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Transcriptome of pig muscle assessed by erial analysis of gene expression (SAGE)
No full textSerial analysis of gene expression (SAGE) is a molecular biology technique applied to measure the global gene expression levels, characterise transcriptomes, compare the transcript levels between tissues and uncover new molecules within defined signal transduction pathways (Tutela and Tuteja, 2004)
Serial Analysis of Gene Expression (SAGE) in the skeletal muscle of pig.
No full textSkeletal muscle growth represents one of the main economic traits in pig production. To gain a better understanding
of expressions profile in pig muscle, serial analysis of gene expression (SAGE) was performed
in Longissimus dorsi of two pigs at 3 and 9 months of age. A total of 53,120 long tags were obtained and
sequenced from the four muscle SAGE libraries, representing 17,902 different tags, or putative transcripts,
0.64% (+0.09) of which had a relative expression level higher than 1‰. Overall, a total of 218 tags
were highly expressed and 31 had a frequency higher than 3‰.
Functional characterisation of the expression profiles was performed using Kyoto Encyclopedia of Genes
and Genomes metabolic maps and 139 pathways were identified for swine skeletal muscle. Focal adhesion,
Mitogen-Activated Protein Kinase signalling, oxidative phosphorylation, ribosomal proteins, regulation of
actin cytoskeleton and insulin signalling pathways showed an abundance of genes greater than 1.5% of
all the expressed transcripts. A comparison with human SAGE library indicated no statistical differences
for the frequency of genes involved in these metabolic pathways
Substitution of a commercial diet with raw meat complemented with vegetable foods containing chickpeas or peas affects faecal microbiome in healthy dogs
Full text linkThe aim of the study was to investigate if the inclusion of chickpeas or peas in the diet can modify faecal microbiome in dogs. Eight healthy adult Border collie, fed a commercial extruded diet as reference diet (RD), were divided in two groups of four individuals. At the beginning of the trial, one group received a diet based mainly of raw meat, rice and chickpeas (CP) and in the other group this pulse was substituted with peas (PE). After 14 days, the dogs with CP diet shifted to the PE and those with PE shifted to the CP diet, for another 14 days. Faeces were col- lected at the beginning (T0), after 14 days (T14) and at the end of the study (T28). Faeces were analysed for 16S rRNA, short chain fatty acids (SCFA), lactate, pH and faecal score was also eval- uated. The SCFA and lactate in the faeces were not affected by the inclusion of pulses, with the only exception of isovalerate, which was higher in CP and PE diets in comparison with RD diet (p < .05). The abundances of Erysipelotrichaceae incertae sedis, Eubacterium, Anaerobacter and Sarcina significantly differed in CP and PE in comparison with RD. Moreover, the genera Prevotella, Lactobacillus, Alloprevotella, Suttarella varied significantly between CP and PE diets. The observed modifications of faecal microbioma were related not only to the change from RD to CP or PE, but also to the type of pulse, chickpeas or peas. However, long-term studies are required to investigate the implications that pulses can have for gut health
Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools
No full textAn array consisting of 10,665 oligo 70mer was used to evaluate the longissimus dorsi muscle tissue expression during growth in nine pigs belonging to Casertana, an autochthonous breed characterized by slow growth and a massive accumulation of backfat, Large White, and a crossbreed (Duroc X Landrace X Large White). The results have been validated through real time PCR. Animals were of the same age and raised in the same environmental conditions. Muscle tissues were collected at 3, 6, 9, and 11 months, and a total of 272 genes showing significant changes between Casertana and cosmopolitan genetic types at 3 months of age have been found.
Time series cluster analysis indicated that Casertana breed had a different pattern of gene expressions compared to the Large White and the crossbreed. For Casertana pigs, a first cluster showed 105 genes were under-expressed at 3 months of age and a second cluster indicated 52 genes were over-expressed at 3 months of age, in comparison to the other genetic types.
As expected, differentially expressed genes were in the category of “contractile fibre” and transcriptional factors involved in muscle development and differentiation. These finding highlight muscle expression genes during pig growth and are useful to understand the genetic meaning of the different developmental rates
Evaluation of gene expression profiles of pig skeletal muscle in response to energy content of the diets using human microarrays
No full textThe aim of the research was to compare gene transcription profiles of Musculus longissimus dorsi (MLD) between pigs fed diets with high (HED) or low (LED) energy contents. Two groups of 4 Casertana pigs were reared from 3 to 12 months of age in the same environmental conditions and fed HED or LED. In the HED, the ave rage daily gain and back fat thickness were significantly (P < 0.05) higher than in LED pigs. Differential expression of genes in MLD of pigs fed diets with different energy density was assessed by a human high-density complementary DNA (cDNA) muscle microarray consisting of 4670 probes and further confirmed by quantitative real time RT-PCR analysis. Seven of the genes up-regulated in MLD of HED pigs were involved in the glycolytic and oxidative metabolism (phosphoglycerate mutase 2, glyceraldehyde-3-phosphate dehydrogenase, NADH dehydrogenase ubiquinone1 beta 9, muscle pyruvate kinase, enolase 3, muscle creatine kinase, isocitrate dehydrogenase 3 (NAD+) gamma) and four in the contractile apparatus (tropomyosin 1 alpha, troponin C2, fast, fast skeletal myosin light chain 2, troponin T3, skeletal, fast). Instead, HED diet reduced the level of expression of muscle proteins associated with slow fibre type (troponin T1, skeletal, slow, supervillin, myosin binding protein C, slow type, titin, myosin, heavy polypeptide 7, beta, calponin homology-associated smooth muscle) and signal transduction (SH3-binding domain protein 5-like, hypothetical protein FLJ21438, protein kinase cAMP-dependent, catalytic, rho guanine nucleotide exchange factor 15). The down-regulation of CTSB was also observed for HED group. From the results it can be assumed that high energy content of the diet influence physiological processes in the muscle tissue by switching slow fibres into fast reacting fibres and thus enhancing meat quality
Investigation of rumen metagenome in Italian Simmental and Italian Holstein cows using a whole-genome shotgun sequencing technique
Full text linkThe study aimed at investigating the rumen microbiome composition and functional activity in mid lactating cows of Italian Holstein (IH) and Italian Simmental (IS) breeds. Eight IH and eight IS pluriparous cows with days in milking (DIM) ranging from 90 to 180 were selected and rumen contents were sampled with oesophageal tube. Rumen metagenome was analysed using a whole shotgun sequencing. Data were analysed for taxonomic classification and microbial genes. The relative abundance of Archaea, the Archaea to Bacteria ratio and the Archaea to Eukarya ratio were higher (p Bactroidaceae, Bacteroides, Prevotellaceae and Prevotella lower (p Euryarchaeota (p Methanosphera (p Methanothermobacter (p < .05) than IH cows. The annotation of sequences to KEGG revealed that 170 genes were differentially abundant between IS and IH cows and among these, 20% were involved in protein biosynthesis, 8.8% in one-carbon metabolism, as methyl coenzyme M reductase associated protein and of six isoforms of methyl coenzyme M reductase. The present results suggest a genetic link between breed and microbiome, although this interaction can be influenced by several biological factors. Considering that there are still a low number of whole genome shotgun sequencing analysis of rumen communities, these data can provide further information to scientific community.</p
Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs
Full text linkBackground: Dietary intervention studies are required to deeper understand the variability of gut microbial ecosystem in healthy dogs under different feeding conditions and to improve diet formulations. The aim of the study was to investigate in dogs the influence of a raw based diet supplemented with vegetable foods on faecal microbiome in comparison with extruded food.
Methods: Eight healthy adult Boxer dogs were recruited and randomly divided in two experimental blocks of 4 individuals. Dogs were regularly fed a commercial extruded diet (RD) and starting from the beginning of the trial, one group received the raw based diet (MD) and the other group continued to be fed with the RD diet (CD) for a fortnight. After 14 days, the two groups were inverted, the CD group shifted to the MD and the MD shifted to the CD, for the next 14 days. Faeces were collected at the beginning of the study (T0), after 14 days (T14) before the change of diet and at the end of experimental period (T28) for DNA extraction and analysis of metagenome by sequencing 16SrRNA V3 and V4 regions, short chain fatty acids (SCFA), lactate and faecal score.
Results: A decreased proportion of Lactobacillus, Paralactobacillus (P < 0.01) and Prevotella (P < 0.05) genera was observed in the MD group while Shannon biodiversity Index significantly increased (3.31 ± 0.15) in comparison to the RD group (2.92 ± 0.31; P < 0.05). The MD diet significantly (P < 0.05) decreased the Faecal Score and increased the lactic acid concentration in the feces in comparison to the RD treatment (P < 0.01). Faecal acetate was negatively correlated with Escherichia/Shigella and Megamonas (P < 0.01), whilst butyrate was positively correlated with Blautia and Peptococcus
(P < 0.05). Positive correlations were found between lactate and Megamonas (P < 0.05), Escherichia/Shigella (P < 0.01) and Lactococcus (P < 0.01).
Conclusion: These results suggest that the diet composition modifies faecal microbial composition and end products of fermentation. The administration of MD diet promoted a more balanced growth of bacterial communities and a positive change in the readouts of healthy gut functions in comparison to RD diet
Isolation and full-length genome characterization of Sarscov-2 from covid-19 cases in northern Italy
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Single-Step Genome Wide Association Study Identifies QTL Signals for Untrimmed and Trimmed Thigh Weight in Italian Crossbred Pigs for Dry-Cured Ham Production
Full text linkAlong with the traditional traits, swine breeding programs for Italian dry-cured ham production have recently aimed to include novel phenotypes. The identification of the genomic regions underlying such new traits helps to untangle their genetic architecture and may provide useful information to be integrated in genetic selection. With this aim, we estimated genetic parameters and conducted a single step genome wide association studies (GWAS) on untrimmed and trimmed thigh weight considering two pig crossbred lines approved for Italian Protected Designation of Origin ham production. Quantitative trait loci (QTLs) were characterized based on the variance of 10-SNP sliding windows genomic estimated breeding values. In particular, we identified interesting QTL signals on several chromosomes, notably on chromosome 4, 6, 7 and 15. A high heritability and genetic correlation were observed for the two traits under investigation and although independent studies including other pig populations are required to disentangle the possible effects of specific linkage disequilibrium in our population, our findings suggest that such QTL could be investigated in future pig breeding programs to improve the reliability of genomic estimated breeding values for the dry-cured ham production
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