A simple analytical and experimental procedure for selection of reference genes for reverse-transcription quantitative PCR normalization data

Parity affects mammary development in late-pregnant swine

The goal of this project was to determine whether various measures of mammary development differed between gilts and multiparous sows at the end of gestation. During gestation, Yorkshire × Landrace gilts (n = 19) and sows (second and third gestations, n = 17) were fed one daily meal of a conventional corn-based diet, where the amount fed was based on body weight (BW) and backfat thickness (BF) at mating. On day 110 ± 1 of gestation, a jugular blood sample was obtained from all gilts and sows to measure insulin-like growth factor-1 (IGF-1), glucose, free fatty acids, and urea. On that same day, BW and BF were measured and animals were euthanized. Mammary glands from one side of the udder were dissected for compositional analyses. The fifth gland of the contralateral row of mammary glands was sampled for histology and immunohistochemical localization of Ki67. There was less total parenchyma (1,437.4 vs. 2,004.7 ± 127.1 g; P < 0.001) and total extraparenchymal tissue (1,691.0 vs. 2,407.0 ± 125.3 g; P < 0.001) in mammary glands of gilts compared to those from sows. When these values were expressed per kg BW (226.0 and 284.0 ± 2.7 kg for gilts and sows, respectively), parenchymal mass did not differ (P > 0.10), while extraparenchymal tissue weight tended to be less in gilts than sows (P = 0.07). All components within the parenchyma differed by parity (P < 0.001). Specifically, parenchymal tissue from gilts contained a greater proportion of fat and dry matter (DM), a lower proportion of protein, and lower concentrations of DNA (6.59 vs. 9.35 ± 0.53 mg/g DM) and RNA (7.76 vs. 12.33 ± 0.70 mg/g DM) than that from sows. On the other hand, the circumference of alveolar lumens was greater in gilts than sows (P < 0.001), while the percentage of epithelial cells that were positive for Ki67, a marker of cell proliferation, was greater in sows than gilts (P < 0.05). Circulating concentrations of IGF-1 were greater in gilts than in multiparous sows (45.0 vs. 27.3 ± 2.8 ng/mL, P < 0.001). None of the other blood variables were changed by parity. Results show a marked effect of parity on mammary gland development in swine. At the end of gestation, the mammary glands of gilts had less parenchyma with lower epithelial proliferation than glands from multiparous sows. These differences could alter the response of mammary tissue to various nutritional or endocrine signals. This information is crucial for the development of management strategies designed to maximize sow milk yield.

Evaluation of suitable reference genes for normalization of quantitative real-time PCR analysis in rice plants under Xanthomonas oryzae pv. oryzae--infection and melatonin supplementation

Exogenous melatonin (MT) was found to be an interesting tool for enhancing the resistance of rice to Xanthomonasoryzaepv. oryzae (Xoo)-caused bacterial blight (BB). However, the accurate comparison of the expression levels across samples was a challenging task. In this work, the stability of 10 common used housekeeping genes under Xoo-infection and MT supplementation in rice was analyzed using quantitative real-time PCR (qRT-PCR), and algorithms geNorm, NormFinder and BestKeeper. Our results indicated that most reference genes remained stable in Xoo-infected rice plants, while a number of reference genes were affected by MT supplementation. Among all studied genes, the transcript levels of 18S(18S ribosomal RNA) and UBC (Ubiquitin-conjugating enzyme E2) remained unaltered by Xoo infection, while UBC and UBQ5(Ubiquitin 5) were the most stable genes when examining simultaneous Xoo-infection and MT supplementation, demonstrating that UBC is a suitable reference gene for qRT-PCR data normalization in rice under Xoo-infection and MT supplementation.

Impact of diet deprivation and subsequent overallowance during gestation on mammary gland development and lactation performance

The impacts of diet deprivation and subsequent overallowance during gestation on mammary gene expression and development and lactation performance were determined. Gilts were reared under a conventional (control, CTL; n = 59) or an experimental (treatment, TRT; n = 56) dietary regimen during gestation. The experimental regimen provided 70% (restriction diet, RES) and 115% (overallowance diet, OVER) of the protein and DE contents provided by the CTL diet. The RES diet was given during the first 10 wk of gestation followed by the OVER diet until farrowing. Some gilts (14 CTL and 14 TRT) were slaughtered on d 110 of gestation, and the others were allowed to farrow. Of these remaining sows, 28 (14 CTL and 14 TRT) were slaughtered on d 21 of lactation, and the rest underwent a second lactation. At each slaughter, mammary tissue was collected for compositional analyses and assessment of gene expression. Milk samples were collected on d 17 of the first lactation. Litter size was standardized to 11 ± 1, and piglets were weighed weekly until d 18 in both parities. The BW and back fat thickness of TRT first-parity sows were less than those of CTL sows in gestation (P < 0.05), and their BW was also less in lactation (P < 0.05). The BW of TRT second-parity sows was still less at mating (P < 0.05) and tended to be less on d 1 of lactation (P < 0.10) compared with CTL sows. There were no differences in piglet growth between CTL and TRT litters in either parity, yet mammary development and mammary gene expression were affected by treatment. There was less parenchymal tissue (P < 0.01) at the end of the first gestation in TRT than in CTL sows, but parenchymal tissue composition was not altered by treatment. Relative abundance of IGF-1 (P < 0.05), ornithine decarboxylase (P < 0.05), signal transducer and activator of transcription 5B (P < 0.05), and whey acidic protein (WAP, P < 0.01) genes in parenchyma at the end of the first gestation was lower in TRT than in CTL sows, and the effect on WAP genes was still present at the end of the first lactation (P < 0.01). Mammary composition at the end of the first lactation and milk composition were unaffected by treatment. In conclusion, feed deprivation and subsequent overallowance in gestation had unfavorable effects on sow BW, back fat, mammary development, and mammary gene expression at the end of gestation, but piglet growth rate over the 2 parities was not affected.

Pseudogenes as weaknesses of ACTB (Actb) and GAPDH (Gapdh) used as reference genes in reverse transcription and polymerase chain reactions

The genes encoding β-actin (ACTB in human or Actb in mouse) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH in human or Gapdh in mouse) are the two most commonly used references for sample normalization in determination of the mRNA level of interested genes by reverse transcription (RT) and ensuing polymerase chain reactions (PCR). In this study, bioinformatic analyses revealed that the ACTB, Actb, GAPDH and Gapdh had 64, 69, 67 and 197 pseudogenes (PGs), respectively, in the corresponding genome. Most of these PGs are intronless and similar in size to the authentic mRNA. Alignment of several PGs of these genes with the corresponding mRNA reveals that they are highly homologous. In contrast, the hypoxanthine phosphoribosyltransferase-1 gene (HPRT1 in human or Hprt in mouse) only had 3 or 1 PG, respectively, and the mRNA has unique regions for primer design. PCR with cDNA or genomic DNA (gDNA) as templates revealed that our HPRT1, Hprt and GAPDH primers were specific, whereas our ACTB and Actb primers were not specific enough both vertically (within the cDNA) and horizontally (compared cDNA with gDNA). No primers could be designed for the Gapdh that would not mis-prime PGs. Since most of the genome is transcribed, we suggest to peers to forgo ACTB (Actb) and GAPDH (Dapdh) as references in RT-PCR and, if there is no surrogate, to use our primers with extra caution. We also propose a standard operation procedure in which design of primers for RT-PCR starts from avoiding mis-priming PGs and all primers need be tested for specificity with both cDNA and gDNA.