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.     

Suppression of microRNA-silencing pathway by HIV-1 during virus replication

MicroRNAs (miRNAs) are single-stranded noncoding RNAs of 19 to 25 nucleotides that function as gene regulators and as a host cell defense against both RNA and DNA viruses. We provide evidence for a physiological role of the miRNA-silencing machinery in controlling HIV-1 replication. Type III RNAses Dicer and Drosha, responsible for miRNA processing, inhibited virus replication both in peripheral blood mononuclear cells from HIV-1-infected donors and in latently infected cells. In turn, HIV-1 actively suppressed the expression of the polycistronic miRNA cluster miR-17/92. This suppression was found to be required for efficient viral replication and was dependent on the histone acetyltransferase Tat cofactor PCAF. Our results highlight the involvement of the miRNA-silencing pathway in HIV-1 replication and latency.     

Towards science-based techniques in agriculture

Because of their being science-based and because they have sparked off an extended debate on how technologies are conceived and developed, biotechnologies represent a particularly useful point of departure for a more general discussion about the evolution of agricultural techniques, as regards the origin and the distinguishing characteristics of different forms of knowledge and know-how.This article seeks to discuss how knowledge from different sources (agricultural, industrial, and scientific) on the one hand, and how the abstract and concrete elements that enter into the knowledge acquisition process, on the other hand, come together and become linked as determinants of different technical paths of development. The growing recourse to biotechnologies tends progressively to modify the common knowledge base mobilized for agro-food production. Even though at present the development of biotechnologies seems to be set in a model of continuity in relation to the current techniques, their full potential could express itself in redefining the relations between Man and Nature, ultimately reconciling the production of agricultural consumer goods and the reproduction of the agro-ecosystems.     

Retinoic acid controls the bilateral symmetry of somite formation in the mouse embryo

A striking characteristic of vertebrate embryos is their bilaterally symmetric body plan, which is particularly obvious at the level of the somites and their derivatives such as the vertebral column. Segmentation of the presomitic mesoderm must therefore be tightly coordinated along the left and right embryonic sides. We show that mutant mice defective for retinoic acid synthesis exhibit delayed somite formation on the right side. Asymmetric somite formation correlates with a left-right desynchronization of the segmentation clock oscillations. These data implicate retinoic acid as an endogenous signal that maintains the bilateral synchrony of mesoderm segmentation, and therefore controls bilateral symmetry, in vertebrate embryos.     

Formation of secondary organic aerosols through photooxidation of isoprene

Detailed organic analysis of natural aerosols from the Amazonian rain forest showed considerable quantities of previously unobserved polar organic compounds, which were identified as a mixture of two diastereoisomeric 2-methyltetrols: 2-methylthreitol and 2-methylerythritol. These polyols, which have the isoprene skeleton, can be explained by OH radical-initiated photooxidation of isoprene. They have low vapor pressure, allowing them to condense onto preexisting particles. It is estimated that photooxidation of isoprene results in an annual global production of about 2 teragrams of the polyols, a substantial fraction of the Intergovernmental Panel on Climate Change estimate of between 8 and 40 teragrams per year of secondary organic aerosol from biogenic sources.     

Long term CO2 enrichment stimulates N-mineralisation and enzyme activities in calcareous grassland

Elevated concentration of atmospheric carbon dioxide will affect carbon cycling in terrestrial ecosystems. Possible effects include increased carbon input into the soil through the rhizosphere, altered nutrient concentrations of plant litter and altered soil moisture. Consequently, the ongoing rise in atmospheric carbon dioxide might indirectly influence soil biota, decomposition and nutrient transformations.N-mineralisation and activities of the enzymes invertase, xylanase, urease, protease, arylsulfatase, and alkaline phosphatase were investigated in spring and summer in calcareous grassland, which had been exposed to ambient and elevated CO₂ concentrations (365 and 600 μl l⁻¹) for six growing seasons.In spring, N-mineralisation increased significantly by 30% at elevated CO₂, while there was no significant difference between treatments in summer (+3%). The response of soil enzymes to CO₂ enrichment was also more pronounced in spring, when alkaline phosphatase and urease activities were increased most strongly by 32 and 21%. In summer, differences of activities between CO₂ treatments were greatest in the case of urease and protease (+21 and +17% at elevated CO₂).The stimulation of N-mineralisation and enzyme activities at elevated CO₂ was probably caused by higher soil moisture and/or increased root biomass. We conclude that elevated CO₂ will enhance below-ground C- and N-cycling in grasslands.     

Effect of wash water temperature and chlorination on phenolic metabolism and browning of stored iceberg lettuce photosynthetic and vascular tissues

Cut tissues from distinct anatomical locations in iceberg lettuce (Lactuca sativa L.) were subjected to washing in cold (4 degrees C) and warm (47 degrees C) water with or without chlorine to assess their propensity to discoloration during storage. Total protein (Bradford method) and phenolic (TPH; Folin-Ciocalteu method) contents and polyphenol oxidase (PPO; spectrophotometric method using catechol as a substrate), peroxidase (POD; guaiacol substrate), and phenylalanine ammonia-lyase (PAL; phenylalanine substrate) activities were determined in photosynthetic and vascular tissue from outer and inner leaves. Unprocessed photosynthetic and inner leaf tissues had significantly higher (P < 0.05) levels of protein and TPH and PPO and POD activities than vascular and outer leaf tissues. PAL activities (on a fresh weight basis) were similar in all tissues. Changes in browning (light reflectance measurement) and phenolic metabolism in all four tissue types were observed during aerobic storage at 5 degrees C over 10 days. PAL activity increased in all tissues after 1-2 days of storage and then gradually decreased. POD activity also increased steadily for the storage duration. Protein content and PPO activity remained constant. Edge browning (measured with a Minolta Chroma Meter) and TPH increased in all tissues, especially in outer vascular tissue. Cut photosynthetic and vascular tissues washed at 4 and 47 degrees C with and without 100 microg mL(-1) chlorine for 3 min were analyzed during 7 days in storage at 5 degrees C. Enzyme activities and accumulation of phenolics in all tissues washed at 47 degrees C were significantly (P < 0.05) lower compared to controls or tissues washed at 4 degrees C. Chlorine had no additional effect at 47 degrees C but significantly (P < 0.05) reduced browning and accumulation of phenolics in lettuce washed at 4 degrees C. These results showed that inherent differences between tissues affect phenolic metabolism and browning in stored, fresh-cut lettuce.     

Extraction of DNA from soil

There is an increased interest in the extraction of nucleic acids from various environmental samples, since molecular techniques allow less biased access to a greater portion of uncultivable microorganisms. Two strategies have been developed to improve DNA recovery in terms of yield, purity and unbiased representation of the microbial diversity. The first approach consists of the direct extraction of nucleic acids from soil through in situ cell lysis followed by DNA purification. The alternative approach is based on the separation of bacteria from the soil particles followed by cell lysis and then DNA purification. Several published methods describe the recovery of highly purified nucleic acids that are well-suited for molecular purposes even though a new challenge concerns the recovery of large bacterial DNAs essential for functional investigation of gene clusters and biosynthetic pathways. This review presents an overview of the available methods to achieve this challenging objective.     

Structure, chemical composition, and xylanase degradation of external layers isolated from developing wheat grain

The external layers of wheat grain were investigated during maturation with respect to chemical and structural features and xylanase degradability. Cytochemical changes were observed in the isolated peripheral tissues of the wheat grain at four defined stages following anthesis. Marked chemical changes were highlighted at 11 days after anthesis, for which protein and lipid contents varied weakly. The profile of esterified ferulic acid showed large variation in the maturing peripheral layers of grain in contrast to the deposition of ferulate dimers, p-coumaric and sinapic acids. Lignin was monitored at the latest stages of ripening, which corresponds to the cessation of reserve accumulation in the grain. Arabinoxylans (AX) reached a maximum at 20 days and did not display any significant change in arabinosyl substitution proportion until ripeness. When submitted to xylanase, all outer layers were similarly altered in the proportion of soluble AX except for the peripheral tissues of the 11-day-aged wheat grain that had very little AX. Aleurone and nucellar layers were mostly degraded, whereas pericarp stayed intact at all stages of maturation. This degradation pattern was connected with the preferential immunolocalization of xylanase in aleurone and nucellar layers irrespective of the developmental stages. Further chemical examination of the enzyme-digested peripheral tissues of the grain supports the facts that ferulic ester is not a limiting factor in enzyme efficiency. Arabinose branching, ferulic dimers, and ether-linked monomers that are deposited early in the external layers would have more relevance to the in situ degradability of AX.     

Effect of essential oils on the growth of Fusarium verticillioides and fumonisin contamination in corn

Essential oils extracted by hydrodistillation from local plants in Benin, western Africa, and oil from seeds of the neem tree (Azadirachta indica) were evaluated in vitro and in vivo for their efficacy against Fusarium verticillioides infection and fumonisin contamination. Fumonisin in corn was quantified using a fluorometer and the Vicam method. Oils from Cymbopogon citratus, Ocimum basilicum, and Ocimum gratissimum were the most effective in vitro, completely inhibiting the growth of F. verticillioides at lower concentrations over 21 days of incubation. These oils reduced the incidence of F. verticillioides in corn and totally inhibited fungal growth at concentrations of 8, 6.4, and 4.8 microL/g, respectively, over 21 days. At the concentration of 4.8 microL/g, these oils did not affect significantly fumonisin production. However, a marked reduction of fumonisin level was observed in corn stored in closed conditions. The oils adversely affected kernel germination at 4.8 microL/g and therefore cannot be recommended for controlling F. verticillioides on stored corn used as seeds, when used at this concentration. The oil of neem seeds showed no inhibitory effect but rather accelerated the growth of F. verticillioides.