Candida bracarensis: Evaluation of virulence factors and its tolerance to Amphotericin B and Fluconazole

Candida bracarensis is an uncommon Candida species found during an epidemiological study of candidiasis performed in Braga, Portugal. Initially, it was identified as C. glabrata, but recently detailed analyses pointed out their differences. So, little information is still available about C. bracarensis virulence factors and antifungal susceptibilities. Therefore, the main goal of this work is to evaluate the ability of C. bracarensis to form biofilms, to produce hydrolytic enzymes (proteases, phospholipases and hemolysins), as well as its susceptibility to amphotericin B and fluconazole. It was shown, for the first time, that all C. bracarensis strains were able to form biofilms and display proteinase and hemolytic activities. Moreover, although planktonic cells presented antifungal susceptibility, amphotericin B and fluconazole were unable to inhibit biofilm formation and eradicate pre-formed biofilms. Due to the propensity of C. bracarensis to display antifungal resistance and virulence attributes, the control of these emerging pathogens is recommended.

Quantitative image analysis as a tool for Yarrowia lipolytica dimorphic growth evaluation in different culture media

Yarrowia lipolytica, a yeast strain with a huge biotechnological potential, capable to produce metabolites such as γ-decalactone, citric acid, intracellular lipids and enzymes, possesses the ability to change its morphology in response to environmental conditions. In the present study, a quantitative image analysis (QIA) procedure was developed for the identification and quantification of Y. lipolytica W29 and MTLY40-2P strains dimorphic growth, cultivated in batch cultures on hydrophilic (glucose and N-acetylglucosamine (GlcNAc) and hydrophobic (olive oil and castor oil) media. The morphological characterization of yeast cells by QIA techniques revealed that hydrophobic carbon sources, namely castor oil, should be preferred for both strains growth in the yeast single cell morphotype. On the other hand, hydrophilic sugars, namely glucose and GlcNAc caused a dimorphic transition growth towards the hyphae morphotype. Experiments for γ-decalactone production with MTLY40-2P strain in two distinct morphotypes (yeast single cells and hyphae cells) were also performed. The obtained results showed the adequacy of the proposed morphology monitoring tool in relation to each morphotype on the aroma production ability. The present work allowed establishing that QIA techniques can be a valuable tool for the identification of the best culture conditions for industrial processes implementation.

Engineering of fatty acid production and secretion in Saccharomyces cerevisiae

Tese de Doutoramento em Ciências - Especialidade em Biologia

Enzymatic processing of protein-based fibers

Wool and silk are major protein fiber materials used by the textile industry. Fiber protein structure-function relationships are briefly described here, and the major enzymatic processing routes for textiles and other novel applications are deeply reviewed. Fiber biomodification is described here with various classes of enzymes such as protease, transglutaminase, tyrosinase, and laccase. It is expected that the reader will get a perspective on the research done as a basis for new applications in other areas such as cosmetics and pharma.

Public service culture collections of microorganisms: are they important for biotechnology?

Microbiology as a scientific discipline recognised the need to preserve microorganisms for scientific studies establishing from its very beginning research culture collections (CC). Later on, to better serve different scientific fields and bioindustries with the increasing number of strains of scientific, medical, ecological and biotechnological importance public service CC were established with the specific aims to support their user communities. Currently, the more developed public service CC are recognised as microBiological Resources Centres (mBRC). mBRC are considered to be one of the key elements for sustainable international scientific infrastructure, which is necessary to underpin successful delivery of the benefits of biotechnology, whether within the health sector, the industrial sector or other sectors, and in turn ensure that these advances help drive economic growth. In more detail, mBRCs are defined by Organisation for Economic Co-operation and Development (OECD) as service providers and repositories of the living cells, genomes of organisms, and information relating to heredity and functions of biological systems. mBRCs contain collections of culturable organisms (e.g., microorganisms, plant, animal cells), replicable parts of these (e.g. genomes, plasmids, virus, cDNAs), viable but not yet culturable organisms, cells and tissues, as well as database containing molecular, physiological and structural information relevant to these collections and related bioinformatics. Thus mBRCs are fundamental to harnessing and preserving the world’s microbial biodiversity and genetic resources and serve as an essential element of the infrastructure for research and development. mBRCs serve a multitude of functions and assume a range of shapes and forms. Some are large national centres performing a comprehensive role providing access to diverse organisms. Other centres play much narrower, yet important, roles supplying limited but crucial specialised resources. In the era of the knowledge-based bio-economy mBRCs are recognised as vital element to underpinning the biotechnology.

Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

Data supporting the role of enzymes and polysaccharides during cassava postharvest physiological deterioration

This data article is referred to the research article entitled The role of ascorbate peroxidase, guaiacol peroxidase, and polysaccharides in cassava (Manihot esculenta Crantz) roots under postharvest physiological deterioration by Uarrota et al. (2015). Food Chemistry 197, Part A, 737746. The stress duo to PPD of cassava roots leads to the formation of ROS which are extremely harmful and accelerates cassava spoiling. To prevent or alleviate injuries from ROS, plants have evolved antioxidant systems that include non-enzymatic and enzymatic defence systems such as ascorbate peroxidase, guaiacol peroxidase and polysaccharides. In this data article can be found a dataset called newdata, in RData format, with 60 observations and 06 variables. The first 02 variables (Samples and Cultivars) and the last 04, spectrophotometric data of ascorbate peroxidase, guaiacol peroxidase, tocopherol, total proteins and arcsined data of cassava PPD scoring. For further interpretation and analysis in R software, a report is also provided. Means of all variables and standard deviations are also provided in the Supplementary tables (data.long3.RData, data.long4.RData and meansEnzymes.RData), raw data of PPD scoring without transformation (PPDmeans.RData) and days of storage (days.RData) are also provided for data analysis reproducibility in R software.

Hydrocarbonoclastic bacteria: from bioremediation to bioenergy feedstock

Tese de Doutoramento em Engenharia Química e Biológica.

Bacteriophage-encoded depolymerases: their diversity and biotechnological applications

Bacteriophages (phages), natural enemies of bacteria, can encode enzymes able to degrade polymeric substances. These substances can be found in the bacterial cell surface, such as polysaccharides, or are produced by bacteria when they are living in biofilm communities, the most common bacterial lifestyle. Consequently, phages with depolymerase activity have a facilitated access to the host receptors, by degrading the capsular polysaccharides, and are believed to have a better performance against bacterial biofilms, since the degradation of extracellular polymeric substances by depolymerases might facilitate the access of phages to the cells within different biofilm layers. Since the diversity of phage depolymerases is not yet fully explored, this is the first review gathering information about all the depolymerases encoded by fully sequenced phages. Overall, in this study, 160 putative depolymerases, including sialidases, levanases, xylosidases, dextranases, hyaluronidases, peptidases as well as pectate/pectin lyases, were found in 143 phages (43 Myoviridae, 47 Siphoviridae, 37 Podoviridae, and 16 unclassified) infecting 24 genera of bacteria. We further provide information about the main applications of phage depolymerases, which can comprise areas as diverse as medical, chemical, or food-processing industry.

Combined bioremediation and enzyme production by Aspergillus sp. in olive mill and winery wastewaters

Olive mill wastewaters (OMW) and vinasses (VS) are effluents produced respectively by olive mills and wineries, both sectors are of great economic importance in Mediterranean countries. These effluents cause a large environmental impact, when not properly processed, due to their high concentration of phenolic compounds, COD and colour. OMW may be treated by biological processes but, in this case, a dilution is necessary, increasing water consumption. The approach here in proposed consists on the bioremediation of OMW and VS by filamentous fungi. In a screening stage, three fungi (Aspergillus ibericus, Aspergillus uvarum, Aspergillus niger) were selected to bioremediate undiluted OMW, two-fold diluted OMW supplemented with nutrients, and a mixture of OMW and VS in the proportion 1:1 (v/v). Higher reductions of phenolic compounds, colour and COD were achieved mixing both residues; with A. uvarum providing the best results. In addition, the production of enzymes was also evaluated during this bioremediation process, detecting in all cases lipolytic, proteolytic and tannase activities. A. ibericus, A. uvarum and A. niger achieved the highest value of lipase (1253.7 ± 161.2 U/L), protease (3700 ± 124.3 U/L) and tannase (284.4 ± 12.1 U/L) activities, respectively. Consequently, this process is an interesting alternative to traditional processes to manage these residues, providing simultaneously high economic products, which can be employed in the same industries.

Biological extraction of bromelain from pineapple byproducts

[Excerpt] Isolation and purification of valuable compounds are very important processes to valorize agro-food byproducts. Currently, protein extraction and development of environmentally friendly technologies are industrially relevant topics [1]. Among the extracted proteins from byproducts proteases are a relevant group for industrial applications. These enzymes are a class of hydrolytic enzymes capable of cleaving the peptide bonds of proteins chains and are essential in physiological processes [2]. (...)

Enzymes which detoxify ochratoxin A

Mycotoxins are fungal secondary metabolites found in some agricultural commodities which are toxic for humans and animals in small amounts. Mycotoxins are a global problem which can be partially controlled through prevention strategies that can be applied along the food and feed chain production. However, when mycotoxin formation can not be avoided and they come to be present in commodities some remediation strategies can also be used to reduce its levels on products, its bioavailability or its toxic effects. Among these remediation strategies, the biological methods are recently holding a relevant position, being widely studied in the last years. As a result, a great number of microorganisms that can degrade or detoxify several mycotoxins and the application of some of them were reported. Moreover, several enzymes which mediate these biological processes were identified, being by themselves studied in order to develop new biotechnological approaches to control the mycotoxin problem on commodities. The main enzymes known to detoxify ochratoxin A, their action and their present application in order to counteract the referred problem are reviewed and critically assessed.

Biocatalysis in micellar systems

[Excert] Biocatalysis and biotransformations are environmentally friendly, and allow the development of sustainable production processes on a large scale. Thus, these processes are becoming important alternatives to conventional chemistry in the drug, biochemical, and emerging biorenewable energy industries. Biocatalysts are required to function under non-conventional conditions, such as in organic solvents, being competitive in terms of cost and efficiency. In fact, the technological utility of enzymes can be enhanced greatly by using them in the presence of organic solvents, rather than in their natural aqueous reaction media. Multiphase systems are more complex but offer a new field of possibilities. The presence of hydrophobic solvents in biocatalysis allows the conversion of poorly water soluble substrates more efficiently. The accessibility of hydrophobic substrates to enzymes or whole cells presents an interesting challenge for researchers and technologists. In this context, microemulsions are a promising tool in enzyme technology. This chapter presents an overview of the characterization of biphasic and microemulsion systems and their applications in biotransformation processes (...).

Biotechnological production and application of fructooligosaccharides

Currently, prebiotics are all carbohydrates of relatively short chain length. An important group is the fructooligosaccharides, which are a special kind of prebiotics associated to their selective stimulation of the activity of certain groups of colonic bacteria that have a positive and beneficial effect on intestinal microbiota, reducing incidence of gastrointestinal infections, respiratory and also possessing a recognized bifidogenic effect. Traditionally, these prebiotic compounds have been obtained through extraction processes from some plants, as well as through enzymatic hydrolysis of sucrose. However, different fermentative methods have also been proposed for the production of fructooligosaccharides, such as solid-state fermentation utilizing various agroindustrial by-products. By optimizing the culture parameters, fructooligosaccharides yields and productivity can be improved. The use of immobilized enzymes and cells has also been proposed as being an effective and economic method for large-scale production of fructooligosaccharides. This paper is an overview on the results of recent studies on fructooligosacharides biosynthesis, physicochemical properties, sources, biotechnological production and applications.