Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes

Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient finding of the target site.     

Gastro-oesophageal reflux in large-sized,deep-chested versus small-sized,barrel-chested dogs undergoing spinal surgery in sternal recumbency

Objective

The aim of this study was to investigate whether an increased frequency of gastro-oesophageal reflux (GOR) is more common in large-sized, deep-chested dogs undergoing spinal surgery in sternal recumbency than in small-sized, barrelchested dogs.

Identifying recreational fisheries in the Mediterranean Sea through social media

The impact of recreational fishing on fish stocks remains largely unknown, as this is inherently difficult to monitor, especially in areas such as the Mediterranean Sea where many species are targeted using a variety of fishing gears and techniques. This study attempts to complement existing data sets and construct the profile of recreational fisheries in the EU‐Mediterranean countries using videos publicly available on social media. A total of 1526 video records were selected, featuring the capture of 7799 fish specimens. The results show recreational fishing is multispecies in nature (26 species contributed to >80% % of the most numerically important species caught) and exhibits a spatially homogeneous pattern, with differences in species composition being mostly dependent on the fishing technique used rather than on the country. Such findings fill an important knowledge gap on recreational fishing activities, and the methodology provides an innovative approach to gather statistics on data‐poor thematic areas that can potentially complement other data sets, such as the EU Data Collection Multi‐Annual Programme.     

Evaluation of plant-growth-promoting rhizobacteria, acibenzolar-S-methyl and hymexazol for integrated control of Fusarium crown and root rot on tomato

BACKGROUND: Plant growth‐promoting rhizobacteria (PGPR) can be potential agents for biological control of plant pathogens, while their combined use with conventional pesticides may increase their efficacy and broaden the disease control spectrum. The effect of four different Bacillus sp. PGPR strains (B. subtilis GB03 and FZB24, B. amyloliquefaciens IN937a and B. pumilus SE34) applied individually and in mixtures, as well as in combined use with acibezolar‐S‐methyl (ASM) and hymexazol, on plant growth promotion and on the control of Fusarium crown and root rot (FCRR) of tomato was evaluated. RESULTS: All PGPR strains promoted the tested plant growth characteristics significantly. A higher promoting effect was provided by SE34. Experiments on population dynamics of PGPR strains revealed that, after 28 days of incubation, populations of strain SE34 remained stable, while the remaining bacterial strains showed a slight decline in their population densities. The GB03 and FZB24 strains provided a higher disease suppression when applied individually. However, application of IN937a in a mixture with GB03 provided a higher control efficacy of Fusarium oxysporum f. sp. radicis‐lycopersici (Forl). Treatment of tomato plants with ASM resulted in a small reduction in disease index, while application of hymexazol provided significantly higher control efficacy. Combined applications of the four PGPR strains with either ASM or hymexazol were significantly more effective. CONCLUSION: The results of the study indicate that, when bacilli PGPR strains were combined with pesticides, there was an increased suppression of Forl on tomato plants, and thus they may prove to be important components in FCRR integrated management. Copyright © 2011 Society of Chemical Industry     

Soil Depletion of Ca, Mg and K Due to Vicinal Intensive Hog Farming Operation Located in East Mediterranean

One of the main environmental impacts of concentrated animal feeding operations is soil degradation in the vicinity of the livestock breeding facilities due to substances such as ammonia emitted from the various stages of the process. In this research, the soil degradation effects of an intensive hog farming operation (IHFO) located at a Mediterranean limestone soil coastal area have been investigated. Soil samples of the upper mineral soil were taken in various distances and directions from the IHFO boundaries. Thirteen experimental cycles were carried out in the duration of 1.5?years starting in March 2009 until October 2010. The soil samples were analysed on total, exchangeable and water-soluble Ca, Mg and K as well as water-soluble ammonium concentrations. Significantly lower concentrations of the exchangeable and water-soluble base cations were observed on soil samples at increasing proximity downwind from the farm (south). Southern soil average concentrations of exchangeable base cations ranged between 78.6 and 128.52?mmol Ca²⁺?kg^?1 soil, 8.42?C21.39?mmol?Mg²⁺?kg^?1 soil and 4.25?C8.1?mmol?K⁺?kg^?1 soil, respectively. Southern soil average concentrations of water-soluble base cations ranged between 0.57 and 2.17?mmol Ca²⁺?kg^?1 soil, 0.16?C0.89?mmol?Mg²⁺?kg^?1 soil and 0.48?C0.95?mmol?K⁺?kg^?1 soil, respectively.     

Reducing set-recovery of compressively densified poplar wood by impregnation–modification with melamine–formaldehyde resin

ABSTRACT

Densification of resin impregnated wood under hot-pressing is a method that along with the potential for the reduction of set-recovery could additionally increase the density of wood and further improve other technical properties. In this study, the effect of the methylated melamine-formaldehyde modification on the shape memory effect of densified Populous nigra wood at various compression ratio levels was investigated. Furthermore, the effects on moisture content and compression ratio were also assessed. The most important conclusion drawn was that MF can act as a means for reducing set-recovery of compressed poplar wood since it is obvious that the use of MF significantly improved the stability of densified wood due to the formation of new bonds between cell wall components and MF. In the case of densification under stress of 10?kg/cm², the stabilization was improved by the use of MF to about 50% compared to water-treated specimens. The effect of MF on the stabilization of densified wood was not very clear for stresses higher than 10?kg/cm² since due to the outflow of MF solution during the first minutes of compression.     

Utilization of wood biomass residues from fruit tree branches,evergreen hardwood shrubs,and Greek fir wood as raw materials for particleboard production. Part B. Hygroscopic properties and formaldehyde content

This paper investigates the basic hygroscopic properties and formaldehyde content (FC) of particleboards produced with wood biomass from fruit tree branches and evergreen hardwood shrubs as substitute raw materials for fir particles. One-layer laboratory particleboards with two distinct target densities (0.63 g/cm³ and 0.69 g/cm³) were produced using various mixtures of the above materials. Industrially produced wood particles were also used for comparison purposes. The results showed that the replacement of fir wood (FW) by evergreen hardwood material significantly upgraded board's quality in terms of thickness swelling (TS) and water absorption (WA) (except boards with density of 0.63 g/cm³) after immersion in water for 24 h and residual swelling (RS) after reconditioning. The contribution of branch-wood (BW) particles in the production of FW boards with density of 0.63 g/cm³ induced increase of TS, WA, and RS while for boards with density of 0.69 g/cm³ did not result to significant changes except for RS. In terms of FC, boards made of BW and evergreen hardwood showed significantly lower FC compared to those produced by FW and industrial particles.     

Characterization and evaluation of chabazite- and mordenite-rich tuffs,and their mixtures as soil amendments and slow release fertilizers

In the present study, zeolite tuffs of diverse chemistry, mineralogy and origin were characterized and tested for their efficiency as slow release fertilizers (SRF) through a series of leaching tests. Mixtures of zeolite tuffs were created and tested as loamy soil additives, in order to evaluate any synergistic effect on their cation exchange capacity (CEC) and SRF properties. The studied materials were a chabazite-rich tuff (SOR), a mordenite-rich tuff (KIM), 3 mixtures of them (SOR/KIM 30/70, 50/50 and 70/30) and a commercial clinoptilolite-rich tuff (BLG). CEC (sodium acetate method) was 95.7 for BLG, 100.9 for KIM and 92.2 cmol kg^?1 for SOR, while their mixtures displayed intermediate values. SRF values vary, with the SOR/KIM 30/70 exhibiting the slowest NH₄⁺ release in 29 days (1.7%) compared to the control sample (19%). Zeolites promoted PO₄^?3 release, while their selectivity for Mg²⁺ and K⁺ was clearly affected by their different structure and chemistry. BLG exhibited the strongest selectivity for Mg²⁺, having the lowest release (39%). The results demonstrate that mixtures of zeolite tuffs could have a potential use in agricultural processes, by improving parameters like: chemistry, mineralogy, CEC and SRF efficiency, and resulting in the production of a competitive and functional soil additive.     

Coralligenous assemblages along their geographical distribution: Testing of concepts and implications for management

• 1. The coralligenous habitat was studied at the large Mediterranean scale, by applying a standardized, non‐destructive photo‐sampling protocol, developed in the framework of the CIGESMED project.
• 2. The results provided evidence to support the following statements: (a) the assemblage pattern is not homogeneously distributed across the four Mediterranean ecoregions studied (biotic gradients hypothesis); and (b) the assemblage pattern does not change significantly when the information is aggregated to higher taxonomic levels (taxonomic sufficiency hypothesis).
• 3. Surrogate taxonomic categories higher than species, such as genus and family, can be used to reveal the multivariate pattern of the coralligenous assemblages.
• 4. Although preliminary at the pan‐Mediterranean scale, these outcomes set the scene for future comparisons as more data sets become available but also for comparisons between taxonomic and functional patterns.