New oxapolycyclic cage amines with NMDA receptor antagonist and trypanocidal activities

The synthesis of several (1,2,3,5,6,7-hexahydro-1,5:3,7-dimethano-4-benzoxonin-3-yl)amines and related compounds is reported. Several of them display very similar activity to memantine as NMDA receptor antagonists. Several derivatives showed a significant level of trypanocidal activity.     

Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries

Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr-B-Phos, Pfr-C-Phos and Pfr-GAP, to describe the three groups of acid phosphatases. These sequence-based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.     

Deficiencia visual y neurológica posterior a la disfunción del sistema de derivación ventrículo-peritoneal: reporte de caso

Neurological visual impairments in children have multiple causes, some of them reversible while others are not. Hydrocephalus is one of the most important and common ones as it can result in permanent impairment. There are multiple causes of hydrocephalus, intraventricular hemorrhage being the main one. This generally occurs when the germinal matrix bleeds and is very common in preterm newborns.We present the clinical case of a patient with cerebral palsy, intraventricular hemorrhage, and hydrocephalus as a result of a preterm multiple pregnancy who developed optic atrophy during childhood secondary to ventricle-peritoneal shunt dysfunction. During the rehabilitation and treatment period, she received neurorehabilitation sessions, which improved her visual acuity and capacity. We found similarities and differences with other cases and we confirmed the importance of the treatment chosen for the recovery of visual capacity.     

Bacterial diversity in the rhizosphere of maize and the surrounding carbonate‐rich bulk soil

Maize represents one of the main cultivar for food and energy and crop yields are influenced by soil physicochemical and climatic conditions. To study how maize plants influence soil microbes we have examined microbial communities that colonize maize plants grown in carbonate‐rich soil (pH 8.5) using culture‐independent, PCR‐based methods. We observed a low proportion of unclassified bacteria in this soil whether it was planted or unplanted. Our results indicate that a higher complexity of the bacterial community is present in bulk soil with microbes from nine phyla, while in the rhizosphere microbes from only six phyla were found. The predominant microbes in bulk soil were bacteria of the phyla Acidobacteria, Bacteroidetes and Proteobacteria, while Gammaproteobacteria of the genera Pseudomonas and Lysobacter were the predominant in the rhizosphere. As Gammaproteobacteria respond chemotactically to exudates and are efficient in the utilization of plants exudate products, microbial communities associated to the rhizosphere seem to be plant‐driven. It should be noted that Gammaproteobacteria made available inorganic nutrients to the plants favouring plant growth and then the benefit of the interaction is common.     

Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three‐item statements

The cladistic literature does not always specify the kind of multistate character treatment that is applied for an analysis. Characters can be treated either as unordered transformation series or as rooted [three‐item analysis (3ia)] or unrooted state trees (ordered characters). We aimed to measure the impact of these character treatments on phylogenetic inference. Discrete characters can be represented either as rows or columns in matrices (e.g. for parsimony) or as hierarchies for 3ia. In the present study, we use simulated and empirical examples to assess the relative merits of each method considering both the character treatment and representation. We measure two parameters (resolving power and artefactual resolution) using a new tree comparison metric, ITRI (inter‐tree retention index). Our results suggest that the hierarchical character representation not only results (with our simulation settings) in the greatest resolving power, but also in the highest artefactual resolution. Our empirical examples provide equivocal results. Parsimony unordered states yield less resolving power and more artefactual resolutions than parsimony ordered states, both with our simulated and empirical data. Relationships between three operational taxonomic units (OTUs), irrespective of their relationships with other OTUs, are called three‐item statements (3is). We compare the intersection tree (which reconstructs a single tree from all of the common 3is of source trees) with the traditional strict consensus and show that the intersection tree retains more of the information contained in the source trees. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 914–930.     

Cytocompatibility and Synergy of EGCG and Cationic Peptides Against Bacteria Related to Endodontic Infections,in Planktonic and Biofilm Conditions

Probiotics and Antimicrobial Proteins - This study evaluated the cytocompatibility and antimicrobial/antibiofilm effects of epigallocatechin-3-gallate (EGCG) associated with peptide LL-37 and its...     

A proteomics study of the induction of somatic embryogenesis in Medicago truncatula using 2DE and MALDI-TOF/TOF

Medicago truncatula is a model legume, whose genome is currently being sequenced. Somatic embryogenesis (SE) is a genotype-dependent character and not yet fully understood. In this study, a proteomic approach was used to compare the induction and expression phases of SE of both the highly embryogenic line M9-10a of M. truncatula cv. Jemalong and its non-embryogenic predecessor line, M9. The statistical analysis between the lines revealed 136 proteins with significant differential expression (P < 0.05). Of these, 5 had a presence/absence pattern in M9 vs M9-10a and 22 showed an at least twofold difference in terms of spot volume, were considered of particular relevance to the SE process and therefore chosen for identification. Spots were excised in gel digested with trypsin and proteins were identified using matrix-assisted laser desorption ionization-time of flight/time of flight. Identified proteins indicated a higher adaptability of the embryogenic line toward the stress imposed by the inducing culture conditions. Also, some proteins were shown to have a dual pattern of expression: peroxidase, pyrophosphatase and aspartate aminotransferase. These proteins showed higher expression during the induction phases of the M9 line, whereas in the embryogenic line had higher expression at stages coinciding with embryo formation.     

Genetic and symbiotic diversity of nitrogen-fixing bacteria isolated from agricultural soils in the Western Amazon by using cowpea as the trap plant

Cowpea is a legume of great agronomic importance that establishes symbiotic relationships with nitrogen-fixing bacteria. However, little is known about the genetic and symbiotic diversity of these bacteria in distinct ecosystems. Our study evaluated the genetic diversity and symbiotic efficiencies of 119 bacterial strains isolated from agriculture soils in the western Amazon using cowpea as a trap plant. These strains were clustered into 11 cultural groups according to growth rate and pH. The 57 nonnodulating strains were predominantly fast growing and acidifying, indicating a high incidence of endophytic strains in the nodules. The other 62 strains, authenticated as nodulating bacteria, exhibited various symbiotic efficiencies, with 68% of strains promoting a significant increase in shoot dry matter of cowpea compared with the control with no inoculation and low levels of mineral nitrogen. Fifty genotypes with 70% similarity and 21 genotypes with 30% similarity were obtained through repetitive DNA sequence (BOX element)-based PCR (BOX-PCR) clustering. The 16S rRNA gene sequencing of strains representative of BOX-PCR clusters showed a predominance of bacteria from the genus Bradyrhizobium but with high species diversity. Rhizobium, Burkholderia, and Achromobacter species were also identified. These results support observations of cowpea promiscuity and demonstrate the high symbiotic and genetic diversity of rhizobia species in areas under cultivation in the western Amazon.     

The enzyme activity of bovine adrenocortical cytochrome P-450 producing pregnenolone from cholesterol: Kinetic and electrophoretic studies on the reactivity of hydroxycholesterol intermediates

Electrofocusing of a highly-purified preparation of bovine adrenocortical cytochrome P-450(scc) showed a single peak of enzyme activity at pH 6.8, when either cholesterol, [20S]-20-hydroxycholesterol, [22R]-22-hydroxycholesterol or [20R, 22R]-20, 22-dihydroxycholesterol was used as the substrate for the side chain cleavage reaction. The formation of pregnenolone from these hydroxycholesterols was inhibited by [20R, 22S]-20, 22-epoxycholesterol similarly in a competitive manner and the Ki value for the epoxide was found to be 12–15 μM for all these substrates. When one of the above mentioned substrates was incubated in a concentration sufficient for maximal reaction velocity, the addition of another hydroxycholesterol did not result in further increase of pregnenolone production. These results support the assumption that a single species of enzyme catalyzes all the three steps of the reaction, i.e., 20-hydroxylation, 22-hydroxylation and cleavage of carbon chain between carbon-20 and carbon-22.