Differential Effects of Dietary Oregano Essential Oil on the Inflammation Related Gene Expression in Peripheral Blood Mononuclear Cells From Outdoor and Indoor Reared Pigs

Intensive farming systems represent a stressful environment for pigs and negatively influence neuroendocrine functions, behavior, and performance. Outdoor farming is an alternative option, which is thought to imply several beneficial effects for the animal. Dietary essential oils are known to be an innovative strategy to improve pig health and performance, and oregano essential oil (ORE) possesses beneficial effects due to its antimicrobial, anti-fungal, and antioxidant properties. We tested the effect of dietary ORE on peripheral blood mononuclear cells (PBMCs) in 36 growing pigs, either reared under indoor or outdoor conditions. Quantitative real-time PCR (RT-qPCR) assay was used to evaluate the effect of diet (control vs. ORE) and the time of sampling (T1-120 days vs. T2-190 days) on the expression of inflammatory and immune-related genes (TNF, IL1β, IL8, IL18, IL10, IL1RN, STAT3, HSP90, ICAM-1, and NFKB1). Under outdoor condition, the majority of transcripts were upregulated (p < 0.05), assuming a general inflammatory status (TNF, HSP90, NFKB1, IL1β, and STAT3). However, an interaction between diet and the farming system was observed: HSP90, NFKB1, and STAT3 were downregulated (p < 0.05) in the outdoor reared pigs when fed the ORE diet. Our study showed that bioactive compounds of ORE exert their activity, especially when the animals are exposed to stressful stimuli. Dietary ORE can be an acceptable strategy to help pigs tolerate the stress related to the harsh, outdoor, rearing conditions.

Dietary supplementation with olive mill wastewaters induces modifications on chicken jejunum epithelial cell transcriptome and modulates jejunum morphology

BACKGROUND

The Mediterranean diet is considered one of the healthier food habits and olive oil is one of its key components. Olive oil polyphenols are known to induce beneficial effects in several pathological conditions, such as inflammatory bowel disease, and to contrast the proliferation of cancer cells or hypercholesterolemia. Polyphenols are also present in waste products derived from the olive industry: olive mill wastewaters (OMWW) are rich in polyphenols and there is an increasing interest in using OMWW in animal nutrition. OMWW are attributed with positive effects in promoting chicken performance and the quality of food-derived products. However, a tissue-specific transcriptome target analysis of chickens fed with OMWW has never been attempted.

RESULTS

We explored the effect of dietary OMWW on the intestinal function in broilers. A morphological analysis of the jejunum revealed that OMWW reduced crypt depth, whereas no significant modifications were observed for villus height and the villus height/crypt depth ratio. An RNA Sequencing analysis was performed on isolated, intestinal, epithelial cells and 280 differentially expressed genes were found using a count-based approach. An enrichment analysis revealed that the majority of up regulated genes in the OMWW group were over-represented by the regulation of viral genome replication-related GO-Terms, whereas down regulated genes were mainly involved in cholesterol and lipid metabolism.

CONCLUSIONS

Our study showed how an industrial waste product can be recycled as a feed additive with a positive relapse. OMWW dietary supplementation can be a nutritional strategy to improve chicken performance and health, prevent intestinal damage, enhance innate immunity and regulate cholesterol metabolism and fat deposition.

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils

BACKGROUND

Essential oil (EO) dietary supplementation is a new strategy to improve animal health. EO compounds have antiparasitic, antimicrobial, antiviral, antimycotic, antioxidant and anti-inflammatory proprieties. Nutrigenomics investigations represent innovative approaches in understanding the relation between diet effect and gene expression related to the animal performance. Few nutrigenomics studies have used a high-throughput RNA-Sequencing (RNA-Seq) approach, despite great potential of RNA-Seq data in gene expression quantification and in co-expression network analyses. Our aim is to use the potential of RNA-Sequencing data in order to evaluate the effect of an EO supplementary diet on gene expression in both lamb liver and muscle.

RESULTS

Using a treatment and sex interaction model, 13 and 4 differentially expressed genes were identified in liver and muscle respectively. Sex-specific differentially expressed (DE) genes were identified in both sexes. Using network based analysis, different clusters of co-expressed genes that were highly correlated to the diet were detected in males vs. females, in agreement with DE analysis. A total of five regulatory genes in liver tissue associated to EO diet were identified: DNAJB9, MANF, UFM1, CTNNLA1 and NFX1. Our study reveals a sex-dependent effect of EO diet in both tissues, and an influence on the expression of genes mainly involved in immune, inflammatory and stress pathway.

CONCLUSION

Our analysis suggests a sex-dependent effect of the EO dietary supplementation on the expression profile of both liver and muscle tissues. We hypothesize that the presence of EOs could have beneficial effects on wellness of male lamb and further analyses are needed to understand the biological mechanisms behind the different effect of EO metabolites based on sex. Using lamb as a model for nutrigenomics studies, it could be interesting to investigate the effects of EO diets in other species and in humans.

Oregano dietary supplementation modifies the liver transcriptome profile in broilers: RNASeq analysis

Intensive farming of broilers involves stressful conditions that reduce animal welfare and performance. New dietary strategies to improve performance and meat quality include the administration of plant extracts. Oregano (Origanum vulgare L.) is known for its antimicrobial, anti-fungal, insecticidal and antioxidant properties. However, studies on diet supplementation with oregano are mainly focused on the evaluation of animal performance, while partial information is available on transcriptomics and nutrigenomics and, in particular, Next Generation Sequencing (NGS) is not widely applied. In this study we tested the effect of an oregano aqueous extract supplemented diet on gene expression in broiler chickens. Whole liver transcriptome of 10 birds fed with a supplemented diet versus 10 controls was analyzed using the RNA-Seq technique. One hundred and twenty-nine genes were differentially expressed with an absolute log fold change >1. The analysis reveals a massive down-regulation of genes involved in fatty acid metabolism and insulin signaling pathways in broilers fed with the oregano aqueous extract supplementation. Down-regulated genes could be associated to chicken lean line, suggesting the potential beneficial effect of oregano supplementation in reducing both abdominal and visceral fat deposition. Down-regulation of insulin signaling pathway related genes suggest that dietary oregano supplementation might be an option in obesity and diabetes conditions.

Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Background

To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.

Results

Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.

Conclusions

Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3943-8) contains supplementary material, which is available to authorized users.

Genetic diversity in the Maremmano horse and its relationship with other European horse breeds

The Maremmano is an Italian warmblood horse breed from central Italy. We characterized the genetic diversity and the degree of admixture in Maremmano in comparison to 14 other European horse breeds using 30 microsatellites. Between-breed diversity explained about 9 per cent of the total genetic diversity. Cluster analysis, genetic distances and genetic differentiation coefficients showed a close relationship of Maremmano with Hanoverian and Lusitano in accordance with breed history.

Transcription of LINE-derived sequences in exercise-induced stress in horses

A large proportion of mammalian genomes is represented by transposable elements (TE), most of them being long interspersed nuclear elements 1 (LINE-1 or L1). An increased expression of LINE-1 elements may play an important role in cellular stress-related conditions exerting drastic effects on the mammalian transcriptome. To understand the impact of TE on the known horse transcriptome, we masked the horse EST database, pointing out that the amount is consistent with other major vertebrates. A previously developed transcript-derived fragments (TDFs) dataset, deriving from exercise-stimulated horse peripheral blood mononuclear cells (PBMCs), was found to be enriched with L1 (26.8% in terms of bp). We investigated the involvement of TDFs in exercise-induced stress through bioinformatics and gene expression analysis. Results indicate that LINE-derived sequences are not only highly but also differentially expressed during physical effort, hinting at interesting scenarios in the regulation of gene expression in relation to exercise.

RNA sequencing of the exercise transcriptome in equine athletes

The horse is an optimal model organism for studying the genomic response to exercise-induced stress, due to its natural aptitude for athletic performance and the relative homogeneity of its genetic and environmental backgrounds. Here, we applied RNA-sequencing analysis through the use of SOLiD technology in an experimental framework centered on exercise-induced stress during endurance races in equine athletes. We monitored the transcriptional landscape by comparing gene expression levels between animals at rest and after competition. Overall, we observed a shift from coding to non-coding regions, suggesting that the stress response involves the differential expression of not annotated regions. Notably, we observed significant post-race increases of reads that correspond to repeats, especially the intergenic and intronic L1 and L2 transposable elements. We also observed increased expression of the antisense strands compared to the sense strands in intronic and regulatory regions (1 kb up- and downstream) of the genes, suggesting that antisense transcription could be one of the main mechanisms for transposon regulation in the horse under stress conditions. We identified a large number of transcripts corresponding to intergenic and intronic regions putatively associated with new transcriptional elements. Gene expression and pathway analysis allowed us to identify several biological processes and molecular functions that may be involved with exercise-induced stress. Ontology clustering reflected mechanisms that are already known to be stress activated (e.g., chemokine-type cytokines, Toll-like receptors, and kinases), as well as "nucleic acid binding" and "signal transduction activity" functions. There was also a general and transient decrease in the global rates of protein synthesis, which would be expected after strenuous global stress. In sum, our network analysis points toward the involvement of specific gene clusters in equine exercise-induced stress, including those involved in inflammation, cell signaling, and immune interactions.

Effect of training status on immune defence related gene expression in Thoroughbred: are genes ready for the sprint?

Athletic performance is both a stress factor and an adaptive response to exercise that may be modulated by training, reduce inflammation and help prevent disease. Studies on the endocrinology of exercise and training have demonstrated the existence of an integrated metabolic network of hormone and cytokine regulation. Subsequent molecular studies have shown that repeated bouts of exercise may establish new basal levels of gene expression at rest. The Thoroughbred horse may be a useful 'exercise model' for inter-individual comparisons between subjects with homogeneous genetic and environmental backgrounds and similar exercise management practices. In this study, the effects of training and acute effort on gene expression were evaluated with a real time PCR approach in athletic (n=10) and sedentary horses (n=9), using a previously characterised panel of genes known to be highly modulated during effort (CXCL2, TLR4, IL1β, IL8, IL1RII, IL18, IL6 and CEBPβ). A 'rest comparison' was performed to evaluate a training effect in both groups while a 'race comparison' was performed in athletic horses only (before, immediately after, and 12h after racing) to determine the effect of acute effort. The results indicated that many of the investigated genes (TLR4, IL1β, IL1RII, IL18, IL6 and CEBPβ) were expressed to a greater extent in athletic horses compared to sedentary animals when both were at rest. However, a time-course comparison in the athletic horses revealed that genes exhibiting the highest levels of expression at rest did not show significant changes after the race. The findings suggested that training may exert a conditioning on gene expression at rest leading to a more prompt response to exercise-induced stress in Thoroughbreds.

Chromosomal assignment of six genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) in four species of the genus Equus

We mapped six genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) on the chromosomes of Equus caballus, Equus asinus, Equus grevyi, and Equus burchelli by fluorescence in situ hybridization. Our results add six type I markers to the cytogenetic map of these species and provide new information on the comparative genomics of the genus Equus.

Exercise-induced up-regulation of MMP-1 and IL-8 genes in endurance horses

Background

The stress response is a critical factor in the training of equine athletes; it is important for performance and for protection of the animal against physio-pathological disorders.

In this study, the molecular mechanisms involved in the response to acute and strenuous exercise were investigated using peripheral blood mononuclear cells (PBMCs).

Results

Quantitative real-time PCR (qRT-PCR) was used to detect modifications in transcription levels of the genes for matrix metalloproteinase-1 (MMP-1) and interleukin 8 (IL-8), which were derived from previous genome-wide expression analysis. Significant up-regulation of these two genes was found in 10 horses that had completed a race of 90–120 km in a time-course experimental design.

Conclusion

These results suggest that MMP-1 and IL-8 are both involved in the exercise-induced stress response, and this represents a starting point from which to understand the adaptive responses to this phenomenon.

Analysis of peripheral blood mononuclear cells gene expression in endurance horses by cDNA-AFLP technique

The knowledge of molecular mechanisms of stress response in athlete horses can allow us to plan an appropriate and high-grade training to obtain better performance and to preserve horse welfare. It is well known that excessive muscular exercise can lead to a number of responses which may be associated with modification of the mRNA levels for a number of metabolic genes such as those involved in the immune response. In the present study cDNA-AFLP technique was applied to Arab endurance horses under stressing conditions to visualise variations of transcriptional profiles; 49 transcript derived fragments (TDFs), differentially expressed, were cloned and sequenced. Four of these showed high sequence similarity with genes probably involved in exercise-induced stress response and resulted to be not sequenced in the horse. Their modulation was confirmed by RT-PCR and the full-length transcripts were isolated by RACE-PCR. The mRNAs sequences obtained were included in the GenBank database as Equus caballus interleukin 8 (IL8), E. caballus retinoblastoma binding protein 6 mRNA (RBBP6), E. caballus eukaryotic translation initiation factor 4 gamma 3 (eIF4G3) and E. caballus heat shock protein 90 (Hsp90). The expression pattern of these genes was verified in other endurance horses under stressing conditions, strengthening the hypothesis of their real involvement in exercise stress-induced response.

cDNA AFLP-based techniques for studying transcript profiles in horses

The identification of differentially expressed genes is a fundamental prerequisite for understanding the molecular regulation of most physiological and pathological processes. Among the procedures employed to compare mRNA populations, those that are gel-based appear to hold great promise and are considered excellent tools for studying gene expression in species, such as the equine one, for which little genomic information is available. In the present study, we evaluated two techniques for studying mRNA profiles in horse tissue, one referred to the cDNA-amplified fragment length polymorphism (AFLP) that we called C-AFLP (classical cDNA-AFLP) protocol and the other to ordered differential display (ODD) with some modifications that we named S-AFLP (systematic cDNA-AFLP). Both techniques can be applied in live animals because of the small amount of sample required. We applied the S-AFLP to investigate horse transcript profile modifications during physical exercise. We found two transcripts that are mostly expressed during exercise and immediately after the end of it.

Glycohistochemistry of the zona pellucida of developing oocytes in the rabbit and hare

Lagomorpha are often used as animal models in reproductive experiments. The aim of the present study was to examine the glycoconjugate modifications occurring mainly in the zona pellucida during oocyte growth in the rabbit and hare, using a battery of lectins combined with sialidase digestion and chemical treatments. This histochemical approach made it possible to identify sulpho- and asulpho-carbohydrates in the terminal and/or subterminal position linked to sialic acid residues. The lectins that stained the zona pellucida of both species most effectively were SBA, PNA and WGA, indicating the presence of beta-D-N-acetylgalactosamine, beta-D-galactosamine and N-acetylglucosamine residues. The differences in the glucidic residue content and in their spatial distribution that depended on the species and stage of follicle development were also detected.

Localization of the lectin reactive sites in adult and prepubertal horse testes

The testes of prepubertal and adult horses were investigated using 10 horseradish peroxidase conjugated lectins combined with sialidase digestion and potassium hydroxide treatment, to localise the oligosaccharide sequences of glycoconjugates during spermatid maturation. In adult animals, the lectins showed a variable affinity for spermatids and Sertoli cell apical extensions. Soybean agglutinin (SBA), peanut agglutinin (PNA), Ricinus communis agglutinin (RCA-I) and wheat germ agglutinin (WGA) bound to the acrosomal structures of spermatids, whereas Griffonia simplicifolia agglutinin (GSA-II) labelled these structures only during Golgi and cap phases. These results suggested that glycoproteins of mature acrosomes contain both N- and O-linked oligosaccharides and that these carbohydrate chains undergo modifications during spermiogenesis. Sialic acid residues were not detected throughout the acrosomal development. The lectin binding pattern of Sertoli cells was very similar to that of acrosome of spermatids during the maturation phase. In sexually immature horses, only the degenerated germinal cells and the Leydig cells showed reactivity towards lectins. The first cells reacted with SBA and Dolichos biflorus agglutinin (DBA), the latter with SBA, PNA, WGA, GSA-II, Canavalia ensiformis agglutinin (ConA), Lens culinaris agglutinin (LCA) and also with DBA after sialidase digestion.

Lectin histochemical detection of sulfoglycans in the zona pellucida of mammalian antral oocytes

Sulphated esters are important to increase effectiveness of specific biological activities of carbohydrates. Biochemical studies revealed the presence of distinct sulphated glycoproteins in mammal zona pellucida (ZP) that bind proacrosin and thus participate in the sperm-egg fusion processes. In the present study, 6 lectin-horseradish peroxidase conjugates (SBA, PNA, RCA-I, GSA-IB4, GSA-II and DBA) were used in combination with desulphation and sialidase digestion to identify sulphocarbohydrates in the terminal and/or subterminal position of oligosaccharide side chains of glycoproteins in the ZP of bovine, ovine, caprine and porcine antral oocytes. In particular, we identified the following terminal sulphoglycans located in the outer layer of the ZP only: SO4-GalNAc in bovine ZP; SO4-Galbeta1,3GalNAc in bovine and ovine ZP; SO4-Galbeta1,4GlcNAc in bovine, ovine and caprine ZP; SO4-alpha-Gal in bovine, caprine and porcine ZP. Subterminal sulphoglycans linked to sialic acid residues were evenly distributed throughout the entire thickness of the ZP: Neu5Ac-SO4-Galbeta1,3GalNAc in bovine and porcine ZP; Neu5Ac-SO4-Galbeta1,4GlcNAc in caprine ZP; Neu5Ac-SO4-alpha-Gal in porcine ZP; Neu5AcSO4-GlcNAc in bovine ZP. The results demonstrate that the chemical composition of the ZP differs among species determining the species-specificity of gamete interactions.

Glycohistochemical investigation of canine and feline zonae pellucidae of preantral and antral oocytes

Glycoconjugate modifications were analysed in the zona pellucida during development of oocytes in dog and cat using conventional histochemical staining methods with or without previous carbohydrate digestion. A series of lectins combined with desulphation and sialic acid degradation were applied. No differences were observed between dog and cat follicles using conventional histochemical staining methods. In both species, the zona pellucida and follicular fluid/intercellular matrix strongly reacted with PAS and high iron diamine stain (HID) and reacted moderately with low iron diamine stain (LID). Treatment with testicular hyaluronidase, chondroitinase ABC, chondroitinase AC and chondroitinase B treatment diminished HID and LID positivity of follicular fluid and intercellular matrix. Lectins that gave the most intense staining of the zona pellucida of both species were SBA, PNA, RCA-I, GSA-IB4 and WGA, indicating the presence of beta-D-GalNAc, D-Gal and GlcNAc residues. Sulpho- and asulpho-carbohydrates were identified in terminal and/or subterminal positions linked to sialic acid residues. In conclusion, the results indicate that glycosaminoglycans are not present in the zona pellucida of both species. Differences were observed in carbohydrate residues and in their spatial distribution, depending on species and developmental stage of the follicles. The similarity in lectin affinity between ooplasm and zona pellucida of oocytes present in follicles at different stages of development confirm the involvement of oocytes in zona pellucida production.

Glycoconjugates in small antral ovarian follicles of the river buffalo (Bubalus bubalis L.)

Types and distribution patterns of glycoconjugates in antral ovarian follicles were investigated in the buffalo, using periodic-acid Schiff (PAS), high iron diamine (HID), low ion diamine (LID) and lectin histochemical staining methods. HID and LID staining procedures were preceded in some cases by digestion with testicular hyaluronidase, Streptomyces hyaluronidase, chondroitinase ABC and heparitinase (heparinase III). Lectin staining was performed with the use of 12 horseradish peroxidase (HRP) lectin conjugates. Some lectin staining procedures were preceded by neuraminidase digestion and saponification. Large amounts of isomeric chondroitin sulphates and a minor quantity of heparan sulphate and hyaluronic acid and/or chondroitin were found in follicular fluid. Lectin staining of buffalo follicular fluid revealed glycoconjugates with different glucidic determinants such as beta-N-acetylgalactosamine, beta-galactose-(1-3)-N-acetylgalactosamine, beta-galactose-(1-4)-N-acetylglucosamine, N-acetylglucosamine, alpha-fucose and alpha-glucose/alpha-mannose, and sialic acid residues. Glycosaminoglycans were absent in the zona pellucida of oocytes in small antral follicles. Acidic glycoconjugates in the zona pellucida were caused by sulphated groups and sialic acid residues. Our data show few internal glucidic residues, such as N-acetylglucosamine in the buffalo zona pellucida but many subterminal beta-N-acetylgalactosamine, alpha- and beta-galactose determinants masked by sialic acids. These findings demonstrate that buffalo follicular fluid has a very heterogeneous composition that is similar to that found in small and large bovine follicles. No differences in composition of the follicular fluid were observed in the follicles examined.

Characterization of the complex carbohydrates in the zona pellucida of mammalian oocytes using lectin histochemistry

The objective of this study was to characterize the glycoconjugates present in the zona pellucida of the follicular oocytes in sheep, goats and pigs. The zona pellucida was stained with periodic acid-Schiff, low iron diamine, high iron diamine, and nine different lectin horseradish conjugates: Con-A, SBA, DBA, PNA, RCA-I, GSA-II, WGA, LTA and UEA-I. Staining with DBA, PNA, SBA and RCA-I was performed with and without saponification with KOH and sialidase digestion. The results showed the presence of neutral and acidic glycoconjugates with different terminal sugars and also sialic acid radicals in the zona pellucida of all the animal studied. In particular, the positive staining with WGA, SBA, PNA and RCA-I suggests the presence of oligosaccharides with N-acetyl-D-glucosamine and sialic acid linked to the penultimate beta-N-acetyl-D-galactosamine and to the disaccharide galactosyl-(beta 1-3)-N-acetyl-D-galactosamine. The terminal trisaccharide sialic acid galactosyl-(beta 1-4)-N-acetyl-D-glucosamine was identified only in the zona pellucida of ovine and porcine oocytes. Thus, the zona pellucida exhibited species-specific variations in the content and distribution of lectin-binding patterns that may reflect the species specificity of gamete interaction.