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.     

Developmental stages during the rooting of in-vitro-cultured Quercus robur shoots from material of juvenile and mature origin

In-vitro-cultured shoots of clones initiated from shoots of the basal parts (BS) and the crown (C) of two mature Quercus robur L. trees were subjected to rooting experiments to relate rooting with shoot topophysical origin. The BS shoots exhibited morphologically juvenile characteristics and rooted more easily after indole-3-butyric acid (IBA) treatment than C shoots. When naphthylphthalamic acid (NPA) was applied to BS shoots, rooting capacity decreased and root emergence was delayed at least 2 days compared with shoots treated with IBA only. During the first days of the rooting process, endogenous indole-3-acetic acid (IAA) concentration was higher in C shoots than in BS shoots, regardless of whether the shoots were treated with NPA. Mitotic figures were observed in cells from the basal part of both BS and C shoots 24 h after IBA treatment. After 4 days of IBA treatment, the occurrence of histological events differed between BS shoots and C shoots. Cells of BS shoots became meristematic, giving rise to meristemoids and root primordia, whereas no differentiation of root meristemoids occurred in cells of C shoots. Thus, although adult oak material (C shoots) is capable of responding to the initial stimulus of auxin during the adventitious rooting process, the endogenous IAA concentration is not the factor limiting rooting in adult material.     

Colostrum yield and litter performance in multiparous sows subjected to farrowing induction

The consumption of colostrum at a low level can compromise the survival and growth of piglets. Therefore, this study aimed to evaluate the effect of farrowing induction on colostrum yield, IgG concentration and the survival and performance of piglets until the weaning. Sows of parity 3 to 7 were assigned into two groups: Control (n = 48), sows with spontaneous farrowing; and induction (n = 48), sows induced to farrow on day 114 of gestation with a PGF₂ analogue. Colostrum and blood samples were collected from the sows, at farrowing and 24 hr later. Blood samples from the piglets were collected at 24 hr after birth. The performance of the piglets was evaluated in a subsample of 28 litters from each group. All piglets were weighed at 7, 14 and 20 days of age. The farrowing length, the number of piglets born alive, stillborn piglets, weight at birth, litter weight at birth and colostrum yield were not significantly affected (p > .05) by farrowing induction. There was no difference between the groups (p > .05) in the percentage of sows with obstetric interventions. Serum IgG concentration, in both sows and piglets, and colostrum IgG concentration were similar between the groups (p > .05). Furthermore, survival rate, piglet weight and litter weight at 7, 14 and 20 days of age were also similar between the groups (p > .05). Therefore, it can be concluded that the farrowing induction performed on day 114 of gestation does not affect the colostrum yield, the IgG concentration in colostrum and serum of piglets, and the litter performance until the weaning.     

Spatial variability of soil water content and mechanical resistance of Brazilian ferralsol

The spatial variability of mechanical resistance to penetration (PR) and gravimetric moisture (GM) was studied at a depth of 0–0.40 m, in a ferralsol cropped with corn, and under conventional tillage in Ilha Solteira, Brazil (latitude 20°17′S, and longitude 52°25′W). The purpose of this study was to analyse and to try explaining the spatial variability of the mentioned soil physical properties using geostatistics. Soil data was collected at points arranged on the nodes of a mesh with 97 points. Geostatistics was used to analyse the spatial variability of PR and GM at four depths: 0–0.1, 0.1–0.2, 0.2–0.3 and 0.3–0.4 m. PR showed a higher variability of data, with coefficients of variation of 52.39, 30.54, 16.91, and 15.18%, from the surface layers to the deepest layers. The values of the coefficients of variation for GM were lower: 9.99, 5.13, 5.59, and 5.69%. Correlation between GM and PR for the same soil layers was low. Penetration resistance showed spatial structure only in the 0.30–0.40 m layer, while gravimetric moisture showed spatial structure at all depths except for 0–0.10 m. All the models of fitted semivariograms were spherical and exponential, with ranges of 10–80 m. Data for the variable ‘GM’ in the 0.20–0.30 and 0.30–0.40 m layers revealed a trend in data attributed to the occurrence of subsurface water flow.     

Characterization of Swine Wastewater by Toxicity Identification Evaluation Methodology (TIE)

Since swine wastewater is used by farmers for soil fertilization, evaluation of toxic compounds or micro-contaminants of separate streams is required. This paper uses the toxicity identification evaluation (TIE) procedure for the physicochemical and ecotoxicological characterization of swine wastewater. To distinguish the most important toxic compounds, a physicochemical characterization and phase I-TIE procedure were performed. The acute toxic effect of swine wastewater and treated fractions (phase II-TIE) were evaluated using Daphnia magna determining 48-h LC₅₀. Results show a high level of conductivity (23.5 μS cm⁻¹), which is explained as due to the concentration of ions, such as ammonium (NH₄⁺–N 1.6 g L⁻¹), sulfate (SO₄²⁻ 397.3 mg L⁻¹), and chlorine (Cl⁻ 1,230.0 mg L⁻¹). The acute toxicity of the swine wastewater was evaluated on D. magna (48-h LC₅₀ = 3.4%). Results of the different water treatments indicate that anionic exchange treatments could reduce 22.5% of swine wastewater’s acute toxicity by reducing chlorine (to around 51%) and conductivity (8.5%). On the other hand, cationic exchange treatment increased acute toxicity on D. magna (% RT = −624.4%), by reducing NH₄⁺–N (around 100%) and total nitrogen (95.5%). This finding suggests that part of the toxicity comes from anionic compounds, such as chlorine.     

Evolution of 3-mercaptohexanol, hydrogen sulfide, and methyl mercaptan during bottle storage of Sauvignon blanc wines. Effect of glutathione, copper, oxygen exposure, and closure-derived oxygen

The effects of wine composition and postbottling oxygen exposure on 3-mercaptohexanol (3-MH), hydrogen sulfide (H2S), and methyl mercaptan (MeSH) were investigated. A Sauvignon blanc wine with initial copper concentration of 0.1 mg/L was treated with copper sulfate and/or glutathione (GSH) prior to bottling to give final concentrations of 0.3 and 20 mg/L, respectively. The wines were bottled with a synthetic closure previously stored in either ambient air or nitrogen to study the effect of the oxygen normally present in the closure. Bottled wines were stored for 6 months in either air or nitrogen to study the effect of oxygen ingress through the closure. Copper addition resulted in a rapid initial decrease in 3-MH. During storage, a further decrease of 3-MH was observed, which was lower with GSH addition and lowered oxygen exposure. H2S accumulated largely during the second 3 months of bottle storage, with the highest concentrations attained in the wines treated with GSH and copper. Lower oxygen from and through the closure promoted H2S accumulation. The concentration of MeSH was virtually not affected by the experimental variables at 6 months, although differences were observed after 3 months of storage. The implications for wine quality are discussed.     

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.