Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds.

Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina's Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright's fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.

Bacterial communities and potential spoilage markers of whole blue crab (Callinectes sapidus) stored under commercial simulated conditions.

Bacterial communities composition using 16S Next Generation Sequencing (NGS) and Volatile Organic Compounds (VOCs) profile of whole blue crabs (Callinectes sapidus) stored at 4 and 10 °C (proper and abuse temperature) simulating real storage conditions were performed. Conventional microbiological and chemical analyses (Total Volatile Base-Nitrogen/TVB-N and Trimethylamine-Nitrogen/TMA-N) were also carried out. The rejection time point was 10 and 6 days for the whole crabs stored at 4 and 10 °C, respectively, as determined by development of unpleasant odors, which coincided with crabs death. Initially, the Aerobic Plate Count (APC) was 4.87 log cfu/g and increased by 3 logs at the rejection time. The 16S NGS analysis of DNA extracted directly from the crab tissue (culture-independent method), showed that the initial microbiota of the blue crab mainly consisted of Candidatus Bacilloplasma, while potential pathogens e.g. Listeria monocytogenes, Pseudomonas aeruginosa and Acinetobacter baumannii, were also found. At the rejection point, bacteria of Rhodobacteraceae family (52%) and Vibrio spp. (40.2%) dominated at 4 and 10 °C, respectively. TVB-N and TMA-N also increased, reaching higher values at higher storage temperature. The relative concentrations of some VOCs such as 1-octen-3-ol, trans-2-octenal, trans,trans-2,4-heptadienal, 2-butanone, 3-butanone, 2-heptanone, ethyl isobutyrate, ethyl acetate, ethyl-2-methylbutyrate, ethyl isovalerate, hexanoic acid ethyl ester and indole, exhibited an increasing trend during crab storage, making them promising spoilage markers. The composition of microbial communities at different storage temperatures was examined by 16S amplicon meta-barcoding analysis. This kind of analysis in conjugation with the volatile profile can be used to explore the microbiological quality and further assist towards the application of the appropriate strategies to extend crab shelf-life and protect consumer's health.

Study on dietary constituents, hs-CRP serum levels and investigation of correlation between them in excess weight adolescents.

BACKGROUND:  The prevalence of childhood obesity has increased in Greece as well as worldwide. Mediterranean diet is considered the world's most popular healthy eating pattern. C-reactive protein (CRP) has been shown to play an important pathophysiological role between inflammation and cardiovascular diseases and has been linked to obesity. Our study aimed to investigate the adolescents' diet, their high-sensitivity CRP (hs-CRP) serum levels, and whether low-grade inflammation, present in obesity, is related to adolescents' diet. METHODS: The sample of the study consisted of 142 adolescents age- and gender- matched 13.4 ± 1.46 years, divided into two groups: the study group and the controls. The study group of 71 excess body weight adolescents was further divided into two subgroups of 28 overweight and 43 obese respectively; 71 normal weight age- and gender-matched served as controls. Dietary constituents (food weight, energy intake, protein, carbohydrate and fat consumption, fiber, and sugars) were analyzed. Adherence to the Mediterranean diet was investigated, and hs-CRP serum levels were determined. The findings were compared between/among groups. Furthermore, the correlation of hs-CRP serum levels and food constituents between/among groups was investigated. RESULTS:  We documented differences in several parameters among the groups: waist to hip ratio (p =0.001), food weight (p =0.040), energy intake (p =0.024), protein intake (p =0.001), total fibre (p =0.017), sugars (p =0.001), and the Mediterranean Diet Quality Index for children and adolescents (KIDMED; p =0.008). No statistically significant difference was found for hs-CRP serum levels among the three groups. No correlation was found between hs-CRP serum levels and any of the dietary constituents. CONCLUSIONS:   Comparing the three groups (obese, overweight, and controls), we found statistically significant differences for food constituents but not for hs-CRP serum levels. In our study, inflammation was not found to be correlated with any of the dietary constituents. Further studies in a larger sample are required to consolidate these findings. HIPPOKRATIA 2019, 23(1): 3-8.

Microbial spoilage investigation of thawed common cuttlefish (Sepia officinalis) stored at 2 °C using next generation sequencing and volatilome analysis.

Cephalopods are highly appreciated with increasing demand seafood, but are also very perishable and deteriorate fast mainly due to microbiological spoilage. For this reason exploration of bacterial communities through 16S Next Generation Sequencing (NGS) and Volatile Organic Compounds (VOCs) analysis was performed. Furthermore, sensory evaluation, classical microbiological analysis, Total Volatile Base-Nitrogen/TVB-N and Trimethylamine-Nitrogen/TMA-N determination were also carried out. Shelf-life of thawed cuttlefish (Sepia officinalis) stored at 2°C determined by sensory evaluation was 4 days. Aerobic Plate Counts (APC) reached the levels of 6.6 log cfu/g. The initial and final population of all spoilage microorganisms enumerated with selective media was under detectable levels with the exception of Pseudomonas. Based on 16S NGS analysis, Psychrobacter were the dominants among others, e.g. Pseudomonas, Shewanella, Comamonas, Carnobacterium, Vagococcus, of the initial microbiota. Psychrobacter was also the dominant microorganisms of the spoiled cuttlefish. TVB-N and TMA-N increased considerably only at the late stages of storage. A plethora of VOCs were produced and some exhibited an increasing profile throughout storage, making them promising molecules as freshness indicators in contrast to TVB-N and TMA-N. The application of next generation sequencing revealed the microbiota that escapes the classic microbiological methodologies, showing that other microorganisms different from those determined on selective culture media might be the main cause of microbiological spoilage.

Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays.

In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (FGRM) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.

Isotopic modeling of the sub-cloud evaporation effect in precipitation.

In dry and warm environments sub-cloud evaporation influences the falling raindrops modifying their final stable isotopic content. During their descent from the cloud base towards the ground surface, through the unsaturated atmosphere, hydrometeors are subjected to evaporation whereas the kinetic fractionation results to less depleted or enriched isotopic signatures compared to the initial isotopic composition of the raindrops at cloud base. Nowadays the development of Generalized Climate Models (GCMs) that include isotopic content calculation modules are of great interest for the isotopic tracing of the global hydrological cycle. Therefore the accurate description of the underlying processes affecting stable isotopic content can improve the performance of iso-GCMs. The aim of this study is to model the sub-cloud evaporation effect using a) mixing and b) numerical isotope evaporation models. The isotope-mixing evaporation model simulates the isotopic enrichment (difference between the ground and the cloud base isotopic composition of raindrops) in terms of raindrop size, ambient temperature and relative humidity (RH) at ground level. The isotopic enrichment (Δδ) varies linearly with the evaporated raindrops mass fraction of the raindrop resulting to higher values at drier atmospheres and for smaller raindrops. The relationship between Δδ and RH is described by a 'heat capacity' model providing high correlation coefficients for both isotopes (R(2)>80%) indicating that RH is an ideal indicator of the sub-cloud evaporation effect. Vertical distribution of stable isotopes in falling raindrops is also investigated using a numerical isotope-evaporation model. Temperature and humidity dependence of the vertical isotopic variation is clearly described by the numerical isotopic model showing an increase in the isotopic values with increasing temperature and decreasing RH. At an almost saturated atmosphere (RH=95%) sub-cloud evaporation is negligible and the isotopic composition hardly changes even at high temperatures while at drier and warm conditions the enrichment of (18)Ο reaches up to 20‰, depending on the raindrop size and the initial meteorological conditions.

A multi-farm assessment of Greek black pig genetic diversity using microsatellite molecular markers.

Local breeds are important for the maintenance of genetic diversity and future food security. Nowadays, the worldwide distribution of pigs is dominated by a few breeds, tending towards a severe loss of pig biodiversity. Thus, it is critical to maintain distinct populations of pig breeds. The Greek black pig, a breed raised locally and known for the high quality of its meat for cured products, is the only traditional indigenous pig breed reared in Greece. We investigated the genetic diversity, based on microsatellite analysis, of the Greek black pig and evaluated its genetic uniqueness. One hundred and three pigs from 12 Greek farms were analyzed using 11 microsatellites. The total number of alleles amounted to 135, with a mean number of alleles per locus of 12.27, ranging between 10 and 16 alleles. The observed heterozygosity ranged from 0.363 to 0.825 per locus. The expected heterozygosity ranged from 0.471 to 0.707. The inbreeding coefficient ranged from -0.329 to 0.229. We conclude that the Greek black pig, despite its low population size, has a high degree of genetic variability, which will be useful for breeding programs aimed at maintaining long-term survival of this ancient breed.

Transcriptional profiling of antimicrobial peptides avian ß-defensins in the chicken ovary during sexual maturation and in response to Salmonella enteritidis infection.

Avian ß-defensins (AvßDs) are antimicrobial peptides that play significant roles in the innate immune system in chickens. The aim of this study was to identify the types of AvßDs expressed in the chicken ovary, to investigate the effects of sexual maturation in the ovarian mRNA abundance and to determine the changes in their expression levels as a result to Salmonella enteritidis (SE) infection. RNA was extracted from the ovary of healthy prepubertal, sexually mature and aged birds, as well as from sexually mature and aged SE infected birds. Real-time PCR analysis revealed that 11 AvßDs genes were expressed in the chicken ovary. A significant up regulation of AvßD1, 3, 4, 5, 7 and 11 was observed in the ovary of sexually mature and aged birds. Furthermore, a significant up-regulation of AvßD4, 5, 7, 11 and 12 was observed in the ovary of SE infected sexually mature birds. These results suggest that the mRNA expression of at least six AvßDs increase with age in the ovary of laying hens, and that at least five AvßDs show an induction in their expression in response to SE infection, indicating an AvßD-mediated immune response mechanism in the chicken ovary.

LDL receptor cDNA sequence analysis in familial hypercholesterolemia patients: 5 novel mutations with high prevalence in families originating from southern Italy.

We screened a group of patients from southern Italy with clinically diagnosed familial hypercholesterolemia (FH) for mutations of the LDL receptor (LDLR) gene. RNA from each proband was analysed by RT-PCR followed by complete cDNA sequencing. Among 51 unrelated FH families we detected 17 mutations affecting the coding region of the LDLR gene. Five of these mutations, designated R395P, L783fsinsG, IVS15-3C>A, IVS3+5G>A, and 1698-1704delCACCCTAinsGCCCAAT (ITL545MPN), have not yet been reported in the literature. Interestingly, the novel IVS15-3C>A splicing mutation was detected in 20% of our unrelated FH families, suggesting an unusually high prevalence in our local population. Hum Mutat 17:433, 2001.

Development of a neural network heating controller for solar buildings.

Artificial neural networks (ANN's) are more and more widely used in energy management processes. ANN's can be very useful in optimizing the energy demand of buildings, especially of those of high thermal inertia. These include the so-called solar buildings. For those buildings, a controller able to forecast not only the energy demand but also the weather conditions can lead to energy savings while maintaining thermal comfort. In this paper, such an ANN controller is proposed. It consists of a meteorological module, forecasting the ambient temperature and solar irradiance, the heating energy switch predictor module and the indoor temperature-defining module. The performance of the controller has been tested both experimentally and in a building thermal simulation environment. The results showed that the use of the proposed controller can lead to 7.5% annual energy savings in the case of a highly insulated passive solar test cell.