Improving analysis of meta-omics data with the MOSCA framework

Introduction: Meta-omics is an emergent field of research with many resources available in the form of databases and software. The information stored in databases is not always easily accessible, and software tools for meta-omics are often difficult to utilize. In this work, we present Meta-Omics Software for Community Analysis (MOSCA), a software framework that implements pipelines for the integrated analysis of metagenomics (MG), metatranscriptomics (MT) and metaproteomics (MP) data. This framework integrates tools allowing access to databases, handling of data and a complete workflow for meta-omics data analysis. Methodology and results: MOSCA was developed in Python 3, takes as input raw files obtained from Next-generation sequencing (in FastQ format), and from mass spectrometry (mass spectra in vendor or peak-picked formats), and integrates several tools for MG, MT and MP analysis. These tools are connected through their inputs/outputs by snakemake, in a fully automated workflow. MG analysis starts with preprocessing of sequencing reads, which automatically configures Trimmomatic to remove adapters and low-quality reads based on FastQC quality reports, and SortMeRNA for rRNA reads removal. Assembly can be performed with MetaSPAdes or Megahit and is followed by binning with MaxBin2 and CheckM for quality check. Genes are identified with FragGeneScan and are annotated with both UPIMAPI (homology-based annotation) and reCOGnizer (domain-based annotation), with reference to UniProt KB and eight databases included in the Conserved Domains Database, respectively. Bowtie2 is used to align reads to metagenomes. Protein identification and quantification can be performed with either SearchCLI coupled to PeptideShaker (performing peptide-to-spectrum matching and spectra count) or using MaxQuant (with quantification at the MS1 level). Differential gene expression analysis is performed with DESeq2, and heatmaps, volcano plots and PCA plots are generated. The expressed enzymes are plotted into hundreds of KEGG metabolic maps with the tool KEGGCharter, showing the metabolic functions that are differentially expressed and the taxonomic assignment. Tables, heatmaps and other representations obtained with MOSCA provide an interactive, accessible and comprehensive representation of the information obtained from MG, MT and MP analyses. Conclusions: MOSCA performs automatic analyses of MG, MT and MP datasets, integrating over 20 tools to obtain a comprehensive and easy to understand representation of microbial activity in different processes and conditions.info:eu-repo/semantics/publishedVersio

UPIMAPI, reCOGnizer and KEGGCharter: three tools for functional annotation

Omics technologies generate large datasets from which biological information must be extracted by using bioinformatics tools. Although web services provide easier to use interfaces, large datasets are difficult to handle. This is not a limitation of command-line tools and programmatic modules, but these may be challenging to use. In this work, three command-line tools were developed, aimed for speed and automation. The tools are available through Bioconda for Unix systems and were developed in Python 3, making use of multithreading/multiprocessing in computationally demanding steps. UPIMAPI integrates annotation with reference to the UniProt database with automatic retrieval of internal and cross-reference information from other databases (e.g., KEGG, BRENDA and RefSeq) through UniProts API, accessed with urllib package. The input is a FASTA file containing protein sequences, and the outputs are EXCEL or TSV files containing taxonomic, functional, and cross-reference information. reCOGnizer performs domain-based annotation of protein sequences with CDD, Pfam, NCBIfam, Protein Clusters, TIGRFAM, SMART, COG and KOG as reference databases, and obtains EC numbers and taxonomic assignments per domain identified. The results are outputted in TSV and EXCEL files. KEGGCharter is a command line implementation of KEGG Pathways mapping service, while also obtaining additional KOs and EC numbers, through the methods available in BioPython for accessing KEGGs API. KEGGCharter takes as input a table (TSV or EXCEL), containing either KEGG IDs, KOs or EC numbers. KEGGCharter represents identified KOs in metabolic maps and includes information on differential gene expression. When data from more than one organism is uploaded, KEGGCharter links function to taxonomic identification, which can be visualized in the maps. Differential expression of genes/proteins can be visualized in metabolic maps, by showing mini heatmaps. UPIMAPI and reCOGnizer are complementary tools, providing functional annotation based on protein sequencing homology and on identification of protein conserved domains, respectively. Both tools retrieve the IDs (KEGG IDs, EC numbers and KOs) necessary to run KEGGCharter. Together, these tools provide a complete characterization and visualization of results, facilitating the interpretation of omics experiments, and requiring minimal bioinformatics expertise.info:eu-repo/semantics/publishedVersio

Contribuição para a caracterização das águas interiores de superfície da ilha do Pico

XII Expedição Científica do Departamento de Biologia - Pico 2005.Com o objectivo de proceder à sua caracterização hidromorfológica, físico-química e biológica visitaram-se, entre 7 e 14 de Junho de 2005, 24 lagoas situadas na ilha do Pico (Açores). Todas as lagoas foram fotografadas e geo-referenciadas. Neste relatório são apresentados os resultados relativos à hidromorfologia, aos parâmetros físico-químicos da água, bem como parte dos elementos para a caracterização biológica, nomeadamente os que se referem aos peixes e às plantas vasculares

Transmission laser welding of thermoplastics: influence of welding parameters and rib dimensions on the strength of welded joints

Laser transmission welding of injection moulded thermoplastics is commonly used in industrial applications such as electronic packaging, textiles, biomedical devices, windows, signs, food and medical packaging, visual displays and automotive components due to very precise control of the process parameters, including the amount of energy delivered and its location, which results in high joint quality. In this article, the influence of laser transmission contour welding parameters and geometry of welding rib on joint force is investigated. Velocity with which the laser beam moves on the sample, temperature applied, clamp force, laser beam size and number of laser passes were studied for various dimensions of the rib with rectangular and triangular cross section. Samples of different thermoplastic materials, PMMA and PC/ABS, were produced and then joined by transmission laser welding and after that were subjected to tensile tests, in order to measure strength of the joint between the plastic parts. Initially, optimal welding conditions were found for each studied rib and their influence on the force of the joint was analysed. Afterwards, a comparison between the best results obtained for each rib was performed, in order to define the dimensions of the rib that result in the highest joint force. It was observed that samples with triangular ribs achieved higher joint strength. For both studied geometries of rib cross section, an increase of the width of the ribs improves the joint strength, while an increase of the height worsens it.Project 40232 – Poly.Weld, co-financed by Compete 2020, Portugal 2020 and European Union through the European Regional Development Fun

Continuous production of highly tuned silk/calcium-based composites: exploring new pathways for skin regeneration

Calcium plays an important role in barrier function repair and skin homeostasis. In particular, calcium phosphates (CaPs) are well established materials for biomedical engineering due to their biocompatibility. To generate biomaterials with a more complete set of biological properties, previously discarded silk sericin (SS) has been recovered and used as a template to grow CaPs. Crucial characteristics for skin applications, such as antibacterial activity, can be further enhanced by doping CaPs with cerium (Ce) ions. The effectiveness of cell attachment and growth on the materials highly depends on their morphology, particle size distribution, and chemical composition. These characteristics can be tailored through the application of oscillatory flow technology, which provides precise mixing control of the reaction medium. Thus, in the present work, CaP/SS and CaP/SS/Ce particles were fabricated for the first time using a modular oscillatory flow plate reactor (MOFPR) in a continuous mode. Furthermore, the biological behavior of both these composites and of previously produced pure CaPs was assessed using human dermal fibroblasts (HDFs). It was demonstrated that both CaP based with plate-shaped nanoparticles and CaP-SS-based composites significantly improved cell viability and proliferation over time. The results obtained represent a first step towards the reinvention of CaPs for skin engineering.info:eu-repo/semantics/publishedVersio

An adsorptive bioprocess for production and recovery of resveratrol with Corynebacterium glutamicum

BACKGROUND The growing interest in polyphenols has led to the design of industrial-scale processes able to produce them by fermentation and recover them in a more sustainable way. The goal of this work is to present two integrated approaches for the recovery of resveratrol, obtained through fermentation. The production of resveratrol using Corynebacterium glutamicum and its continuous removal using a hydrophobic resin is described. Batch production is compared with in situ product removal, where Amberlite XAD-7HP is either directly added to the medium (direct adsorption) or is present in an external column (external adsorption). RESULTS For both adsorption strategies tested, the amount of extracellular resveratrol increased from 75% to at least 90% of the total amount produced. However, lower total resveratrol concentrations were attained 3.6 and 2.2mg L-1, for the external and direct contact strategies, respectively, versus 5.3mg L-1 for batch experiments. CONCLUSIONS The proposed in situ removal strategies demonstrated the potential of increasing the excretion of resveratrol produced intracellularly. These process configurations may not only lead to a simpler downstream process design, but also to the avoidance of potential problems with the toxicity of polyphenols to the cells, especially when larger titers are obtained. © 2017 Society of Chemical IndustryWe would like to thank the European Union Framework Program 7 ‘BacHBerry’ (www.bachberry.eu), Project No. FP7- 613793 for financial support, the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01- 0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145- FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Studies of stabilization of native catalase using additives

Native catalase preparations isolated from Bacillus Sp were formulated with different additives for storage stabilization and better performance at high temperature and pH. The additives studied were: polyethylene glycol, glycerol, BSA, casein, glutaraldehyde, n-butylamine, ethylenediamine, 1.6-diaminohexane, BSA/glutaraldehyde and casein/glutaraldehyde. The glycerol and glutaraldehyde showed the best performance for long-term storage at 30degreesC and neutral pH. No stabilization additives were effective at pH 12, but below that pH the polyethylene glycol and glycerol appeared to be the most appropriate. Amines, polyethylene glycol and glycerol shifted the pH activity maximum of the native catalase toward more alkaline region, while glycerol were the only additive to improve the temperature profile of the enzyme. (C) 2002 Elsevier Science Inc. All rights reserved

Assessment of photocatalytic, superhydrophobic and self-cleaning properties on hot mix asphalts coated with TiO 2 and/or ZnO aqueous solutions

Photocatalytic, superhydrophobic and self-cleaning capabilities were promoted on AC 6 and AC 14 asphalt mixtures by spraying of TiO2 and/or ZnO. Initially, physicochemical and morphological properties of bitumen samples were evaluated by Fourier Transform Infrared Spectroscopy and Atomic Force Microscopy after the solution spraying of TiO2, ZnO and TiO2 ZnO. Then, to assure those capacities, Water Angle Contact and Photocatalytic Efficiency tests were carried out on both mixtures. Finally, mixtures were assessed mechanically through Indirect Tensile Strength. Photocatalytic, superhydrophobic and self-cleaning properties were guaranteed for AC 14 with TiO2 and TiO2 ZnO and AC 6 with TiO2 ZnO without deteriorations.This work was partially financed by FCT—Fundação para a Ciência e Tecnologia—under the project PTDC/FIS/120412/2010: ‘‘Nanobased concepts for Innovative & Eco-sustainable constructive material’s surfaces’’ and project PEst-OE/ECI/UI4047/2014 supported by Portuguese Foundation for Science and Technology.info:eu-repo/semantics/publishedVersio

Photocatalytic asphalt pavement: the physicochemical and rheological impact of TiO2 nano/microparticles and ZnO microparticles onto the bitumen

A cost-effective solution to provide asphalt pavements with the photocatalytic property was addressed for the first time, based on the combination of low percentages of two semiconductors, TiO2and ZnO. Two photocatalytic techniques – spray deposition and bitumen modification – were used. With the former, the chemical properties were evaluated by FTIR after spraying the bitumen samples with two aqueous solutions, one with acid PH and another alkaline, of nano-TiO2. The solution with less chemical impact was the alkaline one. With the latter, Penetration, Softening Point, Mass Loss, Dynamic Viscosity, Complex moduli and Performance Grade, after the modification by TiO2nano/microparticles and ZnO microparticles, were analysed with two levels of ageing produced by the RTFOT. TiO2nano/microparticles and ZnO microparticles conducted to softer bitumens and better results of short-term ageing resistance and did not cause any deterioration to the bitumen before or after either short- or long-term ageing.This work was partially financed by FCT – Fundação para a Ciência e a Tecnologia – under the project PTDC/FIS/120412/2010: ‘Nanobased concepts for Innovative & Eco-sustainable constructive material’s surfaces’ and project PEst-OE/ECI/UI4047/2014