahontan basins of the Great Basin and the upper Snake River Basin. Eight hundred sixty-nine base pairs of the mitochondrial gene cytochrome b were sequenced from 97 individuals representing 22 populations within these 3 basins, as well as from 2 individuals of longnose dace ( Rhinichthys cataractae ) that served as outgroups. Additionally, 13 speckled dace sequences representing 3 Bonneville populations were used from GenBank. Phylogenetic relationships were reconstructed using maximum parsimony and maximum likelihood criteria. Analysis of molecular variance was used to determine population structure and to estimate the amount of gene flow across the community boundaries. Three distinct clades were reconstructed representing the Lahontan Basin, the northern Bonneville and upper Snake River basins, and the southern Bonneville Basin. Additionally, most of the population structuring was explained by variation among basins (65.33%). Speckled dace demonstrated high genetic variation. As hypothesized, the northern and southern Bonneville specimens formed separate clades; however, the southern Bonneville clade was basal to a sister clade formed by the northern Bonneville/upper Snake River and Lahontan clades. These relationships indicate that Pliocene connections between the Snake, Lahontan, and Bonneville drainages, rather than more recent Pleistocene connections, best explain population structuring in speckled dace.     

Changes in Mule Deer Size in Utah

Trends in age-specific, eviscerated carcass weights were determined for hunter-harvested yearling and two-year-old buck mule deer. Carcass weights declined over an 11-year period from two areas of similar management, but with independenly collected data sets. Carcass weights also declined between the opening and second weekends of the hunt. Management implications are discussed.     

Consumption of fresh alfalfa hay by mule deer and elk

Tame mule deer and elk were fed fresh alfalfa hay at night and given various alternate forages during the day. This schedule, simulating farmland depredation feeding, yielded consumption values for field-growing alfalfa hay.     

Three-year surveillance for cestode infections in sheep dogs in central Utah

During the summers of 1982, 1983, and 1984, 269 sheep dogs from an area endemic for hydatid disease were examined for cestodes ( Echinococcus granulosus and Taenia spp.). Each dog was given an oral purge of arecoline hydrobromide and then following purgation received a subcutaneous injection of praziquantel (Droncit ® ). During the three-year study period, 205 dogs were examined one time only, 48 dogs were examined two of the three years, and 16 dogs were examined each of the three years (= 349 separate examinations). In 1982, 45 of 91 dogs examined (49.5%) harbored at least one species of cestode. Those data for 1983 and 1984 were 55 positive of 141 examined (39.0%) and 34 positive of 117 examined (29.1%), respectively. The marked drop in dogs infected during the second and third year of the study suggests that many sheep ranchers were implementing some of the control measures recommended for prevention of E. granulosus infections. The numbers of separate purgations showing specific cestodes detected in all positive dogs (some dogs naturally with more than one species of cestode) were: E. granulosus, 16 (4.6%); T. hydatigena, 34 (9.7%); T. ovis krabbei, 46 (13.2%); T. pisiformis, 47 (13.5%); and T. serialis, 24 (6.9%).     

Littoral heterogeneity and diel behavior of white bass ( Morone chrysops ) and carp ( Cyprinus carpio ) in Utah Lake, Utah

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 st1\:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Diel activity and association patterns of white bass ( Morone chrysops ) and carp ( Cyprinus carpio ) in Utah Lake, Utah, were studied over four 24-hr periods during August 1980. Fish were concurrently sampled from two adjacent littoral habitats. Significant differences existed in diel activity patterns in two of three size classes of white bass and in diel association patterns of white bass and carp between the two habitat areas. Differences in habitat structure, and in biological activity between the habitat types, are implicated as the primary determinants of overall diel activity of fish in these littoral areas.        

Effects of elevation and genetic introgression on growth of Colorado River cutthroat trout

Inland populations of cutthroat trout have suffered dramatic declines and some subspecies are considered threatened or endangered. Understanding patterns of variation and factors that influence life history in populations is important for conservation and management. We determined effects of elevation, sex, and genetic introgression (with Yellowstone cutthroat trout, Oncorhynchus clarkii lewisi , and rainbow trout, Oncorhynchus mykiss ) on growth rates of Colorado River cutthroat trout ( Oncorhynchus clarkii pleuriticus ) in the Sheep Creek drainage in the Uinta Mountains of Utah. In this high-elevation system, native trout grew slowly and matured relatively late. Elevation, sex, and genetic introgression all had significant effects on growth rates. Growth rates were lower at higher elevations. Males were slightly larger than females, and cutthroat trout in locations that were more introgressed grew faster than those at nonintrogressed locations. Both abiotic effects and effects of introduced salmonids must be addressed in long-term management programs to ensure the sustainability of native trout populations.