An effect of large-scale deletions and duplications on transcript expression.

Since copy number variants (CNVs) have been recognized as an important source of genetic and transcriptomic variation, we aimed to characterize the impact of CNVs located within coding, intergenic, upstream, and downstream gene regions on the expression of transcripts. Regions in which deletions occurred most often were introns, while duplications in coding regions. The transcript expression was lower for deleted coding (P = 0.008) and intronic regions (P = 1.355 × 10-10), but it was not changed in the case of upstream and downstream gene regions (P = 0.085). Moreover, the expression was decreased if duplication occurred in the coding region (P = 8.318 × 10-5). Furthermore, a negative correlation (r = - 0.27) between transcript length and its expression was observed. The correlation between the percent of deleted/duplicated transcript and transcript expression level was not significant for all concerned genomic regions in five out of six animals. The exceptions were deletions in coding regions (P = 0.004) and duplications in introns (P = 0.01) in one individual. CNVs in coding (deletions, duplications) and intronic (deletions) regions are important modulators of transcripts by reducing their expression level. We hypothesize that deletions imply severe consequences by interrupting genes. The negative correlation between the size of the transcript and its expression level found in this study is consistent with the hypothesis that selection favours shorter introns and a moderate number of exons in highly expressed genes. This may explain the transcript expression reduction by duplications. We did not find the correlation between the size of deletions/duplications and transcript expression level suggesting that expression is modulated by CNVs regardless of their size.

Chemical Composition, Fatty Acid Profile, and Lipid Quality Indices in Commercial Ripening of Cow Cheeses from Different Seasons.

The aim of the study was to compare and demonstrate whether commercial rennet ripening cheeses available on the market in summer and winter differ in their chemical composition, fatty acid profile, content of cis9trans11 C18:2 (CLA) acid and other trans isomers of C18:1 and C18:2 acid and whether they are characterized by different values of lipid quality assessment indices. The experimental material consisted of rennet ripening of cheeses produced from cow's milk available in the Polish market. The first batch contained cheeses produced in winter and purchased from the market between May and June. The second batch contained cheeses produced in summer and purchased between November and December. Chemical composition was analyzed by FoodScan apparatus. The gas chromatography (GC) method was used to determine the content of fatty acids. Results obtained in the presented study indicate that the chemical composition, content of fatty acids trans isomers, and lipid quality indices varied between summer and winter cheeses. The summer cheeses were richer sources of MUFA and PUFA compared to winter cheeses. Summer cheeses were also characterized by lower content of SFA, higher content n - 3, lower n - 6/n - 3 ratio, and higher content of DFA. Higher contents of CLA and trans C18:1 and C18:2 were found in summer cheeses.

Impact of SNPs in ACACA, SCD1, and DGAT1 Genes on Fatty Acid Profile in Bovine Milk with Regard to Lactation Phases.

Milk fat is a dietary source of fatty acids (FA), which can be health promoting or can increase risks of some diseases. FA profile composition depends on many factors, among them gene polymorphism. This study analyzed the relation between polymorphism of acetyl-CoA carboxylase α (ACACA), stearoyl-CoA desaturase 1 (SCD1), diacylglycerol acyltransferase 1 (DGAT1) genes with FA profile in milk from Polish Holstein-Friesian cattle and determined changes of FA percentage during lactation with regard to polymorphism. Milk samples were collected twice: during the first phase of lactation (<90 Days in milk; DIM) and at the end of lactation (>210 DIM). During the first milk collection, blood samples were taken to analyze three chosen single nucleotide polymorphisms (SNPs): AJ312201.1g.1488C > G SNP in ACACA gene, A293V SNP in SCD1 gene, and K232A SNP in DGAT1 gene. Increased concentration of FA that are less beneficial for human health and have lower concentration of healthy FA in homozygotes: GG in ACACA, VV in SCD1, and KK in DGAT1 were observed, as well as a strong influence of the analyzed genes on FA with 18C atoms was also found. Moreover, it was demonstrated that lactation phase significantly affected FA percentage in milk depending on the phenotype. These results may contribute their part to knowledge toward obtaining more beneficial milk composition.

Effect of Soy Lecithin Supplementation in Beef Cows before Calving on Colostrum Composition and Serum Total Protein and Immunoglobulin G Concentrations in Calves.

The aim of this study was to investigate the impact of soy lecithin supplementation in beef cow's nutrition on colostrum composition and serum concentrations of immunoglobulin G (IgG) and serum total protein (STP) in calves. Twenty pregnant Charolaise cows were assigned to two groups. In the supplementation group (n = 10) during the last four weeks of pregnancy, soy lecithin was administrated in an amount of 20 g/cow/day. In both groups, basic composition (protein, fat, lactose, dry matter), somatic cell count (SCC), total bacteria count (TBC), IgG concentration, and fatty acids profile were determined in colostrum samples. Moreover, STP and IgG concentration were measured in calves' blood samples on the 3rd, 7th, 14th, and 21st days of life, mothered by supplementation and control cows. Animals fed with soy lecithin before calving produced colostrum with a higher (p = 0.049) level of linoleic acid (C18:2 n-6). In addition, these results showed that soy lecithin supplementation has contributed to an increase (p = 0.029) of serum IgG in calves on the 14th day of life. The impact of such change in colostrum on IgG levels on calves serum and their half-life need further analysis.

Effects of Single Nucleotide Polymorphisms in the SLC27A3 Gene on the Nutritional Value of Sheep Milk.

The current research was undertaken to use the genetic potential of animals to obtain high-quality dairy products. Single nucleotide polymorphisms (SNPs) in SLC27A3 gene were identified in Zoslachtená valaska sheep using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Correlations between genotypes and milk composition and nutritional value were analysed This study showed that milk from sheep with TT genotype in the SNP4 locus was characterised by higher (p < 0.01) fat and dry matter content and lower lactose concentration, compared to sheep with AA and TA genotypes, respectively. Moreover, it was found that animals with GG genotype in SNP1 produced milk with higher C18:1n9c, C18:1n7t, CLA, and other unsaturated fatty acids (UFAs) content than sheep with TT. Additionally, milk from animals with CC at the SNP3 locus had significantly higher (p < 0.01) levels of UFAs than milk from sheep with other genotypes in the SNP3. In summary, it may be concluded that milk from animals with TT genotype of SNP4 is characterised by higher fat and dry matter content. Whereas, milk from sheep with GG in SNP1 and with CC in SNP3 is characterised by higher content of UFAs, which increases milk value as material for functional food production.

How to Explore the Function and Importance of MicroRNAs: MicroRNAs Expression Profile and Their Target/Pathway Prediction in Bovine Ovarian Cells.

Micro RNAs (miRNA) are integral components of genetic regulatory networks and act by binding to the transcripts of their corresponding target genes, leading to a decrease in protein production levels either by mRNA degradation or by translational repression. While the role of miRNAs is ubiquitous, they have a particular importance with regard to cell differentiation. The miRNA-target mRNA interaction has a significant impact on many signaling pathways and the cross-talk between them; playing a regulatory role in a variety of different physiological processes within the cells. Ovarian follicle development is a physiological process that is not fully understood with regard to miRNA regulation; there are many questions that remain with respect to the molecular regulation of this important process. Bovine follicular cells are a good experimental model for the investigation of these mechanisms, having direct implications on reproductive health in humans. This chapter describes how differentially expressed miRNAs are identified in the granulosa and theca cells of dominant and subordinate bovine ovarian follicles and the identification of their associated targets and pathways. This chapter systematically describes how the granulosa and theca cells are dissected from the ovarian follicles. Afterward, we present a detailed protocol for miRNA extraction, based on a combined TRI reagent/column clean-up method, and also miRNA expression profiling using both microarray and RT-qPCR. In addition, an outline is provided of the bioinformatic analysis which enables the prediction of miRNAs targets. Pathways associated with the differentially expressed miRNAs are also elucidated using DIANA-miRPath software.

Genomic portrait of ovarian follicle growth regulation in cattle.

The female reproductive cycle is characterized by cyclic patterns of growth of ovarian follicles destined to ovulate and the degeneration of those not chosen for ovulation. Apoptosis is the underlying mechanism of ovarian follicle degeneration during atresia. The fate of ovarian follicles is under the control of endocrine hormones (e.g. gonadotropins) and intra-ovarian regulators (e.g. growth factors and gonadal steroids), but the intra-cellular and molecular regulation of follicle fate (cellular proliferation or atresia) are still not fully understood. Studies using genomic tools which aim to determine the expression profiles of mRNAs and miRNAs in bovine dominant and subordinate ovarian follicles at different stages of the follicle wave have indicated that there are some novel molecular factors (e.g. FOXO1 and miR-183∼96∼182 cluster) associated with ovarian follicle development. Furthermore, bioinformatics tools have been used to identify the interactions between mRNAs and miRNAs leading to better understanding of ovarian follicle growth regulation in cattle. This review summarizes the recent findings about the complex intracellular communication networks involving miRNA, their target genes and signalling molecules which together may coordinate the fate of cattle ovarian follicles.