The expansion of the TRB and TRG genes in domestic goats (Capra hircus) is characteristic of the ruminant species.

BACKGROUND: Goats (Capra hircus), one of the first domesticated species, are economically important for milk and meat production, and their broad geographical distribution reflects their successful adaptation to diverse environmental conditions. Despite the relevance of this species, the genetic research on the goat traits is limited compared to other domestic species. Thanks to the latest goat reference genomic sequence (ARS1), which is considered to be one of the most continuous assemblies in livestock, we deduced the genomic structure of the T cell receptor beta (TRB) and gamma (TRG) loci in this ruminant species. RESULTS: Our analyses revealed that although the organization of the goat TRB locus is broadly similar to that of the other artiodactyl species, with three in-tandem D-J-C clusters located at the 3' end, a complex and extensive series of duplications have occurred in the V genes at the 5' end, leading to a marked expansion in the number of the TRBV genes. This phenomenon appears to be a feature of the ruminant lineage since similar gene expansions have also occurred in sheep and cattle. Likewise, the general organization of the goat TRG genes is typical of ruminant species studied so far, with two paralogous TRG loci, TRG1 and TRG2, located in two distinct and distant positions on the same chromosome as result of a split in the ancestral locus. Each TRG locus consists of reiterated V-J-J-C cassettes, with the goat TRG2 containing an additional cassette relative to the corresponding sheep and cattle loci. CONCLUSIONS: Taken together, these findings demonstrate that strong evolutionary pressures in the ruminant lineage have selected for the development of enlarged sets of TRB and TRG genes that contribute to a diverse T cell receptor repertoire. However, differences observed among the goat, sheep and cattle TRB and TRG genes indicate that distinct evolutionary histories, with independent expansions and/or contractions, have also affected each ruminant species.

Meat quality and lipid fatty acid profile from wild thrush (Turdus philomelos), woodcock (Scolopax rusticola) and starling (Sturnus vulgaris): a preliminary comparative study.

BACKGROUND: The present study aimed to evaluate the nutritional proximate composition, some qualitative traits and fatty acid profile of meat from wild thrush, woodcock and starling hunted in Southern Italy in 2017 and 2018. METHODS: Nutritive composition and physical traits of meat and lipid fatty acid profile were evaluated in breast muscle (Pectoralis major) of gamebirds. RESULTS: From findings, the meat pH was significantly (P < 0.001) higher in starling when compared to the other two species. Thrush meat was significantly (P = 0.002) darker and had higher redness (P < 0.001) and yellowness (P = 0.004) in comparison to starling and woodcock. Thrush breast muscle showed the highest (P < 0.001) level of lipids and lowest (P < 0.001) protein content. Meat from thrush showed the best lipid fatty acid profile based on the higher (P < 0.001) monounsaturated fatty acids (MUFA) and lower (P < 0.001) saturated fatty acids (SFA) concentrations. Starling breast muscle reported the highest (P = 0.002) polyunsaturated fatty acids (PUFA) level compared to both thrush and woodcock, whereas no differences were detected on total n-3. The ratio n-6/n-3 was higher (P = 0.001) in starling muscle. Thrush breast muscle had the lowest (P < 0.001) atherogenic and thrombogenic indices compared to the other gamebirds. CONCLUSIONS: The findings indicated that meat from the three investigated gamebirds species may represent a healthily lipid food source for human consumption in relation to the prevention of cardiovascular diseases.

Effect of dietary nitrogen level and source on mRNA expression of urea transporters in the rumen epithelium of fattening bulls.

This paper aims to study the effect of the dietary treatments on mRNA expression of urea transporter B (UT-B) and some aquaporins (AQP) in rumen epithelium of Italian Simmental young bulls. Eighty animals allocated to 16 pens were fed from about 500 to 650 kg body weight with four experimental diets, which resulted from the combination of two crude protein levels (125 and 110 g/kg dry matter, diets M and L, respectively) and two nitrogen sources (soybean meal (SBM) or SBM partly replaced by an isonitrogenous mixture of corn and urea; diets -U and +U, respectively). At slaughtering samples of blood and rumen epithelium were collected from six bulls for each diet. Blood samples were analysed for haematological parameters and quantitative PCR was carried out on the mRNA extracted from the rumen epithelium samples. The bulls fed diets M had lower plasma concentrations of aspartate aminotransferase than those receiving diets L (78.9 vs. 88.3 U/l, p = 0.04). Plasma urea was higher (p = 0.03) for diets M and lower for diets +U (2.0 vs. 2.5 and 1.73 vs. 2.00 mmol/l, respectively, in M and L diets, p = 0.04). The effect of dietary treatments on rumen UT expression were limited to AQP3, which was down regulated (p = 0.01) in diets +U. Finally, a high positive correlation (R2 = 0.871) between the expressions of AQP7 and AQP10 was found. In conclusion, the AQP3 appears very responsive to dietary treatments and therefore it is a candidate to be further studied in rumen metabolism experiments. The close relationship between mRNA expression of AQP7 and AQP10 indicates a similar function of these two proteins.

Sheep (Ovis aries) T cell receptor alpha (TRA) and delta (TRD) genes and genomic organization of the TRA/TRD locus.

BACKGROUND: In mammals, T cells develop along two discrete pathways characterized by expression of either the αß or the γδ T cell receptors. Human and mouse display a low peripheral blood γδ T cell percentage ("γδ low species") while sheep, bovine and pig accounts for a high proportion of γδ T lymphocytes ("γδ high species"). While the T cell receptor alpha (TRA) and delta (TRD) genes and the genomic organization of the TRA/TRD locus has been determined in human and mouse, this information is still poorly known in artiodactyl species, such as sheep. RESULTS: The analysis of the current Ovis aries whole genome assembly, Oar_v3.1, revealed that, as in the other mammalian species, the sheep TRD locus is nested within the TRA locus. In the most 5' part the TRA/TRD locus contains TRAV genes which are intermingled with TRDV genes, then TRD genes which include seven TRDD, four TRDJ genes, one TRDC and a single TRDV gene with an inverted transcriptional orientation, and finally in the most 3' part, the TRA locus is completed by 61 TRAJ genes and one TRAC gene. Comparative sequence and analysis and annotation led to the identification of 66 TRAV genes assigned to 34 TRAV subgroups and 25 TRDV genes belonging to the TRDV1 subgroup, while one gene was found for each TRDV2, TRDV3 and TRDV4 subgroups. Multiple duplication events within several TRAV subgroups have generated the sheep TRAV germline repertoire, which is substantially larger than the human one. A significant proportion of these TRAV gene duplications seems to have occurred simultaneously with the amplification of the TRDV1 subgroup genes. This dynamic of expansion has also generated novel multigene subgroups, which are species-specific. Ovis aries TRA and TRD genes identified in this study were assigned IMGT definitive or temporary names and were approved by the IMGT/WHO-IUIS nomenclature committee. The completeness of the genome assembly in the 3' part of the locus has allowed us to interpret rearranged CDR3 of cDNA from both TRA and TRD chain repertoires. The involvement of one up to four TRDD genes into a single transcript makes the potential sheep TRD chain much larger than any known TR chain repertoire. CONCLUSIONS: The sheep genome, as the bovine genome, contains a large and diverse repertoire of TRA and TRD genes when compared to the "γδ T cell low" species genomes. The composition and length of the rearranged CDR3 in TRD V-delta domains influence the three-dimensional configuration of the antigen-combining site thus suggesting that in ruminants, γδ T cells play a more important and specific role in immune recognition.

Genomic characteristics of the T cell receptor (TRB) locus in the rabbit (Oryctolagus cuniculus) revealed by comparative and phylogenetic analyses.

The present study identifies the genomic structure and the gene content of the T cell receptor beta (TRB) locus in the Oryctolagus cuniculus whole genome assembly. The rabbit locus spans less than 600 Kb and the general genomic organization is highly conserved with respect to other mammalian species. A pool of 74 TRB variable (TRBV) genes distributed in 24 subgroups are located upstream of two in tandem-aligned D-J-C gene clusters, each composed of one TRBD, six TRBJ genes, and one TRBC gene, followed by a single TRBV gene with an inverted transcriptional orientation. All TRB genes (functional, ORF, pseudogenes) of this paper have been approved by the IMGT/WHO-IUIS nomenclature committee. Additionally, five potentially functional protease serine (PRSS) trypsinogen or trypsinogen-like genes were identified: two in tandem PRSS-like genes, followed by two PRSS genes with unique traits, lie downstream of the TRBV1 gene and one PRSS gene is located about 400 Kb away downstream of the TRBV genes. Comparative and phylogenetic analyses revealed that multiple duplication events within a few subgroups have generated the germline repertoire of the rabbit TRBV genes, which is substantially larger than those described in humans, mice, and dogs, suggesting that a strong evolutionary pressure has selected the development of a species-specific TRBV repertoire. Hence, the genomic organization of the TRB locus in the genomes appears to be the result of a balance between the maintenance of a core-number of genes essential for the immunological performances and the requirement of newly arisen genes.

Genomic and comparative analysis of the T cell receptor gamma locus in two Equus species.

The genus Equus is the only extant genus of the Equidae family, which belongs to Perissodactyla, an order of mammals characterized by an odd number of toes (odd-toes ungulates). Taking advantage of the latest release of the genome assembly, we studied, for the first time in two organisms belonging to the Equus genus, the horse (Equus caballus) and the donkey (Equus asinus), the T cell receptor gamma (TRG) locus encoding the gamma chain of the γδ T cell receptor. Forty-five Variable (TRGV) genes belonging to the seven IMGT-NC validated mammalian TRGV subgroups, 25 Joining (TRGJ) and 17 Constant (TRGC) genes organized in 17 V-J-(J)-C cassettes, in tandem on about 1100 Kb, characterize the horse TRG locus, making the horse TRG locus the one with the greatest extension and with a significantly higher number of genes than the orthologous loci of the other mammalian species. A clonotype analysis of an RNA-seq transcriptomic dataset derived from spleen of an adult healthy horse, using the complete set of the horse TRGJ germline gene sequences as a probe, revealed that, in addition to the most prominent V-J rearrangements within each cassette, there is a relevant proportion of trans-cassette V-J recombination, whereby the same TRGV genes can recombine with different TRGJ genes spliced to the corresponding TRGC genes. This recombinant event strongly contributes to the diversity of the γ chain repertoire. In the donkey TRG locus, 34 TRGV, 21 TRGJ and 14 TRGC genes distributed in 14 V-J-(J)-C cassettes were found in a region of approximately 860 kb. Although the donkey's TRG is smaller than that of the horse, in Equus genus, this is still the second largest locus so far found in any mammalian species. Finally, the comparative analysis highlighted differences in size and gene content between the horse and donkey TRG loci, despite belonging to the same genus, indicating a good level of diversification within Equus. These data is in agreement with the evolutionary idea of the existence of a Equus recent common ancestor in rapid evolution, for which a mutation rate between horses and donkeys is more comparable to that between species belonging to different genera rather than to species of the same genus.

Effects of Dietary Red Grape Extract on the Quality Traits in Juvenile European Sea Bass (Dicentrarchus labrax L.).

Intensive fish farming is responsible for the occurrence of various stressors that negatively affect the health of cultured animals. Polyphenols are plant-derived compounds with biological activities and positive influences on the performances and immunity of fish. The aim of the present study was to evaluate the effects of dietary inclusion of a polyphenol extract obtained from Nero di Troia red grape on the quality of farmed sea bass (Dicentrarchus labrax) fillets. Three diets were tested: control (n = 90) received a conventional feed, whereas the two experimental groups (n = 90 each) received the control feed supplemented with the red grape polyphenol extract (GPE) at the concentration of 100 (GPE 100) or 200 mg/kg (GPE 200). The two GPE diets lowered (p < 0.05) the red (a *) and yellow (b *) indexes, fillet hardness, and total lipid content. Chewiness, concentration of saturated fatty acids, and the Atherogenic Index were higher (p < 0.05) in the control group; GPE diets increased (p < 0.05) the polyunsaturated fatty acids content. Furthermore, the concentration of malondialdehyde was lower (p < 0.05) in fillets of the GPE groups, thus confirming the antioxidant effect of the red grape extract and its effectiveness in preventing lipid oxidation.

Dietary Supplementation with Oregano and Linseed in Autochthonous "Facciuta Lucana" Goats: Effects on Meat Quality Traits in Suckling Kids.

Extruded linseed (Linum usitatissimum) in ruminant diets has been investigated as a strategy to improve the nutritional value and healthiness of meat fat; however, increased polyunsaturated fatty acids may limit the shelf-life of meat. Oregano (Origanum vulgare) has a documented antioxidant activity. The aim of the study was to investigate the effects of dietary supplementation with extruded linseed and oregano on goat milk quality and whether the characteristics of goat milk affect the physical and chemical features, fatty acid profile, meat lipid oxidation, and sensory properties of meat from suckling kids. Thirty-six male kids were weaned and divided into three homogeneous groups (n = 12); each group was either fed a control diet (C), or a diet containing 3% extruded linseed with or without the addition of 0.6% oregano ("L + O" and "L", respectively). The diets containing linseed lowered (p < 0.05) the saturated fatty acid content in meat, and increased (p < 0.05) monounsaturated and polyunsaturated fatty acids and conjugated linoleic acid. Oregano addition to the linseed diet proved to be effective in preserving meat shelf-life, as shown by a significant (p < 0.01) reduction in the malondialdehyde concentration after 10 days of storage, and improved meat succulence, tenderness, juiciness, and overall acceptance.

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.

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.

Dietary Effects of Extra Virgin Olive Oil Extracted by Ultrasound Technology or Refined Olive Oil on the Quality Traits of Pork and "Capocollo di Martina Franca" Dry-Cured Meat.

The "Capocollo di Martina Franca" is a traditional dry-cured pig meat product made in Apulia. The dietary fat source is able to influence the lipid profile of muscle and subcutaneous fat in pork, thus affecting its nutritional and sensorial quality as well as its suitability for technological processing. The aim of the study was to evaluate the effect of a diet containing extra virgin olive oil (EVOO, 3%, as-fed basis) extracted by ultrasound technology in comparison to refined olive oil (ROO, 3%, as-fed basis) on the quality of pig meat (longissimus lumborum muscle) and capocollo in relation to its storage time after seasoning (t1 = 0 vs. t2 = +6 months). The EVOO diet lowered the concentration of myristic, palmitic, stearic and total saturated fatty acids (SFA) and increased oleic, linoleic, total monounsaturated (MUFAs), polyunsaturated (PUFAs) and n-3 and n-6 fatty acids in pig meat; moreover, the atherogenicity and thrombogenicity indices were lowered, with potential benefits for human health. The overall quality of capocollo was positively affected by the EVOO diet, although storage for 6 months after ripening levelled the protective effects of extra virgin olive oil in comparison with refined olive oil.

Dietary Supplementation with Camelina sativa (L. Crantz) Forage in Autochthonous Ionica Goats: Effects on Milk and Caciotta Cheese Chemical, Fatty Acid Composition and Sensory Properties.

The research studied the effects of dietary supplementation with Camelina sativa fresh forage on the chemical and fatty acid composition of milk and Caciotta cheese, and its sensory properties. Twenty Ionica goats were randomly assigned to the following two groups (n = 10): the control received a traditional forage mixture (Avena sativa, 70%; Vicia sativa, 20%; Trifolium spp., 10%), while the experimental group was given Camelina sativa fresh forage (CAM). All of the dams grazed on pasture and received a commercial feed (500 g/head/day) at housing. The milk from the CAM group showed a higher (p < 0.05) content of dry matter, fat, lactose and concentrations of C6:0, C11:0, C14:0, C18:2 n-6, CLA and PUFA, while lower (p < 0.05) amounts of C12:0, C18:0 and saturated long chain FA (SLCFA). The Caciotta cheese from the CAM group showed a greater (p < 0.05) content of n-6 FA and n-6/n-3 ratio, although close to four, thus resulting adequate under the nutritional point of view. The overall liking, odour, taste, hardness, solubility and "goaty" flavour were better (p < 0.05) in the CAM cheeses. Further investigation would be advisable in order to evaluate the effect of feeding Camelina forage obtained from different phenological stages, and the application of ensiling techniques.

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 αß or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, ß, 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.