Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources

Animal by-product meals from the rendering industry could provide a sustainable and commercially viable alternative to fishmeal (FM) in aquaculture, as they are rich in most essential amino acids and contain important amounts of water-soluble proteins that improve feed digestibility and palatability. Among them, poultry by-product meal (PBM) have given encouraging results in rainbow trout (Oncorhynchus mykiss). However, the introduction of new ingredients in the diet needs to be carefully evaluated since diet is one of the main factors affecting the gut microbiota, which is a complex community that contributes to host metabolism, nutrition, growth, and disease resistance. Accordingly, we investigated the effects of partial replacement of dietary FM with a mix of animal by-product meals and plant proteins on intestinal microbiota composition of rainbow trout in relation to growth and feeding efficiency parameters. We used 1540 trout with an initial mean body weight of 94.6 +/- 14.2 g. Fish were fed for 12 weeks with 7 different feed formulations. The growth data showed that trout fed on diets rich in animal by-product meals grew as well as fish fed on control diet, which was rich in FM (37.3%) and PBM-free. High-throughput 16S rRNA gene amplicon sequencing (MiSeq platform, Illumina) was utilised to study the gut microbial community profile. After discarding Cyanobacteria (class Chloroplast) and mitochondria reads a total of 2,701,274 of reads taxonomically classified, corresponding to a mean of 96,474 +/- 68,056 reads per sample, were obtained. Five thousand three hundred ninety-nine operational taxonomic units (OTUs) were identified, which predominantly mapped to the phyla of Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. The ratio between vegetable and animal proteins proved to play a central role in determining microbiome profiles and Firmicutes and Proteobacteria phyla were particularly discriminatory for diet type in trout. Plant ingredients favoured a higher Firmicutes: Proteobacteria ratio than animal proteins. Acceptable abundance of Firmicutes was guaranteed by including at least 25% of vegetable proteins in the diet regardless of animal protein source and percentage. In summary animal by-product meals, as replacements to FM, gave good results in terms of growth performances and did not induce significant changes in gut microbial richness, thus proving to be a suitable protein source for use in rainbow trout aqua feed

The wildland-urban interface map of Italy: A nationwide dataset for wildfire risk management

A wildland-urban interface (WUI) raster map was created for the Italian peninsula with a resolution of 30 m per pixel. The map creation process consisted of three fundamental steps: (1) selection of buildings within the wildland-urban interface areas and subsequent classification of these into isolated, scattered, and clustered buildings; (2) creation of the tree canopy cover layer; (3) generation of WUI map by the intersection of two previous products. According to the WUI map, more than half of the total area of Italy is occupied by interface areas. Areas with buildings classified as clustered (24.61%) and scattered (19.15%) predominate on the territory compared to isolated buildings (14.93%). Most of the buildings are located in areas with a tree cover canopy between up to 64%. This map is functional to the implementation of forest fire prevention plans and to the identification of buildings that are close to fire risk areas such as forests, grasslands, and pastures

The genomic organisation of the tra/trd locus validates the peculiar characteristics of dromedary δ-chain expression

The role of γδ T cells in vertebrate immunity is still an unsolved puzzle. Species such as humans and mice display a low percentage of these T lymphocytes (i.e., “γδ low species”) with a restricted diversity of γδ T cell receptors (TR). Conversely, artiodactyl species (i.e., “γδ high species”) account for a high proportion of γδ T cells with large γ and δ chain repertoires. The genomic organisation of the TR γ (TRG) and δ (TRD) loci has been determined in sheep and cattle, noting that a wide number of germline genes that encode for γ and δ chains characterise their genomes. Taking advantage of the current improved version of the genome assembly, we have investigated the genomic structure and gene content of the dromedary TRD locus, which, as in the other mammalian species, is nested within the TR α (TRA) genes. The most remarkable finding was the identification of a very limited number of variable germline genes (TRDV) compared to sheep and cattle, which supports our previous expression analyses for which the somatic hypermutation mechanism is able to enlarge and diversify the primary repertoire of dromedary δ chains. Furthermore, the comparison between genomic and expressed sequences reveals that D genes, up to four incorporated in a transcript, greatly contribute to the increased diversity of the dromedary δ chain antigen binding-site

Machine learning techniques for fine dead fuel load estimation using multi‐source remote sensing data

Fine dead fuel load is one of the most significant components of wildfires without which ignition would fail. Several studies have previously investigated 1‐h fuel load using standard fuel parameters or site‐specific fuel parameters estimated ad hoc for the landscape. On the one hand, these methods have a large margin of error, while on the other their production times and costs are high. In response to this gap, a set of models was developed combining multi‐source remote sensing data, field data and machine learning techniques to quantitatively estimate fine dead fuel load and understand its determining factors. Therefore, the objectives of the study were to: (1) estimate 1‐h fuel loads using remote sensing predictors and machine learning techniques; (2) evaluate the performance of each machine learning technique compared to traditional linear regression models; (3) assess the importance of each remote sensing predictor; and (4) map the 1‐h fuel load in a pilot area of the Apulia region (southern Italy). In pursuit of the above, fine dead fuel load estimation was performed by the integration of field inventory data (251 plots), Synthetic Aperture Radar (SAR, Sentinel‐1), optical (Sentinel‐2), and Light Detection and Ranging (LIDAR) data applying three different algorithms: Multiple Linear regression (MLR), Random Forest (RF), and Support Vector Machine (SVM). Model performances were evaluated using Root Mean Squared Error (RMSE), Mean Squared Error (MSE), the coefficient of determination (R2) and Pearson’s correlation coefficient (r). The results showed that RF (RMSE: 0.09; MSE: 0.01; r: 0.71; R2: 0.50) had more predictive power compared to the other models, while SVM (RMSE: 0.10; MSE: 0.01; r: 0.63; R2: 0.39) and MLR (RMSE: 0.11; MSE: 0.01; r: 0.63; R2: 0.40) showed similar performances. LIDAR variables (Canopy Height Model and Canopy cover) were more important in fuel estimation than optical and radar variables. In fact, the results highlighted a positive relationship between 1‐h fuel load and the presence of the tree component. Conversely, the geomorphological variables appeared to have lower predictive power. Overall, the 1‐h fuel load map developed by the RF model can be a valuable tool to support decision making and can be used in regional wildfire risk management

Modeling fire ignition probability and frequency using Hurdle models: a cross-regional study in Southern Europe

Background: Wildfires play a key role in shaping Mediterranean landscapes and ecosystems and in impacting species dynamics. Numerous studies have investigated the wildfire occurrences and the influence of their drivers in many countries of the Mediterranean Basin. However, in this regard, no studies have attempted to compare different Mediterranean regions, which may appear similar under many aspects. In response to this gap, climatic, topographic, anthropic, and landscape drivers were analyzed and compared to assess the patterns of fire ignition points in terms of fire occurrence and frequency in Catalonia (Spain), Sardinia, and Apulia (Italy). Therefore, the objectives of the study were to (1) assess fire ignition occurrence in terms of probability and frequency, (2) compare the main drivers affecting fire occurrence, and (3) produce fire probability and frequency maps for each region. Results: In pursuit of the above, the probability of fire ignition occurrence and frequency was mapped using Negative Binomial Hurdle models, while the models’ performances were evaluated using several metrics (AUC, prediction accuracy, RMSE, and the Pearson correlation coefficient). The results showed an inverse correlation between distance from infrastructures (i.e., urban roads and areas) and the occurrence of fires in all three study regions. This relationship became more significant when the frequency of fire ignition points was assessed. Moreover, a positive correlation was found between fire occurrence and landscape drivers according to region. The land cover classes more significantly affected were forest, agriculture, and grassland for Catalonia, Sardinia, and Apulia, respectively. Conclusions: Compared to the climatic, topographic, and landscape drivers, anthropic activity significantly influences fire ignition and frequency in all three regions. When the distance from urban roads and areas decreases, the probability of fire ignition occurrence and frequency increases. Consequently, it is essential to implement long- to medium-term intervention plans to reduce the proximity between potential ignition points and fuels. In this perspective, the present study provides an applicable decision-making tool to improve wildfire prevention strategies at the European level in an area like the Mediterranean Basin where a profuse number of wildfires take place

Is experience the best teacher? Knowledge, perceptions, and awareness of wildfire risk

Wildfires represent a natural phenomenon with detrimental effects on natural resources and human health. A better knowledge, perception, and awareness of wildfire risk may help communities at risk of exposure to prevent future events and safeguard their own lives. The aim of this study is to explore differences between individuals with and without previous wildfire experience, in terms of (1) subjective and advanced wildfire knowledge, (2) self-reported perceptions, (3) level of information, (4) self-protection measures, and (5) importance of community involvement. As a second step, we investigated differences in the same variables, focusing more deeply on a group of individuals with previous wildfire experience, classifying them according to fire-related employment (fire-related workers vs. non-workers) and wildland–urban interface (WUI) proximity (WUI residents vs. non-WUI residents). The Kruskal–Wallis test was applied to establish differences between the pairs of subsamples. Our results partially confirmed our hypothesis, that direct experience leads individuals to have a greater preparedness on the topic of wildfires. Perception of knowledge is reflected only at a shallow level of expertise, and, therefore, no relevant within-group differences related to fire-related employment or to WUI proximity were detected. Moreover, available information was perceived to be insufficient, thus we report a strong need for developing effective communication to high-risk groups, such as homeowners and fire-related workers

Evolution of the T-cell receptor (TR) Loci in the adaptive immune response: The tale of the TRG locus in mammals

T lymphocytes are the principal actors of vertebrates’ cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response

Dietary supplementation of garlic and rosemary: effects on colour stability and lipid oxidation in lamb meat

The colour of fresh meat is an important criterion consumers take into consideration when purchasing meat. Meat colour depends on the occurrence of chemical and microbial deterioration processes. The role of vitamin E and other antioxidants on ruminant meat colour stability and prevention of lipid oxidation has been widely investigated (Macit et al., 2003; Realini et al., 2004). Many natural herbs and plant extracts exert antioxidant effects such as garlic (Yin and Cheng, 2003) and rosemary (Sánchez-Escalante et al., 2001). Their use as additives for animal feeding may be a valid alternative to synthetic antioxidants since they show beneficial effects also on animal welfare and other physiological functions (Tedesco, 2001). The aim of this study was to evaluate whether garlic and rosemary dietary supplementation as compared with vitamin E affects lamb meat colour and lipid stability during storage

Are community gardening and horticultural interventions beneficial for psychosocial well-being? A meta-analysis

Recent literature has revealed the positive effect of gardening on human health; however, empirical evidence on the effects of gardening-based programs on psychosocial well-being is scant. This meta-analysis aims to examine the scientific literature on the effect of community gardening or horticultural interventions on a variety of outcomes related to psychosocial well-being, such as social cohesion, networking, social support, and trust. From 383 bibliographic records retrieved (from 1975 to 2019), seven studies with a total of 22 effect sizes were selected on the basis of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Meta-analytic findings on 11 comparisons indicate a positive and moderate effect of horticultural or gardening interventions on psychosocial well-being. Moderation analysis shows a greater effect size in individualistic than collectivistic cultures. A greater effect size was also observed in studies involving community gardening compared to horticultural intervention. Nevertheless, an effect of publication bias and study heterogeneity has been detected. Despite the presence of a large number of qualitative studies on the effect of horticulture/gardening on psychosocial well-being, quantitative studies are lacking. There is a strong need to advance into further high-quality studies on this research topic given that gardening has promising applied implications for human health, the community, and sustainable city management

The Organization of the Pig T-Cell Receptor γ (TRG) Locus Provides Insights into the Evolutionary Patterns of the TRG Genes across Cetartiodactyla

The domestic pig (Sus scrofa) is a species representative of the Suina, one of the four suborders within Cetartiodactyla. In this paper, we reported our analysis of the pig TRG locus in comparison with the loci of species representative of the Ruminantia, Tylopoda, and Cetacea suborders. The pig TRG genomic structure reiterates the peculiarity of the organization of Cetartiodactyla loci in TRGC "cassettes", each containing the basic V-J-J-C unit. Eighteen genes arranged in four TRGC cassettes, form the pig TRG locus. All the functional TRG genes were expressed, and the TRGV genes preferentially rearrange with the TRGJ genes within their own cassette, which correlates the diversity of the γ-chain repertoire with the number of cassettes. Among them, the TRGC5, located at the 5' end of the locus, is the only cassette that retains a marked homology with the corresponding TRGC cassettes of all the analyzed species. The preservation of the TRGC5 cassette for such a long evolutionary time presumes a highly specialized function of its genes, which could be essential for the survival of species. Therefore, the maintenance of this cassette in pigs confirms that it is the most evolutionarily ancient within Cetartiodactyla, and it has undergone a process of duplication to give rise to the other TRGC cassettes in the different artiodactyl species in a lineage-specific manner