Screening for the Most Suitable Reference Genes for Gene Expression Studies in Equine Milk Somatic Cells

Screening of reliable reference genes for the normalization of RT-qPCR in chicken gastrointestinal tract

The application of reverse transcription quantitative real-time PCR technology for the production of gene tissue expression profiles is a widely employed approach in molecular biology research. It is imperative to ascertain internal reference genes that exhibit stable expression across diverse tissues to ensure the precision of tissue gene expression profiles. While there have been studies documenting the most suitable reference genes for various tissues in chickens, there is a dearth of research on the identification of reference genes in the gastrointestinal (GI) tract of chickens. This study utilized 4 different algorithms (Delta CT, BestKeeper, NormFinder, and Genorm) to assess the stability of 19 internal reference genes in various GI tract tissues, including individual GI tract tissues, the anterior and posterior GI tract, and the entire GI tissue. The RefFinder software was employed to comprehensively rank these genes. The research findings successfully identified the most appropriate internal reference genes for each type of GI tissue. Furthermore, TBP, DNAJC24, Polr2b, RPL13, andAp2m exhibited stable expression in the entire and posterior GI tract, whereas HMBS, TBP, Ap2m, GUSB, DNAJC24, and RPL13 demonstrated stable expression in the anterior GI tract. However, the internal reference genes commonly utilized, namely β-Actin, 18s RNA, and ALB, exhibit poor stability and are not advised for future investigations concerning gene expression in the GI region. Consequently, MUC2 and CDX1, 2 genes that specifically express in the gut, were chosen for examination to ascertain the stability of the aforementioned internal reference genes in this particular study. In summary, this study presents a relatively stable set of internal reference genes that can be employed to enhance the precision of quantifying mRNA expression levels in functional genes within the chicken GI tract.

The Indicators of Clinical and Subclinical Mastitis in Equine Milk

Simple Summary

Mastitis, the inflammation of the mammary gland, is a major problem in a mare’s perinatal period, negatively affecting both the health of the mare and newborn foal and the quality of milk produced on dairy equine farms. The detection of mastitis is therefore one of the important goals in the equine breeding and dairy industry. This study aimed to determine the somatic cell count (SCC), the percentage of the immune cells, the electrical conductivity (ECM), and bacteriological index (BII) in milk collected from mares with (CM) and without (NCM) clinical symptoms of mastitis. The increase in examined indicators is suspected to be a subclinical mastitis indicator, therefore the study aimed to separate two subgroups, mares with (SM) and without (NSM) subclinical symptoms of mastitis. In milk from NCM mares the values of SCC, immune cells, and ECM increased immediately after birth and weaning, whereas during the rest of the lactation period their values were at a low level. Similarly, in milk from CM mares, the values of examined indicators were high and comparable to the weaning time. An increase in the level of examined indicators may become an early indication of subclinical mastitis.

Abstract

The somatic cell count in milk (SCC) and electrical conductivity of milk (ECM) are indicators of the health status of the mammary gland. Among somatic cells, mainly polymorphonuclear neutrophils (PMN), macrophages (MAC), and lymphocytes (LYM) are rated. This study aimed to determine the SCC, PMN, MAC, LYM, ECM, and bacteriological index (BII) in milk collected from mares with (CM) and without (NCM) clinical symptoms of mastitis concerning mares with (SM) and without (NSM) subclinical mastitis. Milk samples were collected from 27 mares divided into NCM (n = 12) and CM (n = 15) groups. In samples, SCC quantification, cytological examinations, ECM measurement, and bacteriological examination were performed. In NCM mares, the values of SCC, PMN, MAC, LYM, and ECM were higher in initial than in consecutive examined days after birth until weaning. After weaning the proportion of SCC, PMN, MAC, LYM, ECM, and BII increased and did not differ with the average values in CM mares. These equine milk indicators may reflect an early symptom of subclinical mastitis and in the future may be used in the early detection of mastitis or as a tool of assessment of the health status of the mammary gland in the dairy equine farm.

Putative Internal Control Genes in Bovine Milk Small Extracellular Vesicles Suitable for Normalization in Quantitative Real Time-Polymerase Chain Reaction

Bovine milk small extracellular vesicles (sEVs) contain many biologically important molecules, including mRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely used method for quantifying mRNA in tissues and cells. However, the use, selection, and stability of suitable putative internal control genes in bovine milk sEVs for normalization in qRT-PCR have not yet been identified. Thus, the aim of the present study was to determine suitable putative internal control genes in milk sEVs for the normalization of qRT-PCR data. Milk sEVs were isolated from six healthy Holstein-Friesian cattle, followed by RNA extraction and cDNA synthesis. In total, 17 mRNAs were selected for investigation and quantification using qRT-PCR; they were further evaluated using geNorm, NormFinder, BestKeeper, and ∆CT algorithms to identify those that were highly stable putative internal control genes in milk sEVs. The final ranking of suitable putative internal control genes was determined using RefFinder. The mRNAs from TUB, ACTB, DGKZ, ETFDH, YWHAZ, STATH, DCAF11, and EGFLAM were detected in milk sEVs from six cattle by qRT-PCR. RefFinder demonstrated that TUB, ETFDH, and ACTB were highly stable in milk sEVs, and thus suitable for normalization of qRT-PCR data. The present study suggests that the use of these genes as putative internal control genes may further enhance the robustness of qRT-PCR in bovine milk sEVs. Since these putative internal control genes apply to healthy bovines, it would be helpful to include that the genes were stable in sEVs under “normal or healthy conditions”.

Mare's Milk from a Small Polish Specialized Farm-Basic Chemical Composition, Fatty Acid Profile, and Healthy Lipid Indices

Simple Summary

As mare’s milk has high nutritional and biological value, it has a number of therapeutic properties. The aim of this study was to determine the basic composition, fatty acid profile, and values of health-related indices of milk from mares of different lactation stages, ages, and birth orders. The study was conducted on milk obtained from Coldblood mares in weeks 10, 15, and 25 of lactation. The mares were aged between five and 14 years. It was found that milk produced from the 15th week of lactation had the most beneficial fatty acid composition and very beneficial values of health-related indices (low values of the atherogenic index—AI and thrombogenic index—TI), which is important with regard to the prevention of atherosclerosis and thrombosis. Moreover, the study found a dependence between birth order and the atherogenic index, which was lower in milk derived from older mares (birth order > 7). The findings from the study indicate that it is possible to modify the fatty acid profile of milk by appropriately managing the age structure of the herd of mares, among other things. To confirm this dependence, the study will be continued on a larger group of mares.

Abstract

The objective of this study was to determine the chemical composition, fatty acid profile, and values of healthy indices of milk from a specialized farm of Polish Coldblood mares of different ages, birth orders, and lactation stages. Milk samples (n = 48) were collected for analysis in weeks 10, 15, and 25 of lactation from mares aged between five and 14 years. The study showed that the stage of lactation has a significant effect on the fatty acid (FA) profile of the milk produced on the farm. The highest concentration of monounsaturated and polyunsaturated FAs was found in milk produced from the 15th week of lactation. The milk was also characterized by low values of atherogenic and thrombogenic indices, which indicate the health benefits of milk with respect to the content of fatty acids and their potential to prevent or cause atherosclerosis and thrombosis. The study also found a significant correlation between the number of foalings (birth order), the fatty acid profile, and atherogenic index of milk produced on the farm. The findings from the study indicate that it is possible to modify the fatty acid profile of bulk tank milk through appropriate management of the age structure of the herd of mares. To confirm this dependence, the study will be continued on a larger group of mares.

Identification of reliable reference genes for expression studies in maternal reproductive tissues and foetal tissues of pregnant cows

The relationship between the conceptus and the maternal uterine environment is crucial for the successful establishment and maintenance of pregnancy in cattle. Gene expression analysis of the conceptus and maternal reproductive tissues is a favourable method to assess the embryonic maternal interaction. The reliability of the commonly used method reverse transcription-quantitative polymerase chain reaction (RT-qPCR) depends on proper normalization to stable reference genes (RGs). The objective of this study was to determine the expression stability of 10 potential RGs in maternal reproductive tissues and foetal tissues, and to analyse the effect of RG selection on the calculation of the relative expression of target genes. The expression stability of 10 potential RGs was analysed in eight different tissues from three pregnant dairy cows. Three programs-GeNorm, NormFinder and Bestkeeper-were used to identify the best RGs. According to all three programs, the most stable RG was CNOT11, whereas the least stable RGs were GAPDH and HPRT1. GeNorm analysis showed that a combination of five RGs (SDHA, PPIA, CNOT11, RPS9 and RPL19) was necessary for appropriate data normalization. However, NormFinder analysis indicated that the combination of CNOT11 and PPIA was the most suitable. When target genes were normalized to these RGs, the relative expression of the Radical S-adenosyl methionine domain containing 2 gene was not affected by the choice of RGs, whereas a large difference was observed in the expression profile of the Nuclear erythroid2-related factor 2 gene between the most stable and least stable RGs. The results indicate that careful selection of RGs is crucial under different conditions, especially for target genes with relatively small fold changes. Furthermore, the results provide useful information for the selection of RGs for evaluating genes affecting bovine reproduction.

Genes encoding equine β-lactoglobulin (LGB1 and LGB2): Polymorphism, expression, and impact on milk composition

β-lactoglobulin is one of the most abundant milk whey proteins in many mammal species, including the domestic horse. The aim of this study was to screen for polymorphism in the equine LGB1 and LGB2 gene sequences (all exons, introns, and 5’-flanking region) and to assess potential relationship of particular genotypes with gene expression levels (measured in milk somatic cells) and milk composition traits (protein, fat, lactose, and total β-lactoglobulin content). Direct DNA sequencing analysis was performed for twelve horse breeds: Polish Primitive Horse (PPH), Polish Coldblood Horse (PCH), Polish Warmblood Horse (PWH), Silesian, Hucul, Fjording, Haflinger, Shetland Pony, Welsh Pony, Arabian, Thoroughbred, and Percheron—and revealed the presence of 83 polymorphic sites (47 and 36 for LGB1 and LGB2 genes, respectively), including eight that were previously unknown. Association analysis of the selected polymorphisms, gene expression, and milk composition traits (conducted for the PPH, PCH, and PWH breeds) showed several statistically significant relationships; for example, the two linked LGB1 SNPs (rs1143515669 and rs1144647991) were associated with total milk protein content (p < 0.01). Our study also confirmed that horse breed had significant impact on both gene transcript levels (p < 0.01) and on milk LGB content (p < 0.05), whereas an influence of lactation period was seen only for gene relative mRNA abundances (p < 0.01).

Equine Milk Production and Valorization of Marginal Areas-A Review

The equine dairy chain is renewing the interest toward horse and donkey breeding for the production of milk with potential health promoting properties. The dairy equine chain for human consumption could contribute to the rural eco-sustainable development for the micro-economies of those areas threatened by marginalization. As a part of the whole equine industry, and its possible impact in the modern and future society, the main traits of the equine dairy enterprise are reviewed with a special focus on management of animals and milk. Equine milk compositional and nutritional peculiarities are described as also related to milk hygiene and health issues. Scientific and technical aspects of the feeding management are considered in the frame of the emerging dairy equine enterprise, where pasture is an essential element that allows to match production goals for horses and donkeys, biodiversity preservation, as well as landscape safeguard.

An Optimized Method of RNA Isolation from Goat Milk Somatic Cells for Transcriptomic Analysis

The goat (Capra hircus) is a perfect animal model for analyzing the transcriptome of milk somatic cells (MSCs), as sufficient numbers of somatic cells in goat milk, i.e., exfoliated epithelial cells, can be obtained using noninvasive methods. RNA integrity and purity are the first and most important parameters qualifying samples for transcriptomic tests and next-generation sequencing, as RNA quality influences experimental results. The aim of this study was to optimize a method for obtaining high-quality RNA from goat MSCs, irrespective of effects like breed, lactation stage, health status (e.g., with or without small ruminant lentivirus [SRLV] infection), or number of somatic cells. Milk samples were obtained from goats of two Polish breeds in various lactation stages and in different parities, and from goats infected and not infected with SRLV. Altogether, 412 MSC samples were examined: 206 using method A with fenozol and 206 using method B with QIAzol. Though the overall purity (measured as absorbance ratios at 260 nm/280 nm and 260 nm/230 nm) of the RNA material was comparable, the average yield of RNA isolated using method A was 11.9 µg, while method B’s average yield was 29.9 µg. Moreover, method B resulted in good quality RNA suitable for transcriptome analysis. Results were confirmed by RT-qPCR, using 18S rRNA and RPLP0 as the reference genes. The application of our modified treatment method was successful in obtaining high-integrity samples for transcriptomic or next-generation sequencing analysis. Using a 400 mL milk sample cooled in ice directly after milking, securing the cooling chain process from milking to MSC isolation, and applying method B to isolate RNA, we obtained good RNA quality irrespective of the goats’ breed, lactation stage, parity, milk yield, SRLV infection, and even milk yield and number of somatic cells in milk.

Selection of Reference Genes for Expression Analysis in Chinese Medicinal Herb Huperzia serrata

Huperzine A (HupA) is a powerful and selective inhibitor of acetylcholinesterase. It has attracted widespread attention endangering the ultimate plant sources of Lycopodiaceae family. In this study, we used Huperzia serrata, extensively used in Traditional Chinese medicine (TCM), a slow growing vascular plant as the model plant of the Lycopodiaceae family to develop and validate the reference genes. We aim to use gene expression platform to understand the gene expression of different tissues and developmental stages of this medicinal herb. Eight candidate reference genes were selected based on RNA-seq data and evaluated with qRT-PCR. The expression of L/ODC and cytochrome P450s genes known for their involvement in lycopodium alkaloid biosynthesis, were also studied to validate the selected reference genes. The most stable genes were TBP, GAPDH, and their combination (TBP + GAPDH). We report for the first time the reference gene of H. serrata’s different tissues which would provide important insights into understanding their biological functions comparing other Lycopodiaceae plants and facilitate a good biopharming approach.

5'-flanking variants of equine casein genes (CSN1S1, CSN1S2, CSN2, CSN3) and their relationship with gene expression and milk composition

Genes encoding casein proteins are important candidates for milk composition traits in mammals. In the case of the domestic horse, our knowledge of casein genes is limited mainly to coding sequence variants. This study involved screening for polymorphism in 5’-flanking regions of four genes encoding equine caseins (CSN1S1, CSN1S2, CSN2, and CSN3) and making a preliminary assessment of their effect on the gene expression (on the mRNA and protein levels) and milk composition traits in selected horse breeds. Altogether, 23 polymorphisms (21 described previously SNPs and two novel InDels) were found in the studied sequences, the majority of which are common in various horse breeds. Statistical analysis revealed that some are putatively associated with gene expression or milk composition — for example, the c.-2047_-2048insAT polymorphism (CSN1S1) turns out to be related to the total milk protein content in Polish Primitive Horse (p < 0.05), whereas c.-2105C>G SNP (CSN2) is related to beta-casein relative mRNA level and milk lactose concentration in the Polish Coldblood Horse breed (p < 0.05). We have also found significant effects of horse breed and lactation time-point on gene expression and mare’s milk composition. Our study indicates that the 5’-regulatory regions of genes encoding casein proteins are interesting targets for functional studies of their expression and the composition traits of mare’s milk.

Variability of lysozyme and lactoferrin bioactive protein concentrations in equine milk in relation to LYZ and LTF gene polymorphisms and expression

BACKGROUND

Equine milk is considered to be an interesting product for human nutrition, mainly owing to its low allergenicity and significant amounts of bioactive proteins, including lysozyme (LYZ) and lactoferrin (LTF). The present study assessed the effect of genetic factors on LYZ and LTF concentration variability in mare's milk.

RESULTS

Significant effects of horse breed and lactation stage on milk LYZ and LTF contents were observed. The highest level of LTF and the lowest concentration of LYZ were recorded for the Polish Warmblood Horse breed. The highest amounts of both proteins were found for the earliest investigated time point of lactation (5th week). Altogether 13 (nine novel) polymorphisms were found in the 5'-flanking regions of both genes, but they showed no significant relationship with milk LYZ and LTF contents. Several associations were found between selected SNPs and the LYZ gene relative transcript level.

CONCLUSION

While the present study indicated the existence of intra- and interbreed variability of LYZ and LTF contents in mare's milk, this variation is rather unrelated to the 5'-flanking variants of genes encoding both proteins. This study is a good introduction for broader investigations focused on the genetic background for variability of bioactive protein contents in mare's milk. © 2016 Society of Chemical Industry.

Identification of reliable reference genes for qRT-PCR studies of the developing mouse mammary gland

Cell growth and differentiation are often driven by subtle changes in gene expression. Many challenges still exist in detecting these changes, particularly in the context of a complex, developing tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) allows relatively high-throughput evaluation of multiple genes and developmental time points. Proper quantification of gene expression levels by qRT-PCR requires normalization to one or more reference genes. Traditionally, these genes have been selected based on their presumed “housekeeping” function, with the implicit assumption that they are stably expressed over the entire experimental set. However, this is rarely tested empirically. Here we describe the identification of novel reference genes for the mouse mammary gland based on their stable expression in published microarray datasets. We compared eight novel candidate reference genes (Arpc3, Clock, Ctbp1, Phf7, Prdx1, Sugp2, Taf11 and Usp7) to eight traditional ones (18S, Actb, Gapdh, Hmbs, Hprt, Rpl13a, Sdha and Tbp) and analysed all genes for stable expression in the mouse mammary gland from pre-puberty to adulthood using four different algorithms (GeNorm, DeltaCt, BestKeeper and NormFinder). Prdx1, Phf7 and Ctbp1 were validated as novel and reliable, tissue-specific reference genes that outperform traditional reference genes in qRT-PCR studies of postnatal mammary gland development.