Ordered and dynamic assembly of single spliceosomes

The spliceosome is the complex macromolecular machine responsible for removing introns from precursors to messenger RNAs (pre-mRNAs). We combined yeast genetic engineering, chemical biology, and multiwavelength fluorescence microscopy to follow assembly of single spliceosomes in real time in whole-cell extracts. We find that individual spliceosomal subcomplexes associate with pre-mRNA sequentially via an ordered pathway to yield functional spliceosomes and that association of every subcomplex is reversible. Further, early subcomplex binding events do not fully commit a pre-mRNA to splicing; rather, commitment increases as assembly proceeds. These findings have important implications for the regulation of alternative splicing. This experimental strategy should prove widely useful for mechanistic analysis of other macromolecular machines in environments approaching the complexity of living cells.     

Polar lightning and decadal-scale cloud variability on Jupiter

Although lightning has been seen on other planets, including Jupiter, polar lightning has been known only on Earth. Optical observations from the New Horizons spacecraft have identified lightning at high latitudes above Jupiter up to 80 degrees N and 74 degrees S. Lightning rates and optical powers were similar at each pole, and the mean optical flux is comparable to that at nonpolar latitudes, which is consistent with the notion that internal heat is the main driver of convection. Both near-infrared and ground-based 5-micrometer thermal imagery reveal that cloud cover has thinned substantially since the 2000 Cassini flyby, particularly in the turbulent wake of the Great Red Spot and in the southern half of the equatorial region, demonstrating that vertical dynamical processes are time-varying on seasonal scales at mid- and low latitudes on Jupiter.     

Primary lacrimal gland adenocarcinoma of the third eyelid in a horse

A 5-year-old Draft Horse gelding presented for evaluation of a large, fleshy, ulcerated third eyelid mass OD of 3 weeks duration. Complete ophthalmic examination, ocular ultrasound and skull radiographs revealed a large soft-tissue mass involving the entire third eyelid OD and extending into the ventral right orbit to the level of the globe equator. No other abnormalities were noted on physical or ophthalmic examination. Surgical removal via exenteration was performed 3 months after initial presentation. A lacrimal adenocarcinoma of the third eyelid was diagnosed based on histopathology. Concurrent asymptomatic intra-ductal and intra-acinar Demodex caballi parasites were found in the eyelid sebaceous glands, likely as an incidental finding. No tumor recurrence or metastasis has occurred 12 months after excision. To the author's knowledge, this case is the first reported primary lacrimal adenocarcinoma in a horse. Complete surgical excision was curative.     

IT—Information Technology and the Human Interface: A Review of the Environmental Effects of Different Livestock Manure Storage Systems, and a Suggested Procedure for Assigning Environmental Ratings

There are concerns over a range of adverse environmental effects resulting from the storage of livestock manures on farms. The objectives of this study were to examine all the likely environmental effects of different storage methods, and to recommend which were the most desirable options.Literature reviews were undertaken to identify the likely environmental consequences of each commonly used storage method, in terms of water pollution risks, odour and ammonia emissions, greenhouse gas emissions and survival of microorganisms during storage. Planning and landscape aspects were considered and the most feasible options for abatement of ammonia emissions were identified. An ‘environmental rating’ for different storage systems was then devised, with the aim of obtaining a balance between water pollution, aerial emissions and other concerns.The environmental rating exercise favoured the more sophisticated and hence most expensive storage methods. No large differences emerged between ratings for slurry systems and solid systems when ease of adding ammonia control measures was excluded. For pigs, slurry systems appear to have a slight advantage, because of the greater ammonia emissions from the solid pig manure. The use of such a rating system could be developed further as more data become available. Whilst the method indicates the relative desirability of systems at a national scale it could be adapted to take account of local considerations or those of individual farm sites.     

Root surface-inhabiting bacteria and the expression of clubroot of radish in controlled environments

The effect of bacteria on the expression of clubroot of radish caused by the obligate parasite, Plasmodiophora brassicae, was studied. Inoculations with the bacterial strains isolated from roots of radish plants increased slightly, decreased slightly or did not change the number of root hairs colonized by P. brassicae in the root hair, i.e. primary phase of colonization. Five of six bacterial strains decreased the incidence of clubroot which was associated with a decrease in the extent of P. brassicae -colonization of the stele, i.e. secondary phase colonization. The role of root surface-inhabiting bacteria in clubroot disease development in radish under controlled environmental conditions is discussed.     

Characterisation of endobacterial communities in ectomycorrhizas by DNA- and RNA-based molecular methods

The diversity of endobacteria associated with ectomycorrhizas of Suillus variegatus and Tomentellopsis submollis, in two Corsican pine (Pinus nigra) stands was analysed by cultivation-dependent and cultivation-independent molecular methods. Denaturing gradient gel electrophoresis (DGGE) analysis revealed the cultivable endobacterial communities associated with S. variegatus were similar within the same stand. The most abundant cultivable bacterial species belonged to the genera Pseudomonas and Burkholderia. Cultivation-independent molecular analysis indicated that the structure of the endobacterial communities in ectomycorrhizas was consistent across all samples regardless of ECM fungal species or the pine stand from which the samples were collected. However, comparison between rDNA- and rRNA-derived DGGE gels showed that metabolically active endobacterial species were not always detected in rDNA-based profiles. Clone libraries constructed from rRNA molecules indicated that Pseudomonas and Burkholderia spp. were metabolically active bacteria. As some of the most abundant cultivable bacteria, including Bacillus/Paenibacillus spp., were not detected in cultivation-independent DGGE profiles, a combination of cultivation-dependent and -independent approaches provided a more complete assessment of the diversity of endobacteria associated with ectomycorrhizas.     

Foliar potassium status explains Douglas fir response to nitrogen fertilization in the inland Northwest,USA

Despite apparently inadequate N levels throughout the Inland Northwest of the United States, trees on some sites showed no increased growth 6 yr after N fertilization. Nor did higher N application rates consistently produce higher response. These facts indicated that other factors are limiting tree growth at these sites. Results suggest that K status is one important factor, influencing N fertilization response in the following general ways; (1) for stands with low pretreatment foliar K levels, the amount and duration of growth response are reduced, and higher N fertilizer rates produce less response; and (2) for all stands, growth response declines when foliar K decreases after N fertilization.     

Assessment of Water Quality in Association with Land use in the Tillamook Bay Watershed, Oregon, USA

The water quality in tributaries to Tillamook Bay, Oregon, frequently exceeds standards for fecal coliform bacteria (FCB) and temperature. FCB inputs to the bay have forced periodic closure of the oyster shellfish industry. In addition, impaired water quality may be contributing to reduced salmonid populations in the bay and its tributaries through reduction in the quality of the habitat. Because of these concerns, the Tillamook Bay National Estuary Project (TBNEP) conducted several characterization studies and a long-term water quality monitoring program for the tributary rivers. This paper summarizes data collected to date within these efforts, including storm-based data on FCB and total suspended solids (TSS), and bimonthly data on nutrient concentrations in selected rivers. Monitoring data from 1996 to 2002 are summarized. Results for FCB and TSS are reported by storm, which are classified according to season and precipitation patterns in order to minimize intra-annual variability. There are not indications of large changes in water quality throughout the period of record, but it is too early in the program for trends analysis. Storms that exhibited the highest FCB concentrations tended to be those that occurred during fall and/or those that were preceded by relatively dry conditions and included high rainfall intensity. Implementation of storm-based monitoring and classification of storms according to season effectively reduces the large variability inherent in the FCB monitoring data, thereby facilitating future trends analysis. Continued storm-based monitoring of FCB and TSS, and also continued collection of rainfall and river discharge data, will provide the database that will be needed to determine to what extent on-the-ground remediation actions and best management practices (BMPs) within the Tillamook Basin are having their desired effects.     

No place to nest or bask: Effects of human disturbance on the nesting and basking habits of yellow-blotched map turtles (Graptemys flavimaculata)

Considerable recent attention has focused on how human disturbance alters the behaviour of imperiled taxa. Data on such impacts are common for waterfowl, marine mammals, and some large game animals. However, little is known about how human disturbances affect reptiles, perhaps because most reptiles are secretive and are not commonly seen by the public. We studied the impact of human disturbances on the nesting and basking behaviour of the yellow-blotched map turtle (Graptemys flavimaculata) on the Pascagoula River in southeastern Mississippi, USA. We found that both nesting and basking behaviour of map turtles were altered by human recreational activities. Turtles attempting to nest commonly abandoned their attempts upon the approach of a boat and, prior to nesting, numerous individuals waited several hours near the beach without emerging. Basking turtles frequently dove into the water upon the approach of a boat and some did not return to bask. Anglers in small boats that remained in the vicinity of basking sites caused the most disturbances, whereas personal water crafts (jet skis) caused fewer disturbances. Our data suggest that interruption of nesting activities may have an especially severe impact on the viability of this population through changes in numbers of clutches females are able to lay and altering the microhabitat females select for their nests.