1,721,239 research outputs found
miRNome of Italian Large White pig subcutaneous fat tissue: new miRNAs, isomiRs and moRNAs
No full textSmall RNAs, such as micro-RNAs (miRNAs), are decisive regulators of gene expression, and they could determine adipose tissue traits. A better knowledge of porcine fat genomics is relevant given that the pig is a biomedical model for metabolic and cardiovascular human pathologies. Adipose tissue is particularly important for the meat industry. We explored the miRNome of two adult Italian Large White pig backfat samples by Illumina RNA-Seq. Using custom bioinformatic methods, the expressed miRNAs were identified and quantified and the nucleotide sequence variability of miRNA isoforms were analysed. We detected 222 known miRNAs, 68 new miRNAs and 17 miRNA-offset RNAs (moRNAs) expressed from known hairpins, and 312 new miRNAs expressed from 253 new hairpins. Porcine transcripts targeted by the most expressed miRNAs were predicted, showing that these miRNAs may have an impact on Wnt, insulin signalling and axon guidance pathways. The expression of five small RNAs, including moRNA ssc-5′-moR-21 and a miRNA from a new hairpin, was validated by a qRT-PCR assay, thus confirming the robustness of our results. The depicted miRNome complexity suggests that quantitative and qualitative features of miRNAs and non-canonical products of their precursors are worthy of further investigation to clarify their roles in the adipose tissue biology
Comparison of expression levels of fourteen genes involved in the lipid and energy metabolism in two pig breeds
No full textFat content, fatty acid composition and lean cut weight are important parameters which influence meat and carcass quality in pigs. Up to now, the genes involved in the regulation of the lipid and energy metabolism in porcine skeletal muscle and fat tissue are still relatively unknown. The aim of this study was to investigate the expression levels of fourteen genes (ACACA, ACLY, CES3, ENO3, FASN, INSIG2, LMNA, MTTP, ACVR1C, NAMPT, PLIN1, PLIN2, PLTP and SORT1) mapped on different chromosomes (1, 4, 7, 8, 9, 12, 15 and 17) which were chosen for their involvement in lipid or energy metabolism in porcine muscle and backfat tissue. Tissue samples from Italian Large White and Italian Duroc pig breeds were collected at the slaughterhouse and frozen in liquid nitrogen. After extraction, the mRNA was quantified by quantitative real time polymerase chain reaction (RT-PCR) and the transcription levels of the genes analysed were compared between breeds for each tissue. In the backfat tissue, differences were found for the ACACA, ACLY, and FASN genes whose highest gene expression levels were found in Italian Large White pigs. In addition, a correlation analysis was carried out between the transcription levels of the genes considered in each tissue and breed. Co-expression relationships still relatively unknown were identified, suggesting new associations between genes which in some cases differed between the two breeds. These results suggest differences between Italian Large White and Italian Duroc pig breeds determined at the genome level affecting carcass quality and fat traits
Association study of FASN, ACLY, ACACA, SCD, ELOVL6 genes with backfat fatty acid profile and intramuscular fat in Italian Large White pigs
No full textFatty acid composition (FAC) of backfat tissue in pigs is an important trait in pig industry mainly for dry-cured ham produc- tion. In pig adipose tissue, variations in FAC contributes to qual- itative characteristics of fresh meat and seasoned products. FAC is influenced by diet, genetics, breed, sex and environmental fac- tors. Several genes affecting fatty acid composition were high- lighted but the regulation of fatty acid (FA) metabolism and fat deposition is complex and not plenty known yet. For the current study we considered eight known SNPs of 5 candidate genes Acetyl-Coenzyme A Carboxylase Alpha (ACACA), Fatty Acid Synthase (FASN), ATP citrate lyase (ACLY), fatty acid elongase 6 (ELOVL6) and stearoyl-CoA desaturase (SCD) chosen for their functions in lipid metabolism and for the genome positions to perform an association study with FA composition in Italian Large White (ILW) breed. A sample of 536 ILW pigs was geno- typed using PCR-RFLP or High Resolution Melting (HRM) PCR. FAC was determined by gas chromatography after after direct trans-esterification of subcutaneous lipids. The results allowed to determine that 37.58% of the total FA of backfat was represent- ed by saturated FA (SFA), 43.70% by monounsaturated FA (MUFA) and 18.29% by polyunsaturated FA (PUFA). The content of individual SFA, MUFA and PUFA of the analyzed tissue was measured. The association between FA and the genotypes of the 5 candidate genes was assessed using a MIXED model and SAS software. Moreover, the coefficient of correlation between the analysed FA was calculated. Genotyping results revealed that the polymorphisms ACACA NM_198837:c.4899G>A, ACACA NM_198837:c.5196T>C, and ELOVL6 XM_003357048:c.533C>T were monomorphic in the analyzed samples. Significant associ- ation with FAC were obtained for the SNP FASN AY183428:g.265T>C with C14 (P=0.005), C18 (P=0.008), C20 (P=0.0006). The SNP SCD AY487830:g.2228T>C was associated to C18:1 (P=0.03). and MUFA (P=0.05). Moreover ACLY NM_001105302:c.2956T>C presented a significant effect on C20 (P=0.05) and C18:2 cis9,trans11(P=0.05). These results high- lighted that the key genes for lipid metabolism considered in the study can regulate backfat FAC of ILW and the analysed polymor- phisms could be markers useful to modulate the subcutaneous FA profile in pigs
Weighted gene co-expression network analysis identifies molecular pathways and hub genes involved in broiler White Striping and Wooden Breast myopathies
Full text linkIn recent years, the poultry industry has experienced an increased incidence of myopathies affecting breasts of fast-growing broilers, such as White Striping (WS) and Wooden Breast (WB) defects. To explore the molecular mechanisms and genes involved in WS and WB onset, we decided to perform a Weighted Gene Co-expression Network Analysis (WGCNA) using the gene expression profile and meat quality parameters of Pectoralis major muscles analysed in our previous study. Among the 212 modules identified by WGCNA, the red, darkred, midnightblue and paleturquoise4 modules were chosen for subsequent analysis. Functional analysis evidenced pathways involved in extracellular matrix (ECM) organization, collagen metabolism, cellular signaling and unfolded protein response. The hub gene analysis showed several genes coding for ECM components as the most interconnected nodes in the gene network (e.g. COL4A1, COL4A2, LAMA2, LAMA4, FBLN5 and FBN1). In this regard, this study suggests that alterations in ECM composition could somehow activate the cascade of biological reactions that result in the growth-related myopathies onset, and the involvement of Collagen IV alterations in activating the endoplasmic reticulum (ER) stress response may be hypothesized. Therefore, our findings provide further and innovative knowledge concerning the molecular mechanisms related to the breast abnormalities occurrence in modern broilers
SNPs within the beta myosin heavy chain (MYH7) and the pyruvate kinase muscle (PKM2) genes in horse
Full text linkTwo highly expressed skeletal muscle genes (the MYH7 gene encoding the myosin heavy chain slow/β-cardiac isoform and the PKM2 gene encoding the pyruvate kinase muscle isoforms) were investigated with the objective to identify DNA markers in horses. A panel of DNA samples from different horse breeds was analysed using a PCR-single strand conformation polymorphism (SSCP) approach. Four and two alleles were identified for the MYH7 and PKM2 loci, respectively. Mendelian inheritance of alleles of the two investigated genes was confirmed analysing horse families. Sequencing of PCR products obtained from the MYH7 and PKM2 genes made it possible to characterise two SSCP alleles for each gene. The polymorphisms found in the MYH7 and PKM2 genes were further studied in 61 and 68 horses of three (Italian Heavy Draught Horse, Italian Saddler and Murgese) and five (Franches-Montagnes, Haflinger, Italian Heavy Draught Horse, Murgese and Standardbred) breeds, respectively. Allele frequencies of the two loci varied among the considered breeds. The SNPs discovery in MYH7 and PKM2 genes makes it possible to locate new molecular markers to ECA1. The identified markers could be used in association analysis with performance traits in horses
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Fatty acid composition of the intramuscular fat in the longissimus thoracis muscle of Apulo-Calabrese and crossbreed pigs
Full text linkThe aim of this study was to investigate the fatty acid profile of thelongissimus thoracismuscle in two genetictypes of pigs. Fifty one pigs of the Italian local breed Apulo-Calabrese and 52 crossbreeds [Duroc x (Landrace xLarge White)] were fed the same commercial diet and reared in the same indoor system. Fatty acid compositionwas assessed through Folch method and the obtained data were analysed with a mixed model to identify possibledifferences between the two genetic types. The Apulo-Calabrese pigs showed significantly higher contents ofheptadecenoic acid (P< 0.0001), myristic (P= 0.03), arachidic (P= 0.04), myristoleic (P= 0.004), palmi-toleic (P= 0.01) and gondoic (P= 0.01) acids. On the other hand, crossbreed samples presented highercontents of docosahexaenoic (P= 0.01) and arachidonic acid (P= 0.01). Except for heptadecenoic acid, there were no great differences inlongissimus thoracismuscle fatty acid profile between the two genetic types, suggesting that when Apulo-Calabrese pigs are managed in the same rearing conditions as crossbreeds their longissimus thoracis muscle fatty acid composition is similar
Detection of differentially expressed genes in broiler pectoralis major muscle affected by White Striping - Wooden Breast myopathies
Full text linkWhite Striping and Wooden Breast (WS/WB) are abnormalities increasingly occurring in the fillets of high breast yield and growth rate chicken hybrids. These defects lead to consistent economic losses for poultry meat industry, as affected broiler fillets present an impaired visual appearance that negatively affects consumers' acceptability. Previous studies have highlighted in affected fillets a severely damaged muscle, showing profound inflammation, fibrosis, and lipidosis. The present study investigated the differentially expressed genes and pathways linked to the compositional changes observed in WS/WB breast muscles, in order to outline a more complete framework of the gene networks related to the occurrence of this complex pathological picture. The biochemical composition was performed on 20 pectoralis major samples obtained from high breast yield and growth rate broilers (10 affected vs. 10 normal) and 12 out of the 20 samples were used for the microarray gene expression profiling (6 affected vs. 6 normal). The obtained results indicate strong changes in muscle mineral composition, coupled to an increased deposition of fat. In addition, 204 differentially expressed genes (DEG) were found: 102 up-regulated and 102 down-regulated in affected breasts. The gene expression pathways found more altered in WS/WB muscles are those related to muscle development, polysaccharide metabolic processes, proteoglycans synthesis, inflammation, and calcium signaling pathway. On the whole, the findings suggest that a multifactorial and complex etiology is associated with the occurrence of WS/WB muscle abnormalities, contributing to further defining the transcription patterns associated with these myopathies
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