Functional genomic analysis of RNA interference in C. elegans

RNA interference (RNAi) of target genes is triggered by double-stranded RNAs (dsRNAs) processed by conserved nucleases and accessory factors. To identify the genetic components required for RNAi, we performed a genome-wide screen using an engineered RNAi sensor strain of Caenorhabditis elegans. The RNAi screen identified 90 genes. These included Piwi/PAZ proteins, DEAH helicases, RNA binding/processing factors, chromatin-associated factors, DNA recombination proteins, nuclear import/export factors, and 11 known components of the RNAi machinery. We demonstrate that some of these genes are also required for germline and somatic transgene silencing. Moreover, the physical interactions among these potential RNAi factors suggest links to other RNA-dependent gene regulatory pathways.     

High-quality binary protein interaction map of the yeast interactome network

Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.     

Radar detection of the nucleus and coma of comet hyakutake

Radar observations of comet Hyakutake (C/1996 B2) made at the Goldstone Deep Space Communications Complex in California have detected echoes from the nucleus and from large grains in the inner coma. The nucleus of this bright comet was estimated to be only 2 to 3 kilometers in diameter. Models of the coma echo indicate backscatter from porous, centimeter-size grains ejected anisotropically at velocities of tens of meters per second. The radar observations suggest that a comet's activity may be a poor indicator of its size and provide evidence that large grains constitute an important component of the mass loss from a typical active comet.     

Allophanic Soil Adsorption System as a Bleached Kraft Mill Aerobic Effluent Post-Treatment

Bleached Kraft mill effluent was treated in an activated sludgereactor followed by an allophanic soil adsorption system (ASAS). Under aerobic conditions, removal efficiencies of biological oxygen demand (BOD₅) and chemical oxygen demand (COD) varied between 57.7–96.5% and 30.3–57.0%, respectively, depending on the hydraulic retention time (HRT). On the other hand, tannin-lignin and phenolic compounds removal efficiencies attained values between 13.2–51.2 and 3.6–33.5%,respectively. An allophanic soil adsorption system was designed for color and phenolic compounds removal. Three different types of soils were used: Natural allophanic soil as the control compared, with calcinated and acidified allophanic soil. The initial removal efficiencies for phenolic compounds varied between 72 an 87% for activated soils, while color initial removal efficiencies were between 95 and 99%. Moreover, COD and tannin-lignin initial removal efficiencies reached maximum values of 74 and 87%, respectively, for calcinated soil. Design parameters show that there is an enhancement factor in adsorption capacities for both activated soils. In fact, phenolic compounds breakpoint adsorption capacity increased 5.3 times for calcinated soil and 17.6 times for acidified soil, while saturation capacity increased between 2.2 and 3.2 times. In addition, color breakpoint adsorption capacity increased 2.8 times for calcinated soil and 10.4 times for acidified soil, while saturation capacity increased between 3.2 and 5.5 times.     

Study of Ammonium Contamination in Leachates from an Ultisol Following Application of Various Types of Amendment

The composition of leachates from an Ultisol reconstructed inlysimeters and amended with limestone, sugar foam waste and gypsum rock was studied. The typical rainfall of the area fromwhich the soil was collected was simulated under laboratory conditions over a five-month period. The soil samples treated with gypsum behaved markedly differently from the rest. Thus, the samples amended with gypsum gave leachates with substantially increased ammonium contents that might result in contamination of aquifers. The gypsum-treated samples alsoexhibited marked differences in pH, EC and the Ca, Mg, Na andK contents from the rest.     

Effects of starvation and recovery on the survival, growth and RNA/DNA ratio in loliginid squid paralarvae

The ability of Loligo opalescens paralarvae to resist and recover from starvation was examined by measuring their survival, growth rate and RNA/DNA ratios during starvation and refeeding. Paralarvae were fed Artemia sp. nauplii, zooplankton and mysid shrimp. Fourteen days after hatching they were separated into five feeding treatments: a control treatment (food was always available) and treatments starved for 2, 3, 4 and 5 days, and then refed. Each day, 5–7 paralarvae from each treatment were anesthetized to measure mantle length and wet weight (WW), and then RNA and DNA were extracted using an ethidium bromide fluorometric technique. Paralarvae did not survive 4 and 5 days of starvation, showing that at 15 days of age and at 16 °C the limit to recovery was 3 days of starvation. Paralarvae starved for 2 and 3 days showed compensatory growth that mitigated the effects of starvation, in that at the end of the experiment (10 days), they attained mean final body weights similar to the control treatment. Differences in the RNA/DNA ratios between control and starved paralarvae were detected within 2 days of food deprivation. For paralarvae starved 2 and 3 days, it took 1 day after refeeding to attain RNA/DNA ratios not significantly different from the control treatment. Additionally, RNA/DNA ratios were highest during the day (0800, 1200, 1600 h) and lowest at night (0000, 0400 h), suggesting daytime feeding activity. Growth rates ranged from − 14% to 21% WW day^− 1 and the resulting equation between RNA/DNA ratio and growth rate (GR) of paralarvae was GR = 1.74 RNA/DNA − 11.79 (R² = 0.70). After starvation, there was a reduction in growth variability in all starved treatments, while growth variability remained high in the control treatment. Findings from the present study indicate that nucleic acids are a valid indicator of nutritional condition and growth in squid paralarvae.     

Ramblas in south‐east Spain: threatened and valuable ecosystems

• 1. The term ‘rambla’ defines watercourses with specific geomorphological features that make them different from all other temporary streams. Most ramblas represent extreme habitats for plants and animals that have to be adapted to high salinity and extreme hydrological fluctuations with severe dry periods and floods. Both factors shape the structure and functioning of the whole aquatic ecosystem.
• 2. Biological communities in ramblas are diverse and rich in endemic species. Habitats of interest within the EU are extensively represented in ramblas and their associated wetlands. Ramblas also fulfil previously unrecognized functional and cultural values, such as helping to control non‐point‐source pollution in agricultural areas and to provide a variety of historic and educational resources. However, they are a threatened ecosystem because of the diversity of uses and derived impacts.
• 3. To characterize and describe the diversity of ramblas in south‐east Spain, an extensive survey was carried out in 2000–2001 in the province of Murcia. Based on the lithology where ramblas are located, they were grouped in three categories: ramblas of marl, limestone and metamorphic basins.
• 4. Rambla categories differ in structural parameters, hydrology, water chemistry, biological communities and their vulnerability to a range of human impacts, thus requiring a flexible approach to their management and conservation.

Copyright © 2005 John Wiley & Sons, Ltd.     

Effect of fermentation and autoclaving on dietary fiber fractions and antinutritional factors of beans (Phaseolus vulgaris L.)

The effect of fermentation on antinutritional factors and also on total dietary fiber (TDF), insoluble (IDF) and soluble (SDF) dietary fiber fractions was studied in beans (Phaseolus vulgaris L.). The processes studied were two types of fermentation (lactic acid and natural), and a portion of the obtained flours were processed by autoclaving. The dietary fiber (DF) content and its components were determined using the enzymatic-gravimetric and enzymatic-chemical methods. The TDF content ranged from 24.5% dry matter (DM) in the raw to 25.2% DM in the processed beans. All the processing treatments significantly decreased the SDF content, and irrelevant changes were noticed in the IDF content of processed beans. Cellulose content of all samples was reduced by the processing treatments. Correspondingly, higher amounts of resistant starch was observed in the processed beans, except in the lactic acid fermented ones. However, the levels of pectic polysaccharides and Klason lignin were higher in the samples fermented by Lactobacillus plantarum. The action of microorganisms was determinant for the different degradation of the bean cell wall, disrupting the protein-carbohydrate integration, thus reducing the solubility of DF.     

Effects of extracorporeal shock wave therapy on desmitis of the accessory ligament of the deep digital flexor tendon in the horse

Objective: To evaluate the effects of extracorporeal shock wave therapy (ESWT) on collagenase‐induced lesions in the accessory ligament of the deep digital flexor tendon (ALDDFT) of horses. Study Design: Paired, blinded controlled study. Animals: Eight Thoroughbred horses (3 mares, 5 geldings; mean±SD weight, 464±26 kg, mean age, 8±1.7 years). Methods: Lesions were created in both ALDDFTs of all horses by injection of 2 × 10³ IU of collagenase type I. Percent lesion and structure (fiber alignment and echogenicity) were quantified with ultrasonographic imaging 3, 6, and 9 weeks after collagenase injection. After ultrasound examinations, ESWT (1000 shocks at 0.15 mJ/mm²) was applied to 1 ALDDFT in each horse. ALDDFT were harvested 15 weeks after collagenase injection and the microstructure, mRNA levels of collagen types I and III, and collagen and glycosaminoglycan content were evaluated. Results: There were no differences in percent lesion, echogenicity, or fiber alignment between control‐ and ESWT‐treated ligaments at each evaluation time; however, compared with 3‐week values, there was a significant increase in percent lesion and echogenicity for EWST treated ligaments at 6 weeks and significant decrease in both variables for treated and control ligaments at 12 weeks. Fiber alignment improved significantly at 9 weeks in controls and at 12 weeks in treated and control ligaments. Collagen type I mRNA levels were significantly higher in the ESWT treatment group compared with the control group 15 weeks after collagenase injection though differences in other mRNA levels, microstructure, and composition were not significant. Conclusions: Our results do not support an effect of ESWT on collagenase‐induced lesions in the equine ALDDFT.