Índice de contraste morfológico basado en el análisis de los contornos y el fondo de la imagen

Resumen. En este artículo se presenta un índice para cuantificar el contraste que se percibe en una imagen. El índice está basado en la ley de Weber y toma en consideración una estimación del fondo de la imagen mediante la erosión de la apertura por reconstrucción. El desempeño de la propuesta se ilustra con un conjunto de imágenes procesadas por un mapeo de contraste y se compara con dos medidas de contraste dadas en la literatura

Genome mining of <i>Streptomyces scabrisporus</i> NF3 reveals symbiotic features including genes related to plant interactions

<div><p>Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte <i>Streptomyces scabrisporus</i> NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven <i>Streptomyces</i> and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The <i>S</i>. <i>scabrisporus</i> NF3 genome is larger than the average <i>Streptomyces</i> genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that <i>S</i>. <i>scabrisporus</i> NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of <i>S</i>. <i>scabrisporus</i> mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions.</p></div

Proteome comparison between NF3 and the 10 complete genomes analyzed.

<p>The genomes are (from outside to inside): SS, SR, SV, SH, SA, SC, SG, KS, CP, BB, BA. The exterior solid line circle indicates the scaffolds of the reference genome–SS NF3. Each circle is comprised of lines, each of them indicating one protein homologous to a protein of the reference genome. An identity matrix indicating the relationship between the colors used and protein similarity is placed below the figure. The image was obtained from PATRIC utilizing the tool Proteome Comparison.</p

Chitinase genes and chitinolytic activity.

<p>A. NJ tree of all chitinase genes in the compared genomes. The MSA was produced using MUSCLE on all 116 chitinase sequences. Branches from proteins belonging to genomes S. scabrisporus NF3 and DSM 41855, as well as all secreted chitinases, are color labeled, respectively: blue, red and green. B. Expression of chitin degrading genes in SS NF3. Left side—chitin degradation at 7 days after inoculation. Right side upper level—chitin degradation at 14 days after inoculation. Ride side lower level—spore formation after growth on chitin for 14 days.</p

Genome characteristics for <i>S</i>. <i>scabrisporus</i> NF3.

<p>The circles refer to (from outside to inside): grey—Position label (Mbp): scaffold size in kbp; dark blue–contigs: organization of the scaffolds from the largest to the shortest; green–coding sequences on the forward strand (CDS FWD); purple–coding sequences on the reverse strand (CDS REV); blue–non-CDS features: location of tRNA, rRNA and pseudogenes; light purple–GC content; light orange–GC skew; dark green–location of genes encoding for polyketides; orange–location of genes encoding for nonribosomal peptide synthetases.</p

Phylogenetic tree of analyzed genomes.

<p>Phylogenetic trees were based on 4 concatenated proteins (16S rRNA, gyrB, rpoB, recG) conserved in all compared genomes using Kalign [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192618#pone.0192618.ref046" target="_blank">46</a>]. The tree was generated from a multiple sequence alignment using a Neighbor Joining algorithm. Bar shows substitution per nucleotide. The right side of the figure contains information about the abundance of genes of various functionalities discussed in the following paragraphs (synthases, siderophores and chitinases/chitin binding proteins (CBP)–computed using FIGfams, polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS) and total number of secondary metabolites clusters (SMC)–computed using antiSMASH, and bacteriocins–analyzed using BAGEL3).</p

Predicted structures of secondary metabolites of <i>S</i>. <i>scabrisporus</i> NF3.

<p>The analyses were performed using AntiSMASH and PRISM.</p

Genes involved in symbiotic interactions between SS NF3 and <i>A</i>. <i>adstringens</i>.

<p>(a) Chitinase family 18 (PDB 4Q22), (b) Siderophore, (c) Phytoene, (d) Spermidine, (e) Bacteriocins (here a lassopeptide).</p

General genome characteristics.

<p>General genome characteristics.</p