BiofOmics: A Web Platform for the Systematic and Standardized Collection of High-Throughput Biofilm Data

Background: Consortia of microorganisms, commonly known as biofilms, are attracting much attention from the scientific community due to their impact in human activity. As biofilm research grows to be a data-intensive discipline, the need for suitable bioinformatics approaches becomes compelling to manage and validate individual experiments, and also execute inter-laboratory large-scale comparisons. However, biofilm data is widespread across ad hoc, non-standardized individual files and, thus, data interchange among researchers, or any attempt of cross-laboratory experimentation or analysis, is hardly possible or even attempted. Methodology/Principal findings This paper presents BiofOmics, the first publicly accessible Web platform specialized in the management and analysis of data derived from biofilm high-throughput studies. The aim is to promote data interchange across laboratories, implementing collaborative experiments, and enable the development of bioinformatics tools in support of the processing and analysis of the increasing volumes of experimental biofilm data that are being generated. BiofOmics data deposition facility enforces data structuring and standardization, supported by controlled vocabulary. Researchers are responsible for the description of the experiments, their results and conclusions. BiofOmics curators interact with submitters only to enforce data structuring and the use of controlled vocabulary. Then, BiofOmics search facility makes publicly available the profile and data associated with a submitted study so that any researcher can profit from these standardization efforts to compare similar studies, generate new hypotheses to be tested or even extend the conditions experimented in the study. Significance BiofOmics novelty lays on its support to standardized data deposition, the availability of computerizable data files and the free-of-charge dissemination of biofilm studies across the community. Hopefully, this will open promising research possibilities, namely: the comparison of results between different laboratories, the reproducibility of methods within and between laboratories, and the development of guidelines and standardized protocols for biofilm formation devices and analytical methods.The financial support from the Institute of Biotechnology and Bioengineering - Center of Biological Engineering (IBB-CEB), Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER (Program COMPETE), project PTDC/SAU-ESA/646091/2006/FCOMP-01-0124-FEDER-007480 and PhD grant of Idalina Machado (SFRH/BD/31065/2006) are gratefully acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Changes in phenolic compounds during storage of pasteurized strawberry

This study aimed to establish mathematical models to describe changes in phenolics of pasteurized strawberry (Fragaria ×ananassa Duch.) during storage at 23 °C for 90 days. Freshly cut strawberries cubes were pasteurized for 5 min in a water bath at 90 °C following a heating time of 15 min. Antioxidant activity, total phenolics, total anthocyanins, and individual phenolic compounds were assessed immediately before or after pasteurization and at regular time intervals during storage. The results indicated that (1) pasteurization did not affect (P <0.05) the concentrations of total phenolics or total anthocyanins, but significantly reduced the concentrations of quercetin-3-rutinoside, kaempferol, and cyanidin-3- glucoside, and increased the concentrations of (+)-catechin, (−)-epicatechin, epigallocatechin gallate, quercetin-3- galactoside, and ellagic acid; (2) changes in antioxidant capacity, total anthocyanin, and individual compounds during storage were described by a pseudo-first-order model with the exception of total phenolic and specifically kaempferol and ellagic acid which followed zero-order kinetic models. Pelargonidin-3- glucoside degraded at the highest rate (k =0.07 day−1), followed by ellagic acid (k =0.004 day−1) and kaempferol (k = 0.003 day−1). The rate constants can be used to predict phytochemical changes in strawberry products during storage.info:eu-repo/semantics/publishedVersio

Long-term frozen storage and pasteurization effects on strawberry polyphenols content

The profile of the strawberry polyphenols was analysed on fresh strawberry, immediately after freezing or after pasteurization and during frozen storage of strawberry at -20 A degrees C for 360 days. Freezing increased the extractability of (-)-epigallocatechin gallate (60 %), (-)-epicatechin (48 %) and ellagic acid (51 %) and decreased the pelargonidin-3-glucoside (18 %). Direct pasteurization of fresh strawberry increased the extractability for (-)-epigallocatechin gallate (73 %), (-)-epicatechin (45 %) and ellagic acid (143 %) and decreased for pelargonidin-3-glucoside (16 %). During storage at -20 A degrees C for 360 days the extractable levels of pelargonidin-3-rutinoside, (-)-epigallocatechin gallate, (+)-catechin, (-)-epicatechin and ellagic acid decreased by 17, 20, 37, 65 and 80 %, respectively, while those of pelargonidin-3-glucoside increased 13 %. Changes in polyphenols content, produced by pasteurization after 360 days frozen storage, were minimal. Polyphenols content decreased during storage of strawberry pieces at -20 A degrees C for 360 days, while the thermal treatment applied after freezing storage did not induce any significant change.info:eu-repo/semantics/publishedVersio

Impact of storage on phytochemicals and milk proteins in peach yoghurt

Yoghurt supplemented with peach is a dairy product consumed around the world with a shelf-life of ca. 30 days. During this period protein–polyphenol complexes can be formed and have a detrimental effect on the in vivo solubility of both phenolic and proteins. Yoghurt enriched with peach preparate were produced and stored up to 28 days at 2 °C. Total antioxidant activity decreased 24%, total carotenoids increased 66%, while total phenolics remained unchanged during the yoghurt shelf-life. Carotenoids presented significant differences between peach enriched yoghurt and peach preparate stored under the same conditions. After 28 days the zeaxantin + lutein, β-cryptoxanthin and β-carotene increased 133, 122, and 84% respectively, for peach preparate, while in peach yoghurt they increased 68, 40, and 15%, indicating interactions of carotenoids with matrix components mainly proteins and fat present in yoghurt. Polyphenols presented higher stability when added to yoghurt with slight variations in their content of ca. 10% for (+)-catechin and 12% for p-coumaric acid, and no variations were recorded in neochlorogenic and chlorogenic acids and in rutin. The α-lactalbumin content decreased 22% after 24 h of peach addition while β-lactoglobulin content did not change. Peach polyphenols were very stable during yoghurt shelf-life while carotenoids were the compounds that presented higher interactions with the matrix.info:eu-repo/semantics/publishedVersio