Occurrence of different inter-varietal and inter-organ defence strategies towards supra-optimal zinc concentrations in two cultivars of Triticum aestivum L.

Two bread wheat (Triticum aestivum L.) cultivars (Albimonte, traditional cultivar very important in Italy since long time; and Manital, more recent, evincing better productive performances) were grown for 10 d in presence of 0.7 (control), 70 or 350 μM ZnSO₄, to verify whether Zn excess was differently managed at inter-varietal and at inter-organ level. Roots were found to be the main site of Zn accumulation, although a moderate metal translocation to leaves occurred in both cultivars. Despite only slight differences in internal Zn concentrations between cultivars, Albimonte seemed to be more sensitive to Zn excess in terms of growth reduction and H₂O₂ accumulation, suggesting that the diversities in responses to Zn stress should be ascribed here to inter-varietal metabolic differences. In both cultivars, increased NAD(P)H oxidation rate by pH-dependent peroxidases, and reduced detoxification activity by catalase and peroxidases, were responsible for Zn-induced H₂O₂ accumulation, while total superoxide dismutase content and activity seemed in general to not change or even depress. Moreover, differences in the content of thiol-peptide compounds (glutathione and phytochelatins) were detected, suggesting indeed the setting up of differential response mechanisms to Zn excess at an inter-varietal and inter-organ level.     

Using the ratio of means as the effect size measure in combining results of microarray experiments

Background  

Development of efficient analytic methodologies for combining microarray results is a major challenge in gene expression analysis. The widely used effect size models are thought to provide an efficient modeling framework for this purpose, where the measures of association for each study and each gene are combined, weighted by the standard errors. A significant disadvantage of this strategy is that the quality of different data sets may be highly variable, but this information is usually neglected during the integration. Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference) when sample sizes in each group are small.     

Rhizospheric streptomycetes as potential biocontrol agents of <Emphasis Type="Italic">Fusarium</Emphasis> and <Emphasis Type="Italic">Armillaria</Emphasis> pine rot and as PGPR for <Emphasis Type="Italic">Pinus taeda</Emphasis>

Pinus taeda is one of the main timber trees in Brazil, occupying 1.8 million ha with an annual productivity of 25–30 m³ ha⁻¹. Another important species is Araucaria angustifolia, belonging to the fragile Rainforest biome, which for decades has been a major source of timber in Brazil. Some diseases that affect the roots and/or the stem of these trees and cause “damping-off” of the seedlings, with economic and environmental losses for the forest sector, are caused by the plant pathogenic fungi Fusarium sp. or Armillaria sp. This research project intended to isolate actinobacteria from the Araucaria rhizosphere, which present an antagonistic effect against these fungi. After the selection of the best pathogen inhibitors, morphologic characteristics, enzyme production, and their effect on the growth of Pinus taeda were studied. The actinobacteria were tested for their antagonistic capacity against Fusarium sp. in Petri plates with PDA as substrate. The inhibition zone was measured after 3, 5, 7, and 10 days. Of all the isolates tested, only two of them maintained inhibition zones up to 4 mm for 10 days. The inhibition of Armillaria sp. was tested in liquid medium and also in Petri dishes through the evaluation of the number of the fungal rhizomorphs in dual culture with the actinobacteria. It was found that all five isolates were able to inhibit the rhizomorph production, with the best performance of the isolate A43, which was capable of inhibiting both fungi, Fusarium and Armillaria. In a greenhouse experiment, the effect of five isolates on the growth of Pinus taeda seedlings was tested. Plant height, stem diameter, root and shoot dry matter were determined. The Streptomyces isolate A43 doubled plant growth. These results may lead to the development of new technologies in the identification of still unknown bacterial metabolites and new management techniques to control forest plant diseases.     

In vitro aldose reductase inhibitory activity of 5-benzyl-2,4-thiazolidinediones

Several 5-benzyl-2,4-thiazolidinediones (5-7) were synthesised and tested as in vitro aldose reductase (ALR2) inhibitors. Most of them, particularly N-unsubstituted 5-benzyl-2,4-thiazolidinediones 5 and (5-benzyl-2,4-dioxothiazolidin-3-yl)acetic acids 7, displayed moderate to high inhibitory activity levels. In detail, the insertion of an acetic chain on N-3 significantly enhanced ALR2 inhibitory potency, leading to acids 7 which proved to be the most effective among the tested compounds. In addition, in N-unsubstituted derivatives 5 the presence of an additional aromatic ring on the 5-benzyl moiety was generally beneficial. In fact, the ALR2 inhibition results of compounds 5-7, compared to those of the previously assayed corresponding 5-arylidene-2,4-thiazolidinediones, indicated that N-unsubstituted derivatives 5b, c and d, which bore an additional aromatic group in the para position of the 5-benzyl residue, were significantly more effective than their 5-arylidene counterparts; in all other cases, the saturation of the exocyclic double bond CC in 5 brought about a moderate decrease in activity.     

Assessing freshwater use impacts in LCA,part 2: case study of broccoli production in the UK and Spain

Background, aim and scope  

Milà i Canals et al. (Int J Life Cycle Ass 14(1):28-42, 2009) referred to as ‘Part 1’ in this paper) showed that impacts associated with use of freshwater must be treated more rigorously than is usual in life cycle assessment (LCA), going beyond the conventional consideration only of ‘blue’ water (i.e. irrigation and other abstractions), and suggested an operational method to include the impacts on freshwater ecosystems (freshwater ecosystem impact) and abiotic resource depletion (freshwater depletion). The inclusion of water-related impacts in LCA is of paramount importance, particularly for agricultural systems due to their large water consumption worldwide. A case study of UK consumption of broccoli grown in the UK and Spain is presented here to illustrate the method suggested in Part 1.     

Gender-associated differences of perforin polymorphisms in the susceptibility to multiple sclerosis

The granule-dependent exocytosis pathway is an important mechanism to induce apoptosis by CD8(+) T cells and NK cells and involves lytic molecules such as perforin. In the current study, we investigated the perforin 1 gene (PRF1) as a candidate for multiple sclerosis (MS) susceptibility in the Spanish population. We genotyped three PRF1 single nucleotide polymorphisms (rs885822, rs10999426, and rs3758562) in 420 patients with MS and 512 controls. Associations of PRF1 polymorphisms with the disease were restricted to male patients with MS, and the finding was consistently observed at the allele, genotype, and haplotype levels. Gender-associated differences were validated in an additional replication cohort comprised of 292 MS cases and 300 controls. In addition, we identified minor risk haplotypes strongly associated with male patients having primary progressive MS (PPMS). Further characterization of male patients with PPMS carrying the risk haplotypes by means of gene expression microarrays revealed overrepresentation of the cell killing gene ontology category among downregulated genes in these patients compared with male patients with PPMS carrying protective haplotypes. Moreover, PRF1 mRNA expression levels were significantly lower in patients with risk haplotypes, and changes in perforin protein expression by CD8(+) T cells mirrored those observed in gene expression. These findings suggest a gender dimorphism in the PRF1 association with MS and point to the presence of a generalized defect in the expression of genes that code for proteins involved in cell killing in a subgroup of male patients with PPMS.     

Critical role of His369 in the reactivity of Pseudomonas aeruginosa cytochrome cd1 nitrite reductase with oxygen

In the denitrification pathway, Pseudomonas aeruginosa cytochrome cd1 nitrite reductase catalyzes the reduction of nitrite to nitric oxide; in vitro, this enzyme is also competent in the reduction of O2 to 2H2O. In this article, we present a comparative kinetic study of the O2 reaction in the wild-type nitrite reductase and in three site-directed mutants (Tyr10-->Phe, His369-->Ala and His327-->Ala/His369-->Ala) of the amino acid residues close to the d1 heme on the distal side. The results clearly indicate that His369 is the key residue in the control of reactivity, as its substitution with Ala, previously shown to affect the reduction of nitrite, also impairs the reaction with O2, affecting both the properties and lifespan of the intermediate species. Our findings allow the presentation of an overall picture for the reactivity of cytochrome cd1 nitrite reductase and extend our previous conclusion that the conserved distal histidines are essential for the binding to reduced d1 heme of different anions, whether a substrate such as nitrite, a ligand such as cyanide, or an intermediate in the O2 reduction. Moreover, we propose that His369 also exerts a protective role against degradation of the d1 heme, by preventing the formation and adverse effects of the reactive O2 species (never present in significant amounts in wild-type cytochrome cd1 nitrite reductase), a finding with clear physiological implications.     

Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10)

A triple mutant of sperm whale myoglobin (Mb) [Leu(B10) --> Tyr, His(E7) --> Gln, and Thr(E10) --> Arg, called Mb-YQR], investigated by stopped-flow, laser photolysis, crystallography, and molecular dynamics (MD) simulations, proved to be quite unusual. Rebinding of photodissociated NO, O2, and CO from within the protein (in a "geminate" mode) allows us to reach general conclusions about dynamics and cavities in proteins. The 3D structure of oxy Mb-YQR shows that bound O2 makes two H-bonds with Tyr(B10)29 and Gln(E7)64; on deoxygenation, these two residues move toward the space occupied by O2. The bimolecular rate constant for NO binding is the same as for wild-type, but those for CO and O2 binding are reduced 10-fold. While there is no geminate recombination with O2 and CO, geminate rebinding of NO displays an unusually large and very slow component, which is pretty much abolished in the presence of xenon. These results and MD simulations suggest that the ligand migrates in the protein matrix to a major "secondary site," located beneath Tyr(B10)29 and accessible via the motion of Ile(G8)107; this site is different from the "primary site" identified by others who investigated the photolyzed state of wild-type Mb by crystallography. Our hypothesis may rationalize the O2 binding properties of Mb-YQR, and more generally to propose a mechanism of control of ligand binding and dissociation in hemeproteins based on the dynamics of side chains that may (or may not) allow access to and direct temporary sequestration of the dissociated ligand in a docking site within the protein. This interpretation suggests that very fast (picosecond) fluctuations of amino acid side chains may play a crucial role in controlling O2 delivery to tissue at a rate compatible with physiology.