Metabolic Potential of Halophilic Filamentous Fungi—Current Perspective

Salty environments are widely known to be inhospitable to most microorganisms. For centuries salt has been used as a food preservative, while highly saline environments were considered uninhabited by organisms, and if habited, only by prokaryotic ones. Nowadays, we know that filamentous fungi are widespread in many saline habitats very often characterized also by other extremes, for example, very low or high temperature, lack of light, high pressure, or low water activity. However, fungi are still the least understood organisms among halophiles, even though they have been shown to counteract these unfavorable conditions by producing multiple secondary metabolites with interesting properties or unique biomolecules as one of their survival strategies. In this review, we focused on biomolecules obtained from halophilic filamentous fungi such as enzymes, pigments, biosurfactants, and osmoprotectants.     

Rapid detection of Salmonella in pet food: design and evaluation of integrated methods based on real-time PCR detection

Reducing the risk of Salmonella contamination in pet food is critical for both companion animals and humans, and its importance is reflected by the substantial increase in the demand for pathogen testing. Accurate and rapid detection of foodborne pathogens improves food safety, protects the public health, and benefits food producers by assuring product quality while facilitating product release in a timely manner. Traditional culture-based methods for Salmonella screening are laborious and can take 5 to 7 days to obtain definitive results. In this study, we developed two methods for the detection of low levels of Salmonella in pet food using real-time PCR: (i) detection of Salmonella in 25 g of dried pet food in less than 14 h with an automated magnetic bead-based nucleic acid extraction method and (ii) detection of Salmonella in 375 g of composite dry pet food matrix in less than 24 h with a manual centrifugation-based nucleic acid preparation method. Both methods included a preclarification step using a novel protocol that removes food matrix-associated debris and PCR inhibitors and improves the sensitivity of detection. Validation studies revealed no significant differences between the two real-time PCR methods and the standard U.S. Food and Drug Administration Bacteriological Analytical Manual (chapter 5) culture confirmation method.     

Inactivation of Oxidative Enzymes by High-Intensity Pulsed Electric Field for Retention of Color in Carrot Juice

The effects of high-intensity pulsed electric fields (HIPEF) on oxidative enzymes and color of fresh carrot juice were studied. A response surface methodology (RSM) was used to evaluate the effect of pulse polarity (mono or bipolar mode), pulse width (from 1 to 7 μs), and pulse frequency (from 50 to 250 Hz) on color and peroxidase (POD) inactivation of carrot juice treated by HIPEF. The total treatment time and the electric field strength were set at 1,000 μs and 35 kV/cm, respectively, at a temperature below 35°C. The physicochemical characteristics of carrot juice were measured. There was a linear relationship between electrical conductivity and temperature of the carrot juice. The results showed that HIPEF-treated carrot juice at 35 kV/cm for 1,000 μs applying 6 μs pulse width at 200 Hz in bipolar mode led to 73.0% inactivation of POD. The color coordinates did not change significantly. Therefore, HIPEF was effective in POD inactivation and carrot juice color preservation.     

Using polysaccharide-based edible coatings to maintain quality of fresh-cut Fuji apples

The effect of alginate and gellan-based edible coatings on the shelf-life of fresh-cut Fuji apples packed in trays with a plastic film of a known permeability to oxygen (110 cm³ O₂ m⁻² bar⁻¹ day⁻¹) was investigated by measuring changes in headspace atmosphere, color, firmness and microbial growth during 23 days of storage at 4 °C. Concentration of O₂ and CO₂ in the package was measured and no significant differences between coated and uncoated fresh-cut apples were observed. Ethylene concentration in coated apples seemed to be delayed since it remained below 50 μl l⁻¹ throughout the whole refrigerated storage period, while production of this gas was detected in uncoated apples from the very initial days of storage. Coated apple wedges exhibited ethanol and acetaldehyde formation from the second week of storage indicating fermentative metabolism. Polymers were crosslinked with a calcium chloride solution, to which the antibrowning agent N-acetylcysteine was added, being incorporated into the coatings formulation and helping to maintain firmness and color of apple wedges during the entire storage time. The application of the edible coatings also retarded the microbiological deterioration of fresh-cut apples. Alginate and gellan edible coatings effectively prolonged the shelf-life of Fuji apple wedges by 2 weeks of storage compared with the control apple slices which showed a considerable cut surface browning and tissue softening from the very early days of storage, limiting their shelf-life to less than 4 days.     

Robust far-field imaging by spatial coherence engineering

The degree of coherence (DOC) function that characterizes the second-order correlations at any two points in a light field is shown to provide a new degree of f...     

Validation of Tuba1a as Appropriate Internal Control for Normalization of Gene Expression Analysis during Mouse Lung Development

The expression ratio between the analysed gene and an internal control gene is the most widely used normalization method for quantitative RT-PCR (qRT-PCR) expression analysis. The ideal reference gene for a specific experiment is the one whose expression is not affected by the different experimental conditions tested. In this study, we validate the applicability of five commonly used reference genes during different stages of mouse lung development. The stability of expression of five different reference genes (Tuba1a, Actb Gapdh, Rn18S and Hist4h4) was calculated within five experimental groups using the statistical algorithm of geNorm software. Overall, Tuba1a showed the least variability in expression among the different stages of lung development, while Hist4h4 and Rn18S showed the maximum variability in their expression. Expression analysis of two lung specific markers, surfactant protein C (SftpC) and Clara cell-specific 10 kDA protein (Scgb1a1), normalized to each of the five reference genes tested here, confirmed our results and showed that incorrect reference gene choice can lead to artefacts. Moreover, a combination of two internal controls for normalization of expression analysis during lung development will increase the accuracy and reliability of results.     

Simulating Future Groundwater Recharge in Coastal and Inland Catchments

Groundwater is a primary source of drinking water in the Mediterranean, however, climate variability in conjunction with mismanagement renders it vulnerable to depletion. Spatiotemporal studies of groundwater recharge are the basis to develop strategies against this phenomenon. In this study, groundwater recharge was spatiotemporally quantified using the Soil and Water Assessment Tool (SWAT) in one coastal and one inland hydrological basin in Greece. A double calibration/validation (CV) procedure using streamflow data and MODIS ET was conducted for the inland basin of Mouriki, whereas only ET values were used in the coastal basin of Anthemountas. Calibration and simulation recharge were accurate in both sites according to statistical indicators and previous studies. In Mouriki basin, mean recharge and runoff were estimated as 16% and 9%, respectively. In Anthemountas basin recharge to the shallow aquifer and surface runoff were estimated as 12% and 16%, respectively. According to the predicted RCP 4.5 and 8.5 scenarios, significant variations in groundwater recharge are predicted in the coastal zone for the period 2020–2040 with average annual recharges decreasing by 30% (RCP 4.5) and 25% (RCP 8.5). Variations in groundwater recharge in the inland catchment of Mouriki were insignificant for the simulated period. Anthemountas basin was characterized by higher runoff rates. Groundwater management in coastal aquifers should include detailed monitoring of hydrological parameters, reinforced groundwater recharge during winter and reduced groundwater abstraction during summer depending on the spatiotemporal distribution of groundwater recharge.

     

The Role of Natural Polymorphic Variants of DNA Polymerase β in DNA Repair

DNA polymerase β (Polβ) is considered the main repair DNA polymerase involved in the base excision repair (BER) pathway, which plays an important part in the repair of damaged DNA bases usually resulting from alkylation or oxidation. In general, BER involves consecutive actions of DNA glycosylases, AP endonucleases, DNA polymerases, and DNA ligases. It is known that protein–protein interactions of Polβ with enzymes from the BER pathway increase the efficiency of damaged base repair in DNA. However natural single-nucleotide polymorphisms can lead to a substitution of functionally significant amino acid residues and therefore affect the catalytic activity of the enzyme and the accuracy of Polβ action. Up-to-date databases contain information about more than 8000 SNPs in the gene of Polβ. This review summarizes data on the in silico prediction of the effects of Polβ SNPs on DNA repair efficacy; available data on cancers associated with SNPs of Polβ; and experimentally tested variants of Polβ. Analysis of the literature indicates that amino acid substitutions could be important for the maintenance of the native structure of Polβ and contacts with DNA; others affect the catalytic activity of the enzyme or play a part in the precise and correct attachment of the required nucleotide triphosphate. Moreover, the amino acid substitutions in Polβ can disturb interactions with enzymes involved in BER, while the enzymatic activity of the polymorphic variant may not differ significantly from that of the wild-type enzyme. Therefore, investigation regarding the effect of Polβ natural variants occurring in the human population on enzymatic activity and protein–protein interactions is an urgent scientific task.