Novel genes related to nodulation, secretion systems, and surface structures revealed by a genome draft of Rhizobium tropici strain PRF 81

Rhizobium tropici is representative of the diversity of tropical rhizobia, besides comprising strains very effective in fixing N₂ in symbiosis with the common bean (Phaseolus vulgaris L.). The genome of a Brazilian commercial inoculant R. tropici strain (PRF 81, =SEMIA 4088), estimated at 7.85 Mb, was analyzed through a total of 9,026 shotgun reads, assembled in 1,668 phrap contigs, and covering ≈30% of the genome. Annotation identified 2,135 coding DNA sequences (CDS), and only 57.2% have possible functions. The genome comprises a mosaic of genes, with CDS showing the highest similarities with 134 microorganisms, none of which represents more than 19% of the CDS with putative known functions. The high saprophytic capacity of PRF 81 may reside in a variety of genes related to transport, biodegradation of xenobiotics, defense, and secretion proteins, many of which were reported for the first time in the present study. Novelty was also found in nodulation (nodG, a double nodIJ system, nodT, nolF, nolG) and capsular polysaccharide genes, showing stronger similarities with Sinorhizobium (=Ensifer) than with the main symbionts of the common bean—R. etli and R. leguminosarum—suggesting that the original host of R. tropici might be another tropical legume or emphasizing the highly promiscuous nature of this rhizobial species.     

Affinity and selectivity of C2- and C5-substituted "chiral-box" PNA in solution and on microarrays

Two peptide nucleic acids (PNAs) containing three adjacent modified chiral monomers (chiral box) were synthesized. The chiral monomers contained either a C2- or a C5-modified backbone, synthesized starting from D- and L-arginine, respectively (2D- and 5L-PNA). The C2-modified chiral PNA was synthesized using a submonomeric strategy to avoid epimerization during solid-phase synthesis, whereas for the C5-derivative, the monomers were first obtained and then used in solid-phase synthesis. The melting temperature of these PNA duplexes formed with the full-match or with single-mismatch DNA were measured both by UV and by CD spectroscopy and compared with the unmodified PNA. The 5L-chiral-box-PNA showed the highest T(m) with full-match DNA, whereas the 2D-chiral-box-PNA showed the highest sequence selectivity. The PNA were spotted on microarray slides and then hybridized with Cy5-labeled full match and mismatched oligonucleotides. The results obtained showed a signal intensity in the order achiral >2D-chiral box >5L-chiral box, whereas the full-match/mismatch selectivity was higher for the 2D chiral box PNA.     

Enhanced ROS production by NADPH oxidase is correlated to changes in antioxidant enzyme activity in human heart failure

In pathological conditions, the balance between reactive oxygen species (ROS) and antioxidants may shift toward a relative increase of ROS, resulting in oxidative stress. Conflicting data are available on antioxidant defenses in human failing heart and they are limited to the left ventricle. Thus, we aimed to investigate and compare the source of oxidant and antioxidant enzyme activities in the right (RV) and left (LV) ventricles of human failing hearts. We found a significant increase in superoxide production only by NADPH oxidase in both failing ventricles, more marked in RV. Despite unchanged mRNA or protein expression, catalase (CAT) and glutathione peroxidase (GPx) activities were increased, and their increases reflected the levels of Tyr phosphorylation of the respective enzyme. Manganese superoxide dismutase (Mn-SOD) activity appeared unchanged. The increase in NADPH oxidase-dependent superoxide production positively correlated with the activation of both CAT and GPx. However, the slope of the linear correlation (m) was steeper in LV than in RV for GPx (LV: m = 2.416; RV: m = 1.485) and CAT (LV: m = 1.007; RV: m = 0.354). Accordingly, malondialdehyde levels, an indirect index of oxidative stress, were significantly higher in the RV than LV. We conclude that in human failing RV and LV, oxidative stress is associated with activation of antioxidant enzyme activity. This activation is likely due to post-translational modifications and more evident in LV. Overall, these findings suggest a reduced protection of RV against oxidative stress and its potential contribution to the progression toward overt heart failure.     

Identification of a novel pyrrole derivative endowed with antimycobacterial activity and protection index comparable to that of the current antitubercular drugs streptomycin and rifampin

A hit optimization procedure based on isosteric and bioisosteric replacement of decorating groups at both the N1 and the C5 phenyl rings of 1,5-diarylpyrroles led to identification of 4-((1-(4-fluorophenyl)-2-methyl-5-(4-(methylthio)phenyl)-1H-pyrrol-3-yl)methyl)thiomorpholine that is characterized by a very high activity toward both Mycobacterium tuberculosis 103471 and H37Rv strains (MIC values of 0.125μg/mL), and a safe profile in terms of cytotoxicity (CC(50) of >128μg/mL) and protection index (>1000). Antitubercular activity and protection index of the new compound are comparable to those found for the current antitubercular drugs streptomycin and rifampin.     

Time-resolved methods in biophysics. 5. Femtosecond time-resolved and dispersed infrared spectroscopy on proteins.

In this contribution we describe how femtosecond time-resolved infrared spectroscopy provides insight into the function and dynamics of pigment-protein complexes, and what the technical requirements are to perform such experiments. We further discuss a few examples of experiments performed on the photoactive yellow protein and photosynthetic complexes in more detail.     

Characterization of hobo element copy number and integrity in Brasilian populations of Drosophila melanogaster

We have determined the copy number and the presence of full-size hobo transposable elements in eight Brasilian strains of Drosophila melanogaster. Genomic DNA was digested with AvaII and XhoI restriction enzymes, respectively, and probed with a 963 bp sequence of the hobo element. Variable numbers of full-sized and defective elements were detected in all strains. The range of the copy number was 22.13 +/- 4.52. Blots showed the presence of a 2.6 kb fragment, corresponding to the complete element, in all strains exception of one and the 1.0 kb sequence, correponding to the Th1 and Th2 repressor elements. There was neither association among copy numbers of hobo elements and latitude nor the mean annual temperatures in the original geographical region of each strain.     

Selective Pressure on the Allantoicase Gene During Vertebrate Evolution

During vertebrate evolution, the uric acid degradation pathway has been modified and several enzymes have been lost. Consequently, the end product of purine catabolism varies from species to species. In the past few years, we have focused our attention on vertebrate allantoicase (an uricolytic pathway enzyme), whose activity is present in certain fish and amphibians only, but whose mRNA we detected also in mammals. As allantoicase activity disappeared in amniotes, we wonder why these sequences not only remain present in the mammalian genome, but are still transcribed. To elucidate this issue, we have cloned and analyzed comparable cDNA sequences of different organisms from ascidians to mammals. The analysis of the nonsynonymous–synonymous substitution rate that we performed on the coding region comprising exons 3 to 8 by means of maximum likelihood suggested that a certain amount of purifying selection is acting on the allantoicase sequences. Some implications of the preservation of an apparently unnecessary gene in higher vertebrates are discussed.     

Soil persistence and biodiversity of ericoid mycorrhizal fungi in the absence of the host plant in a Mediterranean ecosystem

The occurrence of suitable mycorrhizal inocula may be an important factor affecting the dynamics of plant communities. We investigated the persistence and diversity of ericoid mycorrhizal fungi in the soil of a mature Quercus ilex forest where ericaceous hosts were absent. Erica arborea was used as a bait plant and results were compared to soil samples from experimental plots where cuttings had allowed reappearance of this ericaceous species. Fungal endophytes were isolated and tested in mycorrhiza resynthesis trials. Sterile mycorrhizal endophytes were assigned to morphotypes whose consistency was confirmed by ITS-RFLP. The ITS region of a representative of each morphotype was sequenced. BLAST searches and Neighbour-Joining analysis indicated taxonomic affinities with different classes within Ascomycota. Our results indicate that ericoid mycorrhizal fungi persist and maintain mycorrhizal ability in habitats lacking the ericaceous host. Their persistence could favour the establishment of E. arborea seedlings in pure Q. ilex forests after disturbance phenomena.     

The spleen pigment cells in some amphibia

It was demonstrated that the spleen pigment cells of Amphibia are macrophages: they show an ultrastructurally distinctive morphology, are able to phagocytose and react positively for non-specific esterases. These pigmented macrophages express mRNA for tyrosinase and also they show dopa oxidase activity; therefore they are able to synthesize melanins, as Kupffer cells do.