Prediction of antimicrobial activity of synthetic peptides by a decision tree model.

Antimicrobial resistance is a persistent problem in the public health sphere. However, recent attempts to find effective substitutes to combat infections have been directed at identifying natural antimicrobial peptides in order to circumvent resistance to commercial antibiotics. This study describes the development of synthetic peptides with antimicrobial activity, created in silico by site-directed mutation modeling using wild-type peptides as scaffolds for these mutations. Fragments of antimicrobial peptides were used for modeling with molecular modeling computational tools. To analyze these peptides, a decision tree model, which indicated the action range of peptides on the types of microorganisms on which they can exercise biological activity, was created. The decision tree model was processed using physicochemistry properties from known antimicrobial peptides available at the Antimicrobial Peptide Database (APD). The two most promising peptides were synthesized, and antimicrobial assays showed inhibitory activity against Gram-positive and Gram-negative bacteria. Colossomin C and colossomin D were the most inhibitory peptides at 5 µg/ml against Staphylococcus aureus and Escherichia coli. The methods described in this work and the results obtained are useful for the identification and development of new compounds with antimicrobial activity through the use of computational tools.

Isolation of endophytic bacteria from arboreal species of the Amazon and identification by sequencing of the 16S rRNA encoding gene.

Endophytic bacteria from three arboreal species native to the Amazon (Carapa guianenses, Ceiba pentandra, and Swietenia macrophylla), were isolated and identified, through partial sequencing of the 16S rRNA encoding gene. From these, 16 isolates were obtained, although, when compared to sequences deposited in GenBank, only seven had produced identifiable fragments. Bacillus, Pantoea and two non-culturable samples were identified. Results obtained through sequence analysis revealed low genetic diversity across the isolates, even when analyzing different species and plant structures. This is the first report concerning the isolation and identification of endophytic bacteria in these plant species.

Isolation of endophytic bacteria from arboreal species of the Amazon and identification by sequencing of the 16S rRNA encoding gene

Endophytic bacteria from three arboreal species native to the Amazon (Carapa guianenses, Ceiba pentandra, and Swietenia macrophylla), were isolated and identified, through partial sequencing of the 16S rRNA encoding gene. From these, 16 isolates were obtained, although, when compared to sequences deposited in GenBank, only seven had produced identifiable fragments. Bacillus, Pantoea and two non-culturable samples were identified. Results obtained through sequence analysis revealed low genetic diversity across the isolates, even when analyzing different species and plant structures. This is the first report concerning the isolation and identification of endophytic bacteria in these plant species.

Over-expression of genes coding for proline oxidase, riboflavin kinase, cytochrome c oxidase and an MFS transporter induced by acriflavin in Trichophyton rubrum.

Acriflavin (3,6-acridinediamine) and other acridine derivatives act in both prokaryotic and eukaryotic cells at the level of DNA-coiling enzymes (topoisomerases) causing the stabilization of the enzyme-DNA cleavable complex. In order to better understand the mode of action of acriflavin, Differential Display RT-PCR was used to isolate transcripts specifically over-expressed during exposure of Trichophyton rubrum mycelia to this drug. Five transcripts, whose differential expressions were confirmed by Northern blotting, revealed genes not previously described in this dermatophyte. Functional grouping identified putative enzymes possibly involved in the mitochondrial respiratory electron-transport chain and in iron transport. These results may be relevant to our understanding of the molecular events involved in the stress response of T. rubrum to acriflavin.

The synthesis of phosphate-repressible alkaline phosphatase do not appear to be regulated by ambient pH in the filamentous mould Neurospora crassa

In order to investigate further the adaptive response of moulds to ambient pH, we have measured by ELISA the pho-2-encoded Pi-repressible alkaline phosphatase synthesised by Neurospora crassa. We showed that the 74A and pho-2A strains of this mould secrete similar amounts of the pho-2-encoded enzyme irrespective of ambient pH, when both the preg and pgov genes are not functional, i.e., in strains nuc-2+ growing under Pi-starvation. This suggests that pho-2, which is responsive to Pistarvation via the action of genes nuc-2, preg, pgov and nuc-1, is not a gene responsive to ambient pH and that the differential glycosylation observed for the Pi-repressible alkaline phosphatase retained by the mycelium at pH 5.6 or secreted into the growth medium at pH 8.0 is the genetic response to ambient pH sensing in N. crassa.

Purification and properties of pi-repressible acid phosphatases from Aspergillus nidulans.

Two forms of the pacA-encoded acid phosphatase (designated acid phosphatases I and II) secreted by the mold Aspergillus nidulans grown in low-Pi medium at 37 degrees, pH5.0, were purified to apparent homogeneity by PAGE. The M(r) of the purified enzyme forms were ca 115000 (60000) and 113000 (62000) respectively for forms I and II secreted by strain biA1 and ca 118000 (60000) and 121000 (61000) respectively for forms I and II secreted by strain biA1 pacA1, as determined by exclusion chromatography (number between brackets are the M(r) as determined by SDS-PAGE). All of these purified enzyme forms showed an apparent optimum pH ranging from 6.0 to 6.5 and no deviation from Michaelis kinetics for the hydrolysis of both p-nitrophenylphosphate and alpha-naphthylphosphate. Heat inactivation at 60 degrees and at pH6.0 showed half-lives of 14min (k=0.033min(-1)) and 10min (k=0.069min(-1)), respectively, for the purified acid phosphatases I and II secreted by biA1 strain and half-lives of 0.8min (k=0.92min(-1)) and 0.6min (k=0.95min(-1)), respectively, for the purified forms I and II secreted by the biA1 pacA1 strain. The neutral sugar content of purified acid phosphatases I and II secreted by strain biA1 was 48% and 37% (w/w), respectively, whereas the content of forms I and II secreted by strain biA1 pacA1 was 18% and 11%, respectively.