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.     

Infusing an international perspective at the 1890 land-grant institutions

This report examines the role of 1890 land-grant institutions and Tuskegee University in international research and curriculum development. It discusses the need for internationalizing curricula and the benefits and costs for 1890 institutions. Two particular strategies for infusing global perspectives using a small land-grant university as a case-study are presented. Two international projects served as a vehicle for enhancing faculty teaching, research and service capabilities.     

Minimizing the Treatments Required to Determine the Responses of Different Crop Genotypes to Potassium Supply

ABSTRACT

Crop genotypes that make best use of potassium (K) fertilizers can promote agricultural sustainability. However, screening germplasm collections for responses to K fertilizers is often laborious and expensive. To reduce costs, the number of K fertilizer treatments required to identify better genotypes should be minimized. This might be achieved by exploiting the mathematical relationships between biomass, plant K content, and K supply. This study employed 14 barley (Hordeum vulgare L.) genotypes growing in a hydroponics system that allowed the K supply to roots to be controlled through the K concentration in a flowing solution. It sought to determine the minimal number of treatments required to model the relationships between (a) shoot biomass and K supply, (b) plant K content and K supply, and (c) shoot biomass and plant K content. The relationships between (a) shoot biomass and K supply and (b) plant K content and K supply for any given genotype could be fitted by Michaelis–Menten equations and each of these could be estimated from data obtained at two, appropriately-chosen, rates of K supply. The relationship between shoot biomass and plant K content could be estimated from these relationships. However, the optimum K supply required for accurate estimates differed between genotypes and whether shoot biomass or plant K content was to be estimated. It is, therefore, suggested that the relationships between shoot biomass, plant K content, and K supply might best be determined from measurements of biomass and K content at three, carefully-selected, rates of K supply.     

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.     

Rapid effects of plant species diversity and identity on soil microbial communities in experimental grassland ecosystems

Changes in plant community structure, including the loss of plant diversity may affect soil microbial communities. To test this hypothesis, plant diversity and composition were experimentally varied in grassland plots cultivated with monocultures or mixtures of 2, 3 or 4 species. We tested the effects of monocultures versus mixtures and of plant species composition on culturable soil bacterial activity, number of substrates used and catabolic diversity, microbial biomass N, microbial respiration, and root biomass. These properties were all measured 10 months after seeding the experiment. Soil bacterial activity, number of substrates used and catabolic diversity were measured in the different plant communities using BIOLOG GN and GP microplates, which are redox-based tests measuring capacity of soil culturable bacteria to use a variety of organic substrates. Microbial biomass N, microbial respiration, and root biomass were insensitive to plant diversity. Culturable soil microbial activity, substrates used and diversity declined with declining plant diversity. Their activity, number of substrates used and diversity were significantly higher in plots with 3 and 4 plant species than in monocultures and in plots with 2 species. There was also an effect of plant species composition. Culturable soil microbial activity and diversity was higher in the four-species plant community than in any of the plant monocultures suggesting that the effect of plant diversity could not be explained by the presence of a particular plant species. Our results showed that changes in plant diversity and composition in grassland ecosystems lead to a rapid response of bacterial activity and diversity.     

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.     

Stability of maize resistance to the ear rots caused by Fusarium graminearum and F. verticillioides in Argentinian and Canadian environments

Sources of resistance to Fusarium spp. are needed to develop maize hybrids resistant to the accumulation of fungal mycotoxins in the grain. In a search for resistant germplasm in 1999 and 2000, a set of Argentinian maize populations was evaluated in Ottawa, Canada, for resistance to ear rots after inoculation with local isolates of Fusarium verticillioides and F. graminearum. Sixteen of these populations, varying in observed resistance levels, were re-evaluated in 2003 and 2004 in Pergamino, Argentina, using local isolates of the same fungi. Conidial suspensions of each fungal species were inoculated into the silk channel of primary ears. Disease severity was assessed after physiological maturity using a scale based on the percentage of visibly infected kernels. Genotype effect was more important than genotype-by-fungal species or genotype-by-fungal species-by-environment interaction effects. In addition, disease severity levels associated with each fungal species were positively correlated (P < 0.05) (r = 0.90, r = 0.81, r = 0.87 and r = 0.53, in Ottawa 1999 and 2000, and Pergamino 2003 and 2004, respectively). Populations ARZM 01107, ARZM 07138, ARZM 10041, ARZM 13031, ARZM 16002 and Pora INTA exhibited the highest and most stable resistance to both species. Considering that disease resistance exhibited low specificity to the environment and to the fungal species in evaluations conducted in a wide range of environments and with fungal isolates collected from different hemispheres, the most resistant populations are potential sources of genes for stable resistance to these Fusarium spp.     

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.     

Effects of the earthworm Pontoscolex corethrurus on banana plants infected or not with the plant-parasitic nematode Radopholus similis

Radopholus similis is a worldwide endoparasitic nematode that greatly hampers banana (Musa acuminata, Cavendish subgroup) productivity. Earthworms are known to closely interact with above-ground and under-ground soil biota and particularly with plants and microfaunal communities. This study was aimed at investigating, under greenhouse conditions, the effects of the earthworm Pontoscolex corethrurus on banana growth and nutrient uptake, and assessing the influences of this earthworm on the development of an inoculated population of R. similis. Six-week-old tissue culture banana plants were submitted to four treatments: with P. corethrurus, R. similis, P. corethrurus+R. similis, and a control with no earthworms or nematodes. At the end of the experiment, the P. corethrurus treatments showed significantly higher leaf surface areas, shoot dry root weights, and root fresh weights than those without earthworms. This root growth enhancement probably contributed to the evident but non-significant decrease in the density of nematodes in the roots, even though earthworms did not reduce the total number of nematodes per whole root system. Moreover, the presence of earthworms slightly alleviated the severity of root damage. N bioavailability in the soil, along with N, Ca, and Mg content of banana plants, were also significantly increased in the presence of earthworms. Our results demonstrated that banana plant growth and nutrition were positively influenced by earthworms. Cropping practices that boost the development of earthworm communities in soil should therefore be promoted to enhance sustainability and to naturally alleviate nematode impact.