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Understanding the links between genetic, epigenetic and non-genetic factors throughout the lifespan and across generations and their role in disease susceptibility and disease progression offer entirely new avenues and solutions to major problems in our society. To overcome the numerous challenges, we have come up with nine major conclusions to set the vision for future policies and research agendas at the European level. ispartof: BMC Genomics vol:15 issue:1 pages:487-487 ispartof: location:England status: published

Funder: Fondi di Ateneo per la Ricerca (FAR-UNICAM) 2014-2015, Funder: European Commission Marie Sklodowska-Curie Actions H2020 RISE Metable– 645693, We isolated a novel bacterial strain from a prokaryotic consortium associated to the psychrophilic marine ciliate Euplotes focardii, endemic of the Antarctic coastal seawater. The 16S rDNA sequencing and the phylogenetic analysis revealed the close evolutionary relationship to the Antarctic marine bacterium Marinomonas sp. BSw10506 and the sub antarctic Marinomonas polaris. We named this new strain Marinomonas sp. ef1. The optimal growth temperature in LB medium was 22 °C. Whole genome sequencing and analysis showed a reduced gene loss limited to regions encoding for transposases. Additionally, five genomic islands, e.g. DNA fragments that facilitate horizontal gene transfer phenomena, were identified. Two open reading frames predicted from the genomic islands coded for enzymes belonging to the Nitro-FMN-reductase superfamily. One of these, the putative NAD(P)H nitroreductase YfkO, has been reported to be involved in the bioreduction of silver (Ag) ions and the production of silver nanoparticles (AgNPs). After the Marinomonas sp. ef1 biomass incubation with 1 mM of AgNO3 at 22 °C, we obtained AgNPs within 24 h. The AgNPs were relatively small in size (50 nm) and had a strong antimicrobial activity against twelve common nosocomial pathogenic microorganisms including Staphylococcus aureus and two Candida strains. To our knowledge, this is the first report of AgNPs biosynthesis by a Marinomonas strain. This biosynthesis may play a dual role in detoxification from silver nitrate and protection from pathogens for the bacterium and potentially for the associated ciliate. Biosynthetic AgNPs also represent a promising alternative to conventional antibiotics against common pathogens.

The synthesis of silver nanoparticles (AgNPs) by microorganisms recently gained a greater interest due to its potential to produce them in various sizes and morphologies. In this study, for AgNP biosynthesis, we used a new Pseudomonas strain isolated from a consortium associated with the Antarctic marine ciliate Euplotes focardii. After incubation of Pseudomonas cultures with 1 mM of AgNO3 at 22 &deg, C, we obtained AgNPs within 24 h. Scanning electron (SEM) and transmission electron microscopy (TEM) revealed spherical polydispersed AgNPs in the size range of 20&ndash, 70 nm. The average size was approximately 50 nm. Energy dispersive X-ray spectroscopy (EDS) showed the presence of a high intensity absorption peak at 3 keV, a distinctive property of nanocrystalline silver products. Fourier transform infrared (FTIR) spectroscopy found the presence of a high amount of AgNP-stabilizing proteins and other secondary metabolites. X-ray diffraction (XRD) revealed a face-centred cubic (fcc) diffraction spectrum with a crystalline nature. A comparative study between the chemically synthesized and Pseudomonas AgNPs revealed a higher antibacterial activity of the latter against common nosocomial pathogen microorganisms, including Escherichia coli, Staphylococcus aureus and Candida albicans. This study reports an efficient, rapid synthesis of stable AgNPs by a new Pseudomonas strain with high antimicrobial activity.

Borage (Borago officinalis L.) is a wild vegetable appreciated as a folk medicine and for culinary preparations. The introduction of borage as a specialized cultivation would allow for the diversification of vegetable crops and would widen the offerings of raw and minimally processed leafy vegetables. Thus, the aim of the research was to evaluate the quality and shelf-life of fresh-cut borage stored at different temperatures. Borage plants were grown during the autumn&ndash, winter season and immediately minimally processed after harvest. Fresh-cut borage leaves packed in sealed bags were stored at 2 or 6 &deg, C for 21 d. Weight loss, total soluble solids (TSS), titratable acidity (TA), ascorbic acid, nitrates, leaf color characteristics and overall quality were determined through the storage period. Borage plants were deemed suitable for minimal processing. Storage temperature significantly influenced the rate of quality loss. Borage leaves had an initial nitrate content of 329.3 mg kg&minus, 1 FW that was not affected by temperature or storage. TSS and TA were higher in leaves stored at 6 &deg, C. TSS, TA and ascorbic acid content increased during storage. Minimally processed borage leaves stored at 2 &deg, C had lower weight loss and leaf color modifications during storage and a longer shelf life than those stored at 6 &deg, C, so were still marketable after 21 d of storage.

The irrigation of olive orchards is commonly applied to produce table olives with optimal size. No data have been published on the microbiological quality of drupes from irrigated olive groves during fermentation. The trials T100 and T50 (receiving a water amount equivalent to 100 % and 50 % of the required amount, respectively) and control T0 (rainfed trial) were monitored during two consecutive years. The results showed a significant increase of equatorial diameter and flesh:pit ratio of irrigated drupes. The decrease of pH and the numbers of lactic acid bacteria (LAB) registered for the irrigated trials during the fermentation were more consistent than those displayed by control T0. Lactobacillus pentosus, Lactobacillus plantarum, Lactobacillus coryniformis, and Pediococcus pentosaceus for LAB and Candida boidinii, Candida diddensiae, and Wickerhamomyces anomalus for yeasts were isolated at the highest concentrations. The global sensory acceptance was better for irrigated trials than control T0. The statistical multivariate analysis showed that the effect of irrigation was independent of the seasonal variability and it clearly distinguished the T100 and T50 trials from rainfed control. Irrigation improves significantly the quality of table olives. Interestingly, all explorative multivariate analyses showed low dissimilarity between irrigated trials; thus, the thesis T50 represents an effective approach to save water in olive orchards without compromising the quality of table olives.

The present work was carried out to retrieve the origin of lactic acid bacteria (LAB) in sourdough. To this purpose, wheat LAB were monitored from ear harvest until the first step of fermentation for sourdough development. The influence of the geographical area and variety on LAB species/strain composition was also determined. The ears of four Triticum durum varieties (Duilio, Iride, Saragolla and Simeto) were collected from several fields located within the Palermo province (Sicily, Italy) and microbiologically investigated. In order to trace the transfer of LAB during the consecutive steps of manipulation, ears were transformed aseptically and, after threshing, milling and fermentation, samples of kernels, semolinas and doughs, respectively, were analysed. LAB were not found to dominate the microbial communities of the raw materials. In general, kernels harboured lower levels of microorganisms than ears and ears than semolinas. Several samples showing no development of LAB colonies acidified the enrichment broth suggesting the presence of LAB below the detection limit. After fermentation, LAB loads increased consistently for all doughs, reaching levels of 7.0–7.5 Log CFU/g on M17. The values of pH (5.0) and TTA (5.6 mL NaOH/10 g of dough) indicated the occurrence of the acidification process for several doughs. LAB were phenotypically and genotypically differentiated by randomly amplified polymorphic DNA (RAPD)-PCR into eight groups including 51 strains belonging to the species Lactobacillus brevis, Lactobacillus coryniformis, Lactobacillus plantarum, Lactococcus lactis, Lactococcus garvieae, Enterococcus casseliflavus, Enterococcus faecium, Leuconostoc citreum, and Pediococcus pentosaceus. Lactobacilli constituted a minority the LAB community, while lactococci represented more than 50% of strains. Lower LAB complexity was found on kernels, while a richer biodiversity was observed in semolinas and fermented doughs. For broader microbiota characterisation in doughs before fermentation, the 16S rRNA gene fragment profiling was conducted on the unfermented doughs using MiSeq Illumina. LAB group was represented by Enterococcus, Lactococcus and members of Leuconostocaceae family whose relative abundances differed according to both geographical area and variety of wheat. The culture-independent approach confirmed that pediococci and lactobacilli constituted low abundance members of the semolina LAB microbiota and that although some strains may pass from wheat ear to fermented doughs, most are likely to come from other sources.

Thermal disinfestation treatments are relatively easy to apply, leave no chemical residues and may have some fungicidal activity. However, temperature and time combinations required to kill insect pests may meet or exceed those that reduce the viability of seeds, nutrients content, shelf life or technological characteristics. The aim of this study was to investigate the effect of thermal treatments (different temperature and time combinations) on physical and biological characteristics of bean, chickpea and lentil. Seed samples of common bean, chickpea and lentil were treated at low (12, 24 or 48 h at −18 °C) or high (30, 60 or 90 min at 60 °C) temperature. Seed germination, mean germination time, physical characteristics: solids loss, electrolytes leached and firmness after cooking, were determined. The use of thermal treatments for disinfesting seeds of bean, chickpea and lentil represent a physical technique of pest control that can be harmless for seeds destined for crop production (especially for organic farming) or to be stored in germplasm banks. Moreover, thermal treatments can be applied also to grain legumes used as food by humans, with no significant effect on lentils and with a reduction of cooking time for chickpeas. Beans should be treated only with cold treatments and for no more than 24 h.

A commercial cactus pear plantation in Sicily, Italy was manipulated to induce late cropping. The spring flush of flowers and cladodes were removed as was the second induced bloom of flowers and cladodes. The third induced bloom was harvested for a late out-of-season crop of cactus pear (Opuntia ficus-indica Mill.). The double removal induced a third flush of flowers and cladodes during late August with a fruit production that ripened the following winter (to March). The number of flowers per fertile cladode was halved after the double removal and the length of the fruit development period increased from 100-120 days to 160-190 days for the out-of-season crop. Polyethylene covering reduced sunlight but was essential for establishing optimal temperatures for cladode photosynthetic activity and fruit growth and ripening. Out-of-season fruits were regular in size and percent flesh with only a slight reduction in total soluble solid content.

The influence of flesh firmness on consumer acceptance and its relationship with total soluble solids (TSS), titratable acidity (TTA) and sensory analysis were studied for fruits of ‘September Sun’ and ‘Sweet September’ (low acid) peach (Prunus persica (L.) Batsch), and ‘Maria Dolce’ (low acid) and ‘Venus’ nectarine (Prunus persica (L.) Batsch, var. nucipersica) cultivars. Sensory descriptors, assessed by a short-trained panel, were firmness, sweetness, sourness, aroma, acceptability. Different stages of fruit firmness did not always result in significant differences of TSS, TTA and their ratio, but the panel was able to discriminate fruit ripening stages, in terms of fruit firmness, aroma and sweetness and to relate them to fruit acceptability. Acceptability of fruits with a 3.2 to 5.3 kg cm-2 firmness was similar, provided they had a high TSS, TSS/TTA and aroma. Values of flesh firmness higher than 5.5 kg cm-2 always resulted in unacceptable fruit quality. A threshold TSSC/TTA value cannot be used as a single marker for eating quality, since it may range among cultivars, while fruit aroma is the limiting factor for the consumers’ choice.

Oxidative stress is a particularly severe threat to Antarctic marine polar organisms because they are exposed to high dissolved oxygen and to intense UV radiation. This paper reports the features of three superoxide dismutases from the Antarctic psychrophilic ciliate Euplotes focardii that faces two environmental challenges, oxidative stress and low temperature. Two out of these are Cu,Zn superoxide dismutases (named Ef-SOD1a and Ef-SOD1b) and one belongs to the Mn-containing group (Ef-SOD2). Ef-SOD1s and Ef-SOD2 differ in their evolutionary history, expression and overall structural features. Ef-SOD1 genes are expressed at different levels, with Ef-SOD1b mRNA 20-fold higher at the ciliate optimal temperature of growth (4 °C). All Ef-SOD enzymes are active at 4 °C, consistent with the definition of cold-adapted enzymes. At the same time, they display temperatures of melting in the range 50–70 °C and retain residual activity after incubation at 65–75 °C. Supported by data of molecular dynamics simulation, we conclude that the E. focardii SODs combine cold activity, local molecular flexibility and thermo tolerance.