Extraction, characterization and properties evaluation of pineapple leaf fibers from Azores pineapple.

Pineapple leaves can provide competitive and high-quality fibers for textile purposes. Despite pineapple being cultivated in the Portugues islands there is still a technology gap for the extraction and treatment of Pineapple Leaf Fibers (PALF) in Europe. Since Azorean Pineapple differs significantly from other plants in the bromeliad family, the properties and characterization of its leaf fibers were explored for the first time. Long fibers have been extracted by hand scraping and compared to biological retting at 25 °C for different time periods. It was explored the properties of PALF from plants of different ages (11- and 18-months) and from different zones of the leaves (beginning, middle, and tip). Physical-mechanical properties of Azores PALF were determined, including diameter, linear density, strength, Young's modulus, and elongation at break and characterized by ATR-FTIR, XRD, TGA/DTG, and FESEM to understand their chemical and morphological characteristics. While slight differences were observed between different ages, variations in physical-mechanical properties were notable among fibers extracted from different leaf positions. Extraction of Azores PALF through 25 °C biological retting for 14 days effectively eliminated non-fibrous matter and produced the thinnest and strongest fibers. These fibers ranged between 34.9 and 168.3 µm in diameter, 1.39 and 7.07 tex in linear mass density, 37-993 MPa in tensile strength, 1.0-3.9 % in elongation at break, and 2.4-21.8 GPa in Young's modulus.

Simulation of a single spherical droplet drying considering shrinking and temperature profiles: first drying stage.

A model including simultaneous droplet heating and water evaporation is proposed to simulate temperature, shrinking and mass profiles of a spherical droplet subjected to convective drying, being valid for the first drying stage. Experimental data on drying skim milk and colloidal silica obtained in the literature were used for validation, but there is no restriction in the model that prevents it from being suitable for other materials. There were not significant differences observed concerning to the droplet components (dissolved or insoluble materials). The initial heating time of the particle upon reaching the constant temperature is relatively short ($\Delta t\approx7s$) for both simulated materials and water evaporation during the first drying stage occurs mostly at the wet bulb temperature of the air. Discrepancy between simulated and experimental values did not exceed $9\%$ for skim milk and $7\%$ for colloidal silica in this first stage, indicating good applicability of the model. Considering the applicability of the model in a more generic way, Whitaker correlation evaluated at the film temperature showed better results. Finally, the small discrepancy found is discussed and some improvements are proposed.

Chromosome 10 in the tomato plant carries clusters of genes responsible for field resistance/defence to Phytophthora infestans.

The main objective of the present study was to reanalyse tomato expression data that was previously submitted to the Tomato Expression Database to dissect the resistance/defence genomic and metabolic responses of tomato to Phytophthora infestans under field conditions. Overrepresented gene sets belonging to chromosome 10 were identified using the Gene Set Enrichment Analysis, and we found that these genes tend to be located towards the end of the chromosome 10. An analysis of syntenic regions between Arabidopsis thaliana chromosomes and the tomato chromosome 10 allowed us to identify conserved regions in the two genomes. In addition to allowing for the identification of tomato candidate genes participating in resistance/defence in the field, this approach allowed us to investigate the relationships of the candidate genes with chromosomal position and participation in metabolic functions, thus offering more insight into the phenomena occurring during the infection process.

Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes.

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment.

The microbiome of Brazilian mangrove sediments as revealed by metagenomics.

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H(2)S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.

[Comparative analysis of six Mycobacterium tuberculosis complex genomes]. / Análisis comparativo de seis genomas del complejo Mycobacterium tuberculosis.

INTRODUCTION: A growing number of sequenced genomes belonging to the Mycobacterium tuberculosis complex has enabled a comparison of strain traits and genomic constitution. These analyses may reveal mechanisms of evolution and genomic variation relevant to tuberculosis pathogenesis. OBJECTIVE: Multiple alignments were used to analyze the differences between six genomes of the M. tuberculosis complex and to locate regions of variation that may lead to improvements in species identification or in their treatment. MATERIALS AND METHODS: The Mauve software package was used to perform a multiple alignment of 6 genomes belonging to the M. tuberculosis complex. Regions exclusive to each genome were annotated using the TB database. RESULTS: Percent similarity among the six genomes ranged between 96.1% and 97.8%. The annotation identified intergenic regions, regions associated with transposable elements of the PE-PGRS and PPE families, and regions associated with resistance against bacteriophage. CONCLUSIONS: In spite of the high genetic similarity among the tuberculosis strains, genomic variations were elucidated that may be relevant to differences in behavior and virulence, as well as for improvement of strain diagnosis. Regions encoding membrane-associated proteins, possibly related with antigenic variation and immune response, are particularly interesting for studies aimed at seeking tuberculosis treatments.

Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries.

BACKGROUND: Phytophthora infestans (Mont.) de Bary causes late blight of potato and tomato, and has a broad host range within the Solanaceae family. Most studies of the Phytophthora--Solanum pathosystem have focused on gene expression in the host and have not analyzed pathogen gene expression in planta. METHODOLOGY/PRINCIPAL FINDINGS: We describe in detail an in silico approach to mine ESTs from inoculated host plants deposited in a database in order to identify particular pathogen sequences associated with disease. We identified candidate effector genes through mining of 22,795 ESTs corresponding to P. infestans cDNA libraries in compatible and incompatible interactions with hosts from the Solanaceae family. CONCLUSIONS/SIGNIFICANCE: We annotated genes of P. infestans expressed in planta associated with late blight using different approaches and assigned putative functions to 373 out of the 501 sequences found in the P. infestans genome draft, including putative secreted proteins, domains associated with pathogenicity and poorly characterized proteins ideal for further experimental studies. Our study provides a methodology for analyzing cDNA libraries and provides an understanding of the plant--oomycete pathosystems that is independent of the host, condition, or type of sample by identifying genes of the pathogen expressed in planta.

Análisis comparativo de seis genomasdel complejo Mycobacterium tuberculosis / Comparative analysis of six Mycobacterium tuberculosis complex genomes

Introducción. El creciente número de genomas secuenciados pertenecientes al complejo Mycobacterium tuberculosis hace posible la comparación y el análisis genómico, que puede revelar importantes mecanismos de evolución y variación para entender la patogénesis de esta especie. Objetivo. Mediante el uso de alineamientos múltiples se pretendió analizar las diferencias entre seis genomas del complejo M. tuberculosis, para encontrar regiones de variación que conduzcan a mejoras en la identificación de estas especies o en el tratamiento. Materiales y métodos. Mediante el programa bioinformático Mauve, se realizaron alineamientos múltiples de seis genomas pertenecientes a especies del complejo M. tuberculosis. Las regiones genómicas exclusivas para cada genoma se anotaron usando la base de datos Tuberculosis Database.Resultados. El porcentaje de similitud entre los seis genomas analizados estuvo entre 96,1% y 97,8%. La anotación de las regiones exclusivas reveló la presencia de elementos de transposición, familias de proteínas PPE y PE-PGRS, regiones asociadas a resistencia contra bacteriófagos y regiones intergénicas. Conclusiones. A pesar de la gran similitud entre las cepas analizadas, existen variaciones entre ellas que pueden ser importantes para entender diferencias en comportamiento y virulencia, así como para mejorar los diagnósticos de cepas específicas. Regiones como aquéllas con genes para proteínas de membrana, posiblemente, relacionadas con la variación y la respuesta antigénica, son de particular interés para estudios futuros orientados a buscar tratamientos nuevos para el control de esta enfermedad.

Introduction. A growing number of sequenced genomes belonging to the Mycobacterium tuberculosis complex has enabled a comparison of strain traits and genomic constitution. These analyses may reveal mechanisms of evolution and genomic variation relevant to tuberculosis pathogenesis.Objective. Multiple alignments were used to analyze the differences between six genomes of the M. tuberculosis complex and to locate regions of variation that may lead to improvements in species identification or in their treatment. Materials and methods. The Mauve software package was used to perform a multiple alignment of 6 genomes belonging to the M. tuberculosis complex. Regions exclusive to each genome were annotated using the TB database.Results. Percent similarity among the six genomes ranged between 96.1% and 97.8%. The annotation identified intergenic regions, regions associated with transposable elements of the PE-PGRS and PPE families, and regions associated with resistance against bacteriophage. Conclusions. In spite of the high genetic similarity among the tuberculosis strains, genomic variations were elucidated that may be relevant to differences in behavior and virulence, as well as for improvement of strain diagnosis. Regions encoding membrane-associated proteins, possibly related with antigenic variation and immune response, are particularly interesting for studies aimed at seeking tuberculosis treatments.