Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces.

The minimum information about a biofilm experiment (MIABiE) initiative has arisen from the need to find an adequate and scientifically sound way to control the quality of the documentation accompanying the public deposition of biofilm-related data, particularly those obtained using high-throughput devices and techniques. Thereby, the MIABiE consortium has initiated the identification and organization of a set of modules containing the minimum information that needs to be reported to guarantee the interpretability and independent verification of experimental results and their integration with knowledge coming from other fields. MIABiE does not intend to propose specific standards on how biofilms experiments should be performed, because it is acknowledged that specific research questions require specific conditions which may deviate from any standardization.

Burkholderia dolosa phenotypic variation during the decline in lung function of a cystic fibrosis patient during 5.5 years of chronic colonization.

Although rarely isolated from cystic fibrosis (CF) patients, Burkholderia dolosa is associated with accelerated lung function decline. During 18 years of epidemiological surveillance in the major Portuguese CF centre in Lisbon, only one patient was infected with B. dolosa.

Modeling the partitioning of amino acids in aqueous two phase systems.

A new model to obtain fast prediction of partition coefficients in polymer/polymer aqueous two phase systems (ATPSs) is presented, using amino acids as test systems. In particular, the partitioning behavior of eleven amino acids (glycine, alanine, leucine, phenylalanine, lysine, arginine, histidine, aspartic acid, glutamic acid, glutamine and serine) has been studied in 6 polymer/polymer ATPSs, formed by different pairs of nonionic polymers, including polyethylene glycol (PEG), Dextran, Ucon and Ficoll at 0.15M NaCl in 0.

The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant.

In this work, it is described the sequencing and annotation of the genome of the yeast strain ISA1307, isolated from a sparkling wine continuous production plant. This strain, formerly considered of the Zygosaccharomyces bailii species, has been used to study Z. bailii physiology, in particular, its extreme tolerance to acetic acid stress at low pH.

Molecular and functional characterization of an invertase secreted by Ashbya gossypii.

The repertoire of hydrolytic enzymes natively secreted by the filamentous fungus Ashbya (Eremothecium) gossypii has been poorly explored. Here, an invertase secreted by this flavinogenic fungus was for the first time molecularly and functionally characterized. Invertase activity was detected in A.

Sulfate reduction at low pH to remediate acid mine drainage.

Industrial activities and the natural oxidation of metallic sulfide-ores produce sulfate-rich waters with low pH and high heavy metals content, generally termed acid mine drainage (AMD). This is of great environmental concern as some heavy metals are highly toxic. Within a number of possibilities, biological treatment applying sulfate-reducing bacteria (SRB) is an attractive option to treat AMD and to recover metals.

A xenogeneic-free bioreactor system for the clinical-scale expansion of human mesenchymal stem/stromal cells.

The large cell doses (>1 × 10(6)  cells/kg) used in clinical trials with mesenchymal stem/stromal cells (MSC) will require an efficient production process. Moreover, monitoring and control of MSC ex-vivo expansion is critical to provide a safe and reliable cell product. Bioprocess engineering approaches, such as bioreactor technology, offer the adequate tools to develop and optimize a cost-effective culture system for the rapid expansion of human MSC for cellular therapy.

Anaerobic granular sludge as a biocatalyst for 1,3-propanediol production from glycerol in continuous bioreactors.

1,3-Propanediol (1,3-PDO) was produced from glycerol in three parallel Expanded Granular Sludge Blanket (EGSB) reactors inoculated with granular sludge (control reactor-R1), heat-treated granular sludge (R2) and disrupted granular sludge (R3) at hydraulic retention times (HRT) between 3 and 24h. Maximum 1,3-PDO yield (0.52molmol(-1)) and productivity (57gL(-1)d(-1)) were achieved in R1 at HRTs of 12 and 3h, respectively.

Yeast: the soul of beer's aroma--a review of flavour-active esters and higher alcohols produced by the brewing yeast.

Among the most important factors influencing beer quality is the presence of well-adjusted amounts of higher alcohols and esters. Thus, a heavy body of literature focuses on these substances and on the parameters influencing their production by the brewing yeast. Additionally, the complex metabolic pathways involved in their synthesis require special attention.

Sequence determinants for DNA packaging specificity in the S. aureus pathogenicity island SaPI1.

The SaPIs and their relatives are a family of genomic islands that exploit helper phages for high frequency horizontal transfer. One of the mechanisms used by SaPIs to accomplish this molecular piracy is the redirection of the helper phage DNA packaging machinery. SaPIs encode a small terminase subunit that can be substituted for that of the phage.

Conformational and mechanical changes of DNA upon transcription factor binding detected by a QCM and transmission line model.

A novel quartz crystal microbalance (QCM) analytical method is developed based on the transmission line model (TLM) algorithm to analyze the binding of transcription factors (TFs) to immobilized DNA oligoduplexes. The method is used to characterize the mechanical properties of biological films through the estimation of the film dynamic shear moduli, G and G, and the film thickness. Using the Saccharomyces cerevisiae transcription factor Haa1 (Haa1DBD) as a biological model two sensors were prepared by immobilizing DNA oligoduplexes, one containing the Haa1 recognition element (HRE(wt)) and another with a random sequence (HRE(neg)) used as a negative control.

A flat microbial fuel cell for decentralized wastewater valorization: process performance and optimization potential.

A very compact flat microbial fuel cell (MFC), with 64 cm2 each for the anode surface and the cathode surface and 1 cm3 each for the anode and cathode chambers, was tested for wastewater treatment with simultaneous electricity production with the ultimate goal of implementing an autonomous service in decentralized wastewater treatment systems. The MFC was operated with municipal wastewater in sequencing batch reactor mode with re-circulation. Current densities up to 407 W/m3 and a carbon removal of 83% were obtained.

The drug:H⁺ antiporters of family 2 (DHA2), siderophore transporters (ARN) and glutathione:H⁺ antiporters (GEX) have a common evolutionary origin in hemiascomycete yeasts.

Background: The Saccharomyces cerevisiae 14-spanner Drug:H+ Antiporter family 2 (DHA2) are transporters of the Major Facilitator Superfamily (MFS) involved in multidrug resistance (MDR). Although poorly characterized, DHA2 family members were found to participate in the export of structurally and functionally unrelated compounds or in the uptake of amino acids into the vacuole or the cell. In S.

Modification of cell volume and proliferative capacity of Pseudokirchneriella subcapitata cells exposed to metal stress.

The impact of metals (Cd, Cr, Cu and Zn) on growth, cell volume and cell division of the freshwater alga Pseudokirchneriella subcapitata exposed over a period of 72 h was investigated. The algal cells were exposed to three nominal concentrations of each metal: low (closed to 72 h-EC10 values), intermediate (closed to 72 h-EC50 values) and high (upper than 72 h-EC90 values). The exposure to low metal concentrations resulted in a decrease of cell volume.

Limb patterning: from signaling gradients to molecular oscillations.

The developing forelimb is patterned along the proximal-distal and anterior-posterior axes by opposing gradients of retinoic acid and fibroblast growth factors and by graded sonic hedgehog signaling, respectively. However, how coordinated patterning along both axes is accomplished with temporal precision remains unknown. The limb molecular oscillator hairy2 was recently shown to be a direct readout of the combined signaling activities of retinoic acid, fibroblast growth factor and sonic hedgehog in the limb mesenchyme.

Bacterial diversity assessed by cultivation-based techniques shows predominance of Staphylococccus species on coins collected in Lisbon and Casablanca.

Money is usually considered a source of infections, yet survival of bacteria on dry metal surfaces is limited. The aim of this work was to assess the bacterial numbers and diversity on coins collected in Casablanca and Lisbon as these two cities, on different continents and only 585 km apart, have diverse cultural habitats, but have similar climate. A cultivation-based characterisation of the bacterial community showed that a relatively low number of cells per area of coin were found on both Moroccan Dirhams and Euros (0.

Mini-review: Staphylococcus epidermidis as the most frequent cause of nosocomial infections: old and new fighting strategies.

Staphylococcus epidermidis is nowadays regarded as the most frequent cause of nosocomial infections and indwelling medical device-associated infections. One of the features that contributes to the success of this microorganism and which is elemental to the onset of pathogenesis is its ability to form biofilms. Cells in this mode of growth are inherently more resistant to antimicrobials.

Integrated use of residues from olive mill and winery for lipase production by solid state fermentation with Aspergillus sp.

Two-phase olive mill waste (TPOMW) is presently the major waste produced by the olive mill industry. This waste has potential to be used as substrate for solid state fermentation (SSF) despite of its high concentration of phenolic compounds and low nitrogen content. In this work, it is demonstrated that mixtures of TPOMW with winery wastes support the production of lipase by Aspergillus spp.

Candida glabrata: a review of its features and resistance.

Candida species belong to the normal microbiota of the oral cavity and gastrointestinal and vaginal tracts, and are responsible for several clinical manifestations, from mucocutaneous overgrowth to bloodstream infections. Once believed to be non-pathogenic, Candida glabrata was rapidly blamable for many human diseases. Year after year, these pathological circumstances are more recurrent and problematic to treat, especially when patients reveal any level of immunosuppression.

Re-annotation of the genome sequence of Helicobacter pylori 26695.

Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated.

New dextrin nanomagnetogels as contrast agents for magnetic resonance imaging.

This study aims at the production and characterization of a "nanomagnetogel" consisting of superparamagnetic iron oxide nanoparticles (γ-FeO) stabilized within a hydrophobized-dextrin nanogel. The nanomagnetogel obtained was extensively characterized with respect to physico-chemical (transmission electron microscopy, cryo-scanning electron microscopy, dynamic light scattering, small angle X-ray scattering), magnetic (relaxometry, MIAplex) and biocompatibility (interaction with cells) properties. The obtained nanomagnetogel formulation, with about 4 mM of iron and a diameter of 100 nm, presents relevant features as a promising magnetic resonance imaging (MRI) contrast agent, noteworthy superparamagnetic behavior, high stability, narrow size distribution and potential for magnetic guidance to target areas by means of an external magnetic field.

Integrated platform for production and purification of human pluripotent stem cell-derived neural precursors.

Human pluripotent stem cells (hPSCs) are a promising source of cells for clinical applications, such as transplantation of clinically engineered tissues and organs, and drug discovery programs due to their ability to self-renew and to be differentiated into cells from the three embryonic germ layers. In this study, the differentiation of two hPSC-lines into neural precursors (NPs) was accomplished with more than 80% efficiency, by means of the dual-SMAD inhibition protocol, based on the use of two small molecules (SB431542 and LDN193189) to generate Pax6 and Nestin-positive neural entities. One of the major hurdles related to the in vitro generation of PSC-derived populations is the tumorigenic potential of cells that remain undifferentiated.

Potential therapeutic applications of biosurfactants.

Biosurfactants have recently emerged as promising molecules for their structural novelty, versatility, and diverse properties that are potentially useful for many therapeutic applications. Mainly due to their surface activity, these molecules interact with cell membranes of several organisms and/or with the surrounding environments, and thus can be viewed as potential cancer therapeutics or as constituents of drug delivery systems. Some types of microbial surfactants, such as lipopeptides and glycolipids, have been shown to selectively inhibit the proliferation of cancer cells and to disrupt cell membranes causing their lysis through apoptosis pathways.

Activated sludge characterization through microscopy: a review on quantitative image analysis and chemometric techniques.

In wastewater treatment processes, and particularly in activated sludge systems, efficiency is quite dependent on the operating conditions, and a number of problems may arise due to sludge structure and proliferation of specific microorganisms. In fact, bacterial communities and protozoa identification by microscopy inspection is already routinely employed in a considerable number of cases. Furthermore, quantitative image analysis techniques have been increasingly used throughout the years for the assessment of aggregates and filamentous bacteria properties.

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.

The YEASTRACT (http://www.yeastract.com) information system is a tool for the analysis and prediction of transcription regulatory associations in Saccharomyces cerevisiae.