The impact of sustainable diets οn cognitive function in an ageing society: A mini-review.

The increasing number of older people raises important health concerns because, in part, of the associated cognitive and functional impairment. The United Nations is taking action with its Decade of Healthy Ageing (2021-2030) campaign, by promoting Sustainable Development Goals and shifting our focus towards more sustainable diets. In this mini-review, sustainable dietary patterns are evaluated, with a focus on healthy plant-based diets, the Mediterranean diet, the Dietary Approaches to Stop Hypertension (DASH) diet, and the Mediterranean-DASH Intervention for Neurodegenerative Delay diet. The review analyzes and describes whether older people's cognitive performance can benefit from the adoption of these sustainable diets. The results of primary studies indicate that the Mediterranean diet and healthy plant-based diets can prevent cognitive impairment by improving cognitive function, language and memory. Plant-based dietary patterns with incorporated Mediterranean foods (high consumption of fruit, vegetables, and fish) are associated with delayed cognitive ageing. Additionally, adherence to the Mediterranean-DASH Intervention for Neurodegenerative Delay diet is associated with improved cognitive resilience and lower risk of dementia after 16 years of follow-up. Although consumption of red meat and elevated body mass index are both associated with cognitive dysfunction, some studies have had contradictory findings. Concerns exist regarding the development of chronic diseases, cognitive and functional impairment, as well as disability as age advances. Thus, the policies of the United Nations should ensure healthy ageing for all older individuals. Nonetheless, more research is required to evaluate older people's willingness and readiness to adopt a more sustainable way of eating.

Novel Wild-Type Pediococcus and Lactiplantibacillus Strains as Probiotic Candidates to Manage Obesity-Associated Insulin Resistance.

As the food and pharmaceutical industry is continuously seeking new probiotic strains with unique health properties, the aim of the present study was to determine the impact of short-term dietary intervention with novel wild-type strains, isolated from various sources, on high-fat diet (HFD)-induced insulin resistance. Initially, the strains were evaluated in vitro for their ability to survive in simulated gastrointestinal (GI) conditions, for adhesion to Caco-2 cells, for bile salt hydrolase secretion, for cholesterol-lowering and cellular cholesterol-binding ability, and for growth inhibition of food-borne pathogens. In addition, safety criteria were assessed, including hemolytic activity and susceptibility to antibiotics. The in vivo test on insulin resistance showed that mice receiving the HFD supplemented with Pediococcus acidilactici SK (isolated from human feces) or P. acidilactici OLS3-1 strain (isolated from olive fruit) exhibited significantly improved insulin resistance compared to HFD-fed mice or to the normal diet (ND)-fed group.

Fish-Derived Protein Hydrolysates Increase Insulin Sensitivity and Alter Intestinal Microbiome in High-Fat-Induced Obese Mice.

Obesity and type 2 diabetes are characterized by low-grade systemic inflammation and glucose intolerance, which can be partially controlled with nutritional interventions. Protein-containing nutritional supplements possess health-promoting benefits. Herein, we examined the effect of dietary supplementation with protein hydrolysates derived from fish sidestreams on obesity and diabetes, utilizing a mouse model of High-Fat Diet-induced obesity and type 2 diabetes. We examined the effect of protein hydrolysates from salmon and mackerel backbone (HSB and HMB, respectively), salmon and mackerel heads (HSH and HMH, respectively), and fish collagen. The results showed that none of the dietary supplements affected weight gain, but HSH partially suppressed glucose intolerance, while HMB and HMH suppressed leptin increase in the adipose tissue. We further analyzed the gut microbiome, which contributes to the metabolic disease implicated in the development of type 2 diabetes, and found that supplementation with selected protein hydrolysates resulted in distinct changes in gut microbiome composition. The most prominent changes occurred when the diet was supplemented with fish collagen since it increased the abundance of beneficial bacteria and restricted the presence of harmful ones. Overall, the results suggest that protein hydrolysates derived from fish sidestreams can be utilized as dietary supplements with significant health benefits in the context of type 2 diabetes and diet-induced changes in the gut microbiome.

Genomic and 16S metabarcoding data of Holothuria tubulosa Gmelin, 1791.

Holothuria tubulosa Gmelin, 1791 is an edible sea cucumber species widespread in the Mediterranean Sea with ecological and increasing economic importance. Genome data of holothurian species is limited and the availability of genomic data resources is crucial in understanding their biology and adaptability mechanisms. This dataset presents the raw genome sequence data of H. tubulosa sequenced on an Illumina NextSeq 2000 platform. Genome size estimation was performed based on k-mer frequency approach. Additionally, the bacterial microbiome in the stomach and intestine of H. tubulosa collected from the Strymonian Gulf (North Aegean Sea, Greece) through 16S rRNA amplicon metabarcoding sequencing is reported. Sequencing was performed on an Illumina MiSeq platform. Analysis was conducted using the QIIME2 software package, the DADA2 algorithm and a trained classifier for taxonomy assignment. The datasets presented in this work serve as valuable resources for a comprehensive investigation of H. tubulosa at the genome level and for comparative genomics and echinoderms gut microbial studies.

Microbial and Biochemical Profile of Different Types of Greek Table Olives.

Analysis of table olives microbiome using next-generation sequencing has enriched the available information about the microbial community composition of this popular fermented food. In this study, 16S and 18S rRNA sequencing was performed on table olives of five Greek popular cultivars, Halkidikis, Thassou, Kalamon, Amfissis, and Konservolia, fermented either by Greek style (in brine or salt-drying) or by Spanish style, in order to evaluate their microbial communities. Moreover, analytical methods were used to evaluate their biochemical properties. The prevailing bacterial species of all olives belonged to Lactobacillaceae, Leuconostocaceae, and Erwiniaceae families, while the most abundant yeasts were of the Pichiaceae family. Principal coordinates analysis showed a clustering of samples cured by salt-drying and of samples stored in brine, regardless of their cultivar. The biochemical evaluation of total phenol content, antioxidant activity, hydroxytyrosol, oleuropein, oleocanthal, and oleacein showed that salt-dried olives had low amounts of hydroxytyrosol, while Spanish-style green olives had the highest amounts of oleocanthal. All the other values exhibited various patterns, implying that more than one factor affects the biochemical identity of the final product. The protocols applied in this study can provide useful insights for the final product, both for the producers and the consumers.

Effects of Dietary Supplementation of Spirulina platensis on the Immune System, Intestinal Bacterial Microbiome and Skin Traits of Mink.

The impact of dietary inclusion of Spirulina platensis on the immune system, intestinal microbiome and skin of mink was investigated. Forty-eight animals were equally separated into four groups. Groups B and D were control animals, while groups A and C had their feed supplemented daily with 100 mg/kg of body weight Spirulina. Mink in groups A and B were descended from dams supplemented with spirulina during their reproductive period, while those in groups C and D were descended from dams fed the control diets. Fur growth rate and quality were graded semi-quantitatively. Fecal microbiome analysis, skin thickness histomorphometry, immunohistochemical labeling and counts of immune cells in the colon, mesenteric lymph nodes and spleen and quantitative gene expression analysis of cytokines in the colon were performed. Skin thickness, fur growth rate and skin quality were similar among groups (p > 0.05). However, differences were observed among groups concerning the relative and differential abundance of bacterial species. Tgf-ß expression was lower in group A, whereas IL-ß1 was lower in group C compared to group B (p < 0.05). Group D had significantly lower numbers of inflammatory cells in the colon and mesenteric lymph nodes. The results revealed that Spirulina decreased indices of subclinical inflammation in mink gut, while differences in the bacterial communities among groups were observed.

PROTEIN AI Advisor: A Knowledge-Based Recommendation Framework Using Expert-Validated Meals for Healthy Diets.

AI-based software applications for personalized nutrition have recently gained increasing attention to help users follow a healthy lifestyle. In this paper, we present a knowledge-based recommendation framework that exploits an explicit dataset of expert-validated meals to offer highly accurate diet plans spanning across ten user groups of both healthy subjects and participants with health conditions. The proposed advisor is built on a novel architecture that includes (a) a qualitative layer for verifying ingredient appropriateness, and (b) a quantitative layer for synthesizing meal plans. The first layer is implemented as an expert system for fuzzy inference relying on an ontology of rules acquired by experts in Nutrition, while the second layer as an optimization method for generating daily meal plans based on target nutrient values and ranges. The system's effectiveness is evaluated through extensive experiments for establishing meal and meal plan appropriateness, meal variety, as well as system capacity for recommending meal plans. Evaluations involved synthetic data, including the generation of 3000 virtual user profiles and their weekly meal plans. Results reveal a high precision and recall for recommending appropriate ingredients in most user categories, while the meal plan generator achieved a total recommendation accuracy of 92% for all nutrient recommendations.

Tissue-specific transcriptional analysis outlines calcium-induced core metabolic changes in sweet cherry fruit.

The role of calcium in fruit ripening has been established, however knowledge regarding the molecular analysis at fruit tissue-level is still lacking. To address this, we examined the impact of foliar-applied calcium (0.5% CaCl2) in the ripening metabolism in skin and flesh tissues of the sweet cherry 'Tragana Edessis' fruit at the harvest stage. Exogenously applied calcium increased endogenous calcium level in flesh tissue and reduced fruit respiration rate and cracking traits. Fruit metabolomic along with transcriptomic analysis unraveled common and tissue-specific metabolic pathways associated with calcium feeding. Treatment with calcium diminished several alcohols (arabitol, sorbitol), sugars (fructose, maltose), acids (glyceric acid, threonic acid) and increased ribose and proline in both fruit tissues. Moreover, numerous primary metabolites, such as proline and galacturonic acid, were differentially accumulated in calcium-exposed tissues. Calcium-affected genes that involved in ubiquitin/ubl conjugation and cell wall biogenesis/degradation were differentially expressed between skin and flesh samples. Notably, skin and flesh tissues shared common calcium-responsive genes and exhibited substantial similarity in their expression patterns. In both tissues, calcium activated gene expression, most strongly those involved in plant-pathogen interaction, plant hormone signaling and MAPK signaling pathway, thus affecting related metabolic processes. By contrast, calcium depressed the expression of genes related to TCA cycle, oxidative phosphorylation, and starch/sucrose metabolism in both tissues. This work established both calcium-driven common and specialized metabolic suites in skin and flesh cherry tissues, demonstrating the utility of this approach to characterize fundamental aspects of calcium in fruit physiology.

Users' Perspective on the AI-Based Smartphone PROTEIN App for Personalized Nutrition and Healthy Living: A Modified Technology Acceptance Model (mTAM) Approach.

The ubiquitous nature of smartphone ownership, its broad application and usage, along with its interactive delivery of timely feedback are appealing for health-related behavior change interventions via mobile apps. However, users' perspectives about such apps are vital in better bridging the gap between their design intention and effective practical usage. In this vein, a modified technology acceptance model (mTAM) is proposed here, to explain the relationship between users' perspectives when using an AI-based smartphone app for personalized nutrition and healthy living, namely, PROTEIN, and the mTAM constructs toward behavior change in their nutrition and physical activity habits. In particular, online survey data from 85 users of the PROTEIN app within a period of 2 months were subjected to confirmatory factor analysis (CFA) and regression analysis (RA) to reveal the relationship of the mTAM constructs, i.e., perceived usefulness (PU), perceived ease of use (PEoU), perceived novelty (PN), perceived personalization (PP), usage attitude (UA), and usage intention (UI) with the users' behavior change (BC), as expressed via the acceptance/rejection of six related hypotheses (H1-H6), respectively. The resulted CFA-related parameters, i.e., factor loading (FL) with the related p-value, average variance extracted (AVE), and composite reliability (CR), along with the RA results, have shown that all hypotheses H1-H6 can be accepted (p < 0.001). In particular, it was found that, in all cases, FL > 0.5, CR > 0.7, AVE > 0.5, indicating that the items/constructs within the mTAM framework have good convergent validity. Moreover, the adjusted coefficient of determination (R 2) was found within the range of 0.224-0.732, justifying the positive effect of PU, PEoU, PN, and PP on the UA, that in turn positively affects the UI, leading to the BC. Additionally, using a hierarchical RA, a significant change in the prediction of BC from UA when the UI is used as a mediating variable was identified. The explored mTAM framework provides the means for explaining the role of each construct in the functionality of the PROTEIN app as a supportive tool for the users to improve their healthy living by adopting behavior change in their dietary and physical activity habits. The findings herein offer insights and references for formulating new strategies and policies to improve the collaboration among app designers, developers, behavior scientists, nutritionists, physical activity/exercise physiology experts, and marketing experts for app design/development toward behavior change.

Genomic data of two Greek Vitis varieties.

The genetic material of Vitis varieties is crucial for the wine sector. In addition, genomic technologies applied in vitis germplasm characterization are important for the conservation of indigenous genetic reservoirs. Until recently the most common method to genetically identify vitis varieties was the use of Simple Sequence Repeats (SSR) along with SNP chips. Yet, with the progress in Next Generation Sequencing (NGS) technologies and the reduced sequencing cost per base, a twist in plant species genetic identification methods has occurred. Among them, the low coverage Whole-Genome Sequencing (lcWGS) method with downstream bioinformatic analysis for variant discovery and phylogenetic characterization is gaining scientific attention. In this dataset, shotgun sequencing data of two different Greek Vitis varieties, 'Razaki' and 'Vlachiko' are presented. Vitis cultivars were collected from the Aristotle University of Thessaloniki's (AUTH) ampelographic collection and have been previously phenotypically and genetically characterized. WGS libraries were sequenced on an IlluminaⓇ NovaSeq 6000 platform with the IlluminaⓇ NovaSeq 6000 S2 Reagent Kit (300 cycles). Raw sequence data used for analysis are available in NCBI under the Sequence Read Archive (SRA), with BioProject ID PRJNA805368. Reads were aligned to the reference genome of Vitis vinifera available from the EnsemblPlants database and formal analysis was conducted with the Genome Analysis Toolkit 4 (GATK4) pipeline. Data can be used to enrich our knowledge related to the genetic background of vitis cultivars and can also serve as a threshold in the scientific community towards the construction of a genomic database of vitis cultivars.

Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece.

The COVID-19 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot, for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). Our proposed method was tested and evaluated using NGS data produced by the sequencing of 14 wastewater samples from the municipality of Thessaloniki, Greece, covering a 6-month period. The results showed the presence of SARS-CoV-2 variants in wastewater data. lineagespot was able to record the evolution and rapid domination of the Alpha variant (B.1.1.7) in the community, and allowed the correlation between the mutations evident through our approach and the mutations observed in patients from the same area and time periods. lineagespot is an open-source tool, implemented in R, and is freely available on GitHub and registered on bio.tools.

Comparative Transcriptome Analysis in Homo- and Hetero-Grafted Cucurbit Seedlings.

Watermelon (Citrullus lanatus) is a valuable horticultural crop with nutritional benefits grown worldwide. It is almost exclusively cultivated as grafted scions onto interspecific squash rootstock (Cucurbita maxima × Cucurbita moschata) to improve the growth and yield and to address the problems of soilborne diseases and abiotic stress factors. This study aimed to examine the effect of grafting (homo- and hetero-grafting) on the transcriptome level of the seedlings. Therefore, we compared homo-grafted watermelon (WW) with non-grafted watermelon control (W), homo-grafted squash (SS) with non-grafted squash control (S), hetero-grafted watermelon onto squash (WS) with SS, and WS with WW. Different numbers of differentially expressed genes (DEGs) were identified in each comparison. In total, 318 significant DEGs were detected between the transcriptomes of hetero-grafts and homo-grafts at 16 h after grafting. Overall, a significantly higher number of downregulated transcripts was detected among the DEGs. Only one gene showing increased expression related to the cytokinin synthesis was common in three out of four comparisons involving WS, SS, and S. The highest number of differentially expressed (DE) transcripts (433) was detected in the comparison between SS and S, followed by the 127 transcripts between WW and W. The study provides a description of the transcriptomic nature of homo- and hetero-grafted early responses, while the results provide a start point for the elucidation of the molecular mechanisms and candidate genes for the functional analyses of hetero-graft and homo-graft systems in Cucurbitaceae and generally in the plants.

A Novel Real-Time RT-PCR-Based Methodology for the Preliminary Typing of SARS-CoV-2 Variants, Employing Non-Extendable LNA Oligonucleotides and Three Signature Mutations at the Spike Protein Receptor-Binding Domain.

Mutations resulting in amino-acid substitutions of the SARS-CoV-2 spike protein receptor-binding domain (RBD) have been associated with enhanced transmissibility and immune escape of the respective variants, namely Alpha, Beta, Gamma or Delta. Rapid identification of the aforementioned variants of concern and their discrimination of other variants is thus of importance for public health interventions. For this reason, a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed, to target signature mutations associated with amino-acid substitutions at positions 478, 484 and 501 present in the receptor-binding motif (RBM) of the spike protein RBD. This region contains most contacting residues of SARS-CoV-2 that bind to ACE2. A novel strategy employing the use of non-extendable LNA oligonucleotide blockers that can reduce non-specific hybridization of probes increased the number of different mutated sites examined in a multiplex PCR. The combinatory analysis of the different fluorescence signals obtained enabled the preliminary differentiation of SARS-CoV-2 variants of concern. The assay is sensitive with a LOD of 263 copies/reaction for the Delta variant, 170 copies/reaction for the Beta variant, amplification efficiencies > 91% and a linear range of >5 log10 copies/reaction against all targets. Validation of the assay using known SARS-CoV-2-positive and negative samples from humans and animals revealed its ability to correctly identify the targeted mutations and preliminary characterize the SARS-CoV-2 variants. The novel approach for mutation typing using LNA oligonucleotide blockers can be modified to target signature mutations at four different sites in the RBM and further expand the range of variants detected.

Investigating Transcriptomic Induction of Resistance and/or Virulence in Listeria monocytogenes Cells Surviving Sublethal Antimicrobial Exposure.

The potential transcriptomic induction of resistance and/or virulence in two L. monocytogenes strains belonging to the most frequent listeriosis-associated serovars (i.e., 1/2a and 4b), following their sublethal antimicrobial exposure, was studied through qPCR determination of the relative expression of 10 selected related genes (i.e., groEL, hly, iap, inlA, inlB, lisK, mdrD, mdrL, prfA, and sigB). To induce sublethal stress, three common antimicrobials (i.e., benzalkonium chloride, thymol, and ampicillin) were individually applied for 2 h at 37 °C against stationary phase cells of each strain, each at a sublethal concentration. In general, the expression of most of the studied genes remained either stable or was significantly downregulated following the antimicrobial exposure, with some strain-specific differences to be yet recorded. Thymol provoked downregulation of most of the studied genes, significantly limiting the expression of 6/10 and 4/10 genes in the strains of ser. 1/2a and ser. 4b, respectively, including those coding for the master regulators of stress response and virulence (SigB and PrfA, respectively), in both strains. At the same time, the two genes coding for the invasion internalin proteins (InlA and InlB), with crucial role in the onset of L. monocytogenes pathogenesis, were both importantly upregulated in ser. 4b strain. The results obtained increase our knowledge of the stress physiology of L. monocytogenes under certain sublethal antimicrobial conditions that could be encountered within the food chain and in clinical settings, and may assist in better and more effective mitigation strategies.

Amplicon metabarcoding data of prokaryotes and eukaryotes present in 'Kalamata' table olives packaged under modified atmosphere.

Evaluation of food microbiome is of major importance since it accounts for the product's organoleptic characteristics and their nutritional value. In this dataset, microbes present in olive samples ('Kalamata' variety) stored under modified atmosphere and throughout different time-points of the shelf life of the product are presented, originated after 16S and 18S rRNA sequencing. The different time-points analyzed were: T0 (immediately after packaging), T6 (six months of storage), T12 (12 months of storage) and T18 (six months after the end of shelf life). Sequencing was performed on a MiSeq platform with the MiSeq Reagent Kit v3 (600 cycles). The raw sequence data used for analysis are available in NCBI under the Sequence Read Archive (SRA), with BioProject ID PRJNA688686. Raw reads were analyzed using the QIIME2 pipeline, clustered into Operational Taxonomic Units (OTU) and aligned against SILVA 132 reference database. OTUs are presented in different taxonomic levels for each time-point. These data present valuable information on the microbial communities of table olives, a dynamic niche that affect the final product quality. The data presented are related to the research article "Insights into the evolution of Greek style table olives microbiome stored under modified atmosphere: biochemical implications on the product quality" [1].

Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination.

SARS-CoV-2 infection outbreaks in minks have serious implications associated with animal health and welfare, and public health. In two naturally infected mink farms (A and B) located in Greece, we investigated the outbreaks and assessed parameters associated with virus transmission, immunity, pathology, and environmental contamination. Symptoms ranged from anorexia and mild depression to respiratory signs of varying intensity. Although the farms were at different breeding stages, mortality was similarly high (8.4% and 10.0%). The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. Lung histopathology identified necrosis of smooth muscle and connective tissue elements of vascular walls, and vasculitis as the main early key events of the acute SARS-CoV-2-induced broncho-interstitial pneumonia. Molecular investigation in two dead minks indicated a consistently higher (0.3-1.3 log10 RNA copies/g) viral load in organs of the male mink compared to the female. In farm A, the infected farmers were responsible for the significant initial infection of 229 out of 1,000 handled minks, suggesting a very efficient human-to-mink transmission. Subsequent infections across the sheds wherein animals were being housed occurred due to airborne transmission. Based on a R0 of 2.90 and a growth rate equal to 0.293, the generation time was estimated to be 3.6 days, indicative of the massive SARS-CoV-2 dispersal among minks. After the end of the outbreaks, a similar percentage of animals were immune in the two farms (93.0% and 93.3%), preventing further virus transmission whereas, viral RNA was detected in samples collected from shed surfaces and air. Consequently, strict biosecurity is imperative during the occurrence of clinical signs. Environmental viral load monitoring, in conjunction with NGS should be adopted in mink farm surveillance. The minimum proportion of minks that need to be immunized to avoid outbreaks in farms was calculated at 65.5%, which is important for future vaccination campaigns.

Drought induces variation in the DNA methylation status of the barley HvDME promoter.

Cytosine methylation is an epigenetic modification with essential roles in diverse plant biological processes including vegetative and reproductive development and responsiveness to environmental stimuli. A dynamic process involving DNA methyltransferases and DNA demethylases establishes cytosine DNA methylation levels and distribution along the genome. A DNA demethylase gene from barley (Hordeum vulgare), DEMETER (HvDME), the homologue of the Arabidopsis thaliana DME (AtDME), has been characterized previously and found to respond to drought conditions. Here, the promoter of the HvDME gene was analysed further by in silico and DNA methylation analysis. The effect of drought conditions on the DNA methylation status of HvDME was investigated at single-cytosine resolution using bisulfite sequencing. It was demonstrated that the HvDME promoter can be divided into two discrete regions, in terms of DNA methylation level and density; a relatively unmethylated region proximal to the translational start site that is depleted of non-CG (CHG, CHH) methylation and another distal region, approximately 1500 bp upstream of the translational start site, enriched in CG, as well as non-CG methylation. Drought stress provoked alterations in the methylation status of the HvDME promoter distal region, whereas the DNA methylation of the proximal region remained unaffected. Computational analysis of the HvDME promoter revealed the presence of several putative regulatory elements related to drought responsiveness, as well as transposable elements (TEs) that may affect DNA methylation. Overall, our results expand our investigations of the epigenetic regulation of the HvDME gene in response to drought stress in barley and may contribute to further understanding of the epigenetic mechanisms underlying abiotic stress responses in barley and other cereals.

Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds.

In dairy sheep industry, milk production dictates the value of a ewe. Milk production is directly related to the morphology and physiology of the mammary gland; both being designated targets of breeding strategies. Although within a flock breeding parameters are mutual, large differences in milk production among individual ewes are usually observed. In this work, we tested two of the most productive dairy sheep breeds reared intensively in Greece, one local the Chios breed and one foreign the Lacaune breed. We used transcriptome sequencing to reveal molecular mechanisms that render the mammary gland highly productive or not. While highly expressed genes (caseins and major whey protein genes) were common among breeds, differences were observed in differentially expressed genes. ENSOARG00000008077, as a member of ribosomal protein 14 family, together with LPCAT2, CCR3, GPSM2, ZNF131, and ASIP were among the genes significantly differentiating mammary gland's productivity in high yielding ewes. Gene ontology terms were mainly linked to the inherent transcriptional activity of the mammary gland (GO:0005524, GO:0030552, GO:0016740, GO:0004842), lipid transfer activity (GO:0005319) and innate immunity (GO:0002376, GO:0075528, GO:0002520). In addition, clusters of genes affecting zinc and iron trafficking into mitochondria were highlighted for high yielding ewes (GO:0071294, GO:0010043). Our analyses provide insights into the molecular pathways involved in lactation between ewes of different performances. Results revealed management issues that should be addressed by breeders in order to move toward increased milk yields through selection of the desired phenotypes. Our results will also contribute toward the selection of the most resilient and productive ewes, thus, will strengthen the existing breeding systems against a spectrum of environmental threats.

A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions.

The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94 % and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.

Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding.

Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.