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Peste des petits ruminants (PPR) is a serious acute, highly contagious disease caused by the peste des petits ruminants virus (PPRV). This study aims to establish a qRT-PCR assay with an internal amplification control for the rapid and accurate detection of PPRV. The primers and probes for PPRV N were based on the national standard of the diagnostic techniques for PPR of China, and a pair of primers and TaqMan probes for the internal reference gene of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was designed. Optimisation of the reaction conditions, specificity, sensitivity and reproducibility tests, and clinical sample detection were conducted. The results showed that the optimal primers and probe concentrations of PPRV were 0.4 µmol/l and 0.4 µmol/l, respectively, and were 0.4 µmol/l and 0.2 µmol/l for the reference gene GAPDH, respectively. The established method has no cross-reaction with other viruses. The minimum detection limit was 6.8 copies/µl for PPRV and 190 copies/µl for GAPDH. The coefficients of variation (CV%) of PPRV and GAPDH were both lower than 2%. The results suggest that the PPRV qRT-PCR method containing internal reference genes has strong specificity, high sensitivity, and good reproducibility. The addition of internal reference genes for the sample quality control improves the accuracy of the detection.

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Volumetric bone mineral density (vBMD) is commonly assessed using QCT. Although standard vBMD calculation methods require phantom rods that may not be available, internal-reference phantomless (IPL) and direct measurements of Hounsfield units (HU) can be used to calculate vBMD in their absence. Yet, neither approach has been systemically assessed across skeletal sites, and HU need further validation as a vBMD proxy. This study evaluated the accuracy of phantomless methods, including IPL and regression-based phantomless (RPL) calibration using HU to calculate vBMD, compared to phantom-based (PB) methods. vBMD from QCT scans of 100 male post-mortem human subjects (PMHS) was calculated using site-specific PB calibration at multiple skeletal sites throughout the body. A development sample of 50/100 PMHS was used to determine site-specific reference material density for IPL calibration and RPL equations. Reference densities and equations from the development sample were used to calculate IPL and RPL vBMD on the remaining 50/100 PMHS for method validation. PB and IPL/RPL vBMD were not significantly different (p > .05). Univariate regressions between PB and IPL/RPL vBMD were universally significant (p < 0.05), except for IPL Rad-30 (p = 0.078), with a percent difference across all sites of 6.97% ± 5.95% and 5.22% ± 4.59% between PB and IPL/RPL vBMD, respectively. As vBMD increased, there were weaker relationships and larger differences between PB vBMD and IPL/RPL vBMD. IPL and RPL vBMD had strong relationships with PB vBMD across sites (R2 = 97.99, R2 = 99.17%, respectively), but larger residual differences were found for IPL vBMD. As the accuracy of IPL/RPL vBMD varied between sites, phantomless methods should be site-specific to provide values more comparable to PB vBMD. Overall, this study suggests that RPL calibration may better represent PB vBMD compared to IPL calibration, increases the utility of opportunistic QCT, and provides insight into bone quality and fracture risk.

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Heavy-atom-free triplet-triplet annihilation (TTA) upconversion sensitized by a thermally activated delayed fluorescence (TADF) molecule is investigated in a dried gel made of a photo-cross-linked polymer as the solid-state matrix. The upconversion fluorescence quantum yields, ΦUC, of the solid-gel TTA system at different penetration depths are measured accurately based on a developed internal-reference method. It is found that ΦUC is greatest at the surface and then decreases exponentially with increasing depth, influenced by the substrate absorption. The same process is also performed in a TTA solution at different depths, but a completely different result is obtained; there is little difference for ΦUC. To the best of our knowledge, this is the first time the quantum yields at different transmission depths have been mentioned and calculated experimentally. These results illustrate the importance of accurately measuring the quantum yield of solid-phase TTA upconversion and provide a novel way to improve the solid-phase TTA quantum yield by reducing the thickness of the substrate.

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Exploration of a stably expressed gene as a reference is critical for the accurate evaluation of miRNAs isolated from small extracellular vesicles (sEVs). In this study, we analyzed small RNA sequencing on plasma sEV miRNAs in the training dataset (n = 104) and found that miR-140-3p was the most stably expressed candidate reference for sEV miRNAs. We further demonstrated that miR-140-3p expressed most stably in the validation cohort (n = 46) when compared to two other reference miRNAs, miR-451a and miR-1228-3p, and the commonly-used miRNA reference U6. Finally, we compared the capability of miR-140-3p and U6 as the internal reference for sEV miRNA expression by evaluating key miRNAs expression in lung cancer patients and found that miR-140-3p was more suitable as a sEV miRNA reference gene. Taken together, our data indicated miR-140-3p as a stable internal reference miRNA of plasma sEVs to evaluate miRNA expression profiles in lung cancer patients.

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BACKGROUND: Immunohistochemistry (IHC) is an essential technique in surgical and clinical pathology for detecting diagnostic, prognostic, and predictive biomarkers for personalized cancer therapy. However, the lack of standardization and reference controls results in poor reproducibility, and a reliable tool for IHC quantification is urgently required. The objective of this study was to describe a novel approach in which H3F3B (histone H3, family 3B) can be used as an internal reference standard to quantify protein expression levels using IHC. METHODS: The authors enrolled 89 patients who had human epidermal growth factor receptor 2 (HER2)-positive breast cancer (BC). They used a novel IHC-based assay to measure protein expression using H3F3B as the internal reference standard. H3F3B was uniformly expressed at the protein level in all tumor regions in cancer tissues. HER2 expression levels were measured with the H-score using HALO software. RESULTS: Kaplan-Meier analysis indicated that, among patients who had HER2-positive BC in The Cancer Genome Atlas data set and the authors' data set, the subgroup with low HER2 expression had a significantly better prognosis than the subgroup with high HER2 expression. Furthermore, the authors observed that HER2 expression levels were precisely evaluated using the proposed method, which can classify patients who are at higher risk of HER2-positive BC to receive trastuzumab-based adjuvant therapy. Dual-color IHC with H3F3B is an excellent tool for internal and external quality control of HER2 expression assays. CONCLUSIONS: The proposed IHC-based quantification method accurately assesses HER2 expression levels and provides insights for predicting clinical prognosis in patients with HER2-positive BC who receive trastuzumab-based adjuvant therapy.

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(1) Background: Vaccinium vitis-idaea is a nutritionally and economically valuable natural wild plant species that produces berries useful for treating various diseases. There is growing interest in lingonberry, but there is limited information regarding lingonberry reference genes suitable for gene expression analyses of different tissues under various abiotic stress conditions. The objective of this study was to identify stable reference genes suitable for different lingonberry tissues in response to abiotic stress. (2) Methods: The delta Ct method and the GeNorm v3.5 and NormFinder v20 programs were used to comprehensively analyze gene expression stability. (3) Results: Actin Unigene23839 was the best reference gene for analyzing different cultivars, whereas Actin CL5740.Contig2 was the most suitable reference gene for analyzing different tissues and alkali stress. In contrast, 18S rRNA CL5051.Contig1 was the most stable reference gene under drought conditions. (4) Conclusions: These suitable reference genes may be used in future qRT-PCR analyses of different lingonberry tissues and the effects of abiotic stresses. Furthermore, the study data may be useful for functional genomics studies and the molecular breeding of lingonberry. In summary, internal reference genes or internal reference gene combinations should be carefully selected according to the experimental conditions to ensure that the generated gene expression data are accurate.

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Selenium (Se), as one of the essential and nutrient components of living organisms and plants, plays an important role in life activities, while excessive selenium is hazardous to human health. So, the establishment of an effective method for simple, rapid, and highly sensitive determination of selenium content is crucial in the field of food composition analysis and other areas. In this paper, a novel and simple ratiometric fluorescence method for the determination of Se has been developed using 9-anthracenemethanol (AM) as the ratiometric fluorescence reagent on the basis of the conventional fluorometric assay which utilized 2,3-diaminonapthalene (DAN) as fluorescent ligand. The ratiometric method was compared with the conventional method with respect to precision and accuracy. The inter-day and intra-day precisions (RSDs) of the ratiometric fluorescence method ranged from 2.08 to 2.78% and 1.28 to 1.84%, with mean recoveries of 93.2~98.0% and limit of detection (LOD) and limit of quantification (LOQ) of 0.0016 and 0.0049 µg/mL, respectively. This method was successfully applied to the determination of total selenium in selenium-enriched milk and selenium-supplemented shampoo, with the results in agreement with those obtained by inductively coupled plasma mass spectrometer (ICP-MS). The results demonstrated that the precision and accuracy of the ratiometric fluorescence method were superior to those of the conventional fluorescence method, and the interferences of various environmental factors were effectively eliminated. The precision and accuracy of the conventional method can be significantly improved by simply adding an elaborately selected ratiometric fluorescence reagent, and the new method will have broader practical applications.

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Real-time quantitative PCR (RT-qPCR) has a high sensitivity and strong specificity, and is widely used in the analysis of gene expression. Selecting appropriate internal reference genes is the key to accurately analyzing the expression changes of target genes by RT-qPCR. To find out the most suitable internal reference genes for studying the gene expression in Broussonetia papyrifera under abiotic stresses (including drought, salt, and ZnSO4 treatments), seven different tissues of B. papyrifera, as well as the roots, stems, and leaves of B. papyrifera under the abiotic stresses were used as test materials, and 15 candidate internal reference genes were screened based on the transcriptome data via RT-qPCR. Then, the expression stability of the candidate genes was comprehensively evaluated through the software geNorm (v3.5), NormFinder (v0.953), BestKeeper (v1.0), and RefFinder. The best internal reference genes and their combinations were screened out according to the analysis results. rRNA and Actin were the best reference genes under drought stress. Under salt stress, DOUB, HSP, NADH, and rRNA were the most stable reference genes. Under heavy metal stress, HSP and NADH were the most suitable reference genes. EIF3 and Actin were the most suitable internal reference genes in the different tissues of B. papyrifera. In addition, HSP, rRNA, NADH, and UBC were the most suitable internal reference genes for the abiotic stresses and the different tissues of B. papyrifera. The expression patterns of DREB and POD were analyzed by using the selected stable and unstable reference genes. This further verified the reliability of the screened internal reference genes. This study lays the foundation for the functional analysis and regulatory mechanism research of genes in B. papyrifera.

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The study investigates whether participants can establish multiple temporal references in a temporal reproduction task. The results show that participants can learn and maintain two references for the overlapping intervals with the short distribution being overestimated towards the long one.

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Statins have anticancer effects and may be used as anticancer agents via drug repositioning. In reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays, the internal reference gene must not be affected by any experimental conditions. As statins exert a wide range of effects on cells by inhibiting the mevalonate pathway, it is possible that statin treatment might alter the expression of housekeeping genes used as internal reference genes, thereby misleading the assessment of obtained gene expression data. Here, we evaluated the expression stability of internal reference genes in atorvastatin-treated cancer cell lines. We treated both statin-sensitive and statin-resistant cancer cell lines with atorvastatin at seven different concentrations and performed RT-qPCR on 15 housekeeping genes whose expression stability was then assessed using five different algorithms. In both statin-sensitive and statin-resistant cancer cell lines, atorvastatin affected the expression of certain internal reference genes in a dose-dependent and cancer cell line-dependent manner; therefore, caution should be exercised when comparing target gene expression between cells. Our findings emphasize the importance of the validation of internal reference genes in gene expression analyses in drug treatment-based cancer research.

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The quite popular, simple but imperfect method of referencing NMR spectra to residual 1H and 13C signals of TMS-free deuterated organic solvents (referred to as Method A) is critically discussed for six commonly used NMR solvents with respect to their δH and δC values that exist in the literature. Taking into account the most reliable data, it was possible to recommend 'best' δX values for such secondary internal standards. The position of these reference points on the δ scale strongly depends on the concentration and type of analyte under study and the solvent medium used. For some solvents, chemically induced shifts (CISs) of residual 1H lines were considered, also taking into account the formation of 1:1 molecular complexes (for CDCl3). Typical potential errors that can occur as a result of improper application of Method A are considered in detail. An overview of all found δX values adopted by users of this method revealed a discrepancy of up to 1.9 ppm in δC reported for CDCl3, most likely caused by the CIS mentioned above. The drawbacks of Method A are discussed in relation to the classical use of an internal standard (Method B), two 'instrumental' schemes in which Method A is often implicitly applied, that is, the default Method C using 2H lock frequencies and Method D based on Ξ values, recommended by the IUPAC but only occasionally used for 1H/13C spectra, and external referencing (Method E). Analysis of current needs and opportunities for NMR spectrometers led to the conclusion that, for the most accurate application of Method A, it is necessary to (a) use dilute solutions in a single NMR solvent and (b) to report δX data applied for the reference 1H/13C signals to the nearest 0.001/0.01 ppm to ensure the precise characterization of new synthesized or isolated organic systems, especially those with complex or unexpected structures. However, the use of TMS in Method B is strongly recommended in all such cases.

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As a liver toxin, long-term exposure of microcystin-arginine-arginine (MC-RR) is harmful to the ecological environment and human health, so it is necessary to realize on-site detection of MC-RR. The self-powered sensor has enormous potential for on-site detection in battery-free devices. However, due to the low photoelectric conversion efficiency and poor anti-interference ability to environmental fluctuation, the field detection of self-powered sensor is limited. Herein, we tackled above problems according to the following two aspects. For one hand, CoMoS4 hollow nanospheres modified internal reference electrode was arranged in the self-powered sensor, which effectively avoided the influence of unstable sunlight caused by different space, time, weather and other factors. For the other hand, dual-photoelectrode could absorb and convert sunlight, so as to improve the solar capture and energy utilization, and realized the sunlight instead of traditional external light source (Xenon lamp or LED, etc.). This method effectively simplified the sensing device and solved the interference of environment in on-site detection. In addition, multimeter was used to measure the output voltage instead of electrochemical workstation, achieving the purpose of portability. This work established a sunlight-driven internal reference self-powered sensor with miniaturization, portability and anti-interference to realize MC-RR on-site monitoring in lake water.

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A dual-functional lanthanide-MOF nanocomposite probe was designed and constructed for the detection of ascorbic acid (AA). The magnetically functionalized hydroxyapatite nanowires are selected as the carriers and simultaneously loaded with ciprofloxacin (CIP) and terbium metal organic framework to form the internal reference fluorescence probe nanocomposite (Fe3O4-HAPNWs-Tb/MOF-CIP). This dual-functional lanthanide-MOF probe not only combines the respectively unique fluorescence properties of lanthanide MOFs and CIP, but also takes full advantage of the rapid separation properties of the magnetic component. Structural and spectroscopic characterization results have demonstrated the successful synthesis of probe material and the fluorescence mechanism. At a suitable excitation wavelength (295 nm), the probe can simultaneously emit characteristic fluorescence of CIP (445 nm) and Tb3+ (543 nm). In the presence of AA, the ratio of I543/I445 decreases rapidly with increasing of AA concentration. The linear range of determination is 0.3-40 µM with a detection limit of 20.4 nM. The contents of AA in vitamin C tablets and four fruit juice samples were detected by the composite probe. The spiked recoveries ranged from 82.6 to 104.2% with relative standard deviations (RSD) less than 2.1%, revealing the practical application value of the developed sensor in healthcare and food fields. A novel internal reference fluorescence sensor (Fe O -HAPNWs-Tb/MOF-CIP) was constructed for detecting ascorbic acid by solvothermal and self-assembly techniques, showing excellent selectivity and sensitivity based on the different responses of Tb/MOF and CIP to the target.

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Objective To monitor the validity of the sample process flow and to improve the detection accuracy of a SARS-CoV-2 antigen by introducing internal reference into SARS-CoV-2 fluorescent lateral flow assay.Methods Silica-core double-layer quantum dots(SiO2-DQD)microspheres were prepared using a polyethyleneimine(PEI)-mediated self-assembly method before being separately conjugated with an internal reference detection antibody and SARS-CoV-2 antibody.Their capture antibodies were plotted on two test lines of the nitrocellulose membrane.Based on double-antibody sandwich detection principles,an internal reference-assisted fluorescent lateral flow assay for SARS-CoV-2 antigen was established.Results According to the readout fluorescent signals,the detection limit of the method for the SARS-CoV-2 antigen reached 0.01 ng/ml with a validated sample process,suggesting its good specificity and stability.Conclusion In this study,a rapid internal reference-integrated fluorescent lateral flow assay for SARS-CoV-2 has been established,which provides control reference for the analysis workflow so that the false-negative rate of the test results can be reduced.

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Ribonuclease P protein subunit p30 (RPP30) is a highly conserved housekeeping gene that exists in many species and tissues throughout the three life kingdoms (archaea, bacteria, and eukaryotes). RPP30 is closely related to a few types of tumors in human diseases but has a very stable transcription level in most cases. Based on this feature, increasing number of studies have used RPP30 as an internal reference gene. Here, the structure and basic functions of RPP30 are summarized and the likely relationship between RPP30 and various diseases in plants and human is outlined. Finally, the current application of RPP30 as an internal reference gene and its advantages over traditional internal reference genes are reviewed. RPP30 characteristics suggest that it has a good prospect of being selected as an internal reference; more work is needed to develop this research avenue.

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Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia (EP), which resulting in considerable economic losses in pig farming globally. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a major tool for gene expression studies. However, no internal reference genes for normalization of RT-qPCR data of M. hyopneumoniae have been reported. The aim of this study was to screen the most stable genes for RT-qPCR analysis in M. hyopneumoniae under different conditions. Therefore, a total of 13 candidate internal reference genes (rpoC, Lipo, sgaB, oppB, hypo621, oppF, gyrB, uvrA, P146, prfA, proS, gatB, and hypo499) of M. hyopneumoniae filtered according to the reported quantitative proteomic analysis and the 16S rRNA internal reference gene frequently used in other bacteria were selected for RT-qPCR analysis. The mRNAs from different virulence strains (168, 168 L, J, NJ, and LH) at five different growth phases were extracted. The corresponding cycle threshold (Ct) values of the 25 reverse transcribed cDNAs using the 14 candidate genes were determined. Different internal reference genes or combinations were then screened for expression stability analysis using various statistical tools and algorithms, including geNorm, BestKeeper, and NormFinder software, to ensure the reliability of the analysis. Through further comprehensive evaluation of the RefFinder software, it is concluded that the gatB gene was the most suitable internal reference gene for samples of the different virulence strains in different growth phases for M. hyopneumoniae, followed by prfA, hypo499, and gyrB.

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The stability of internal reference genes is crucial to the reliability of gene expression results using real-time fluorescence quantitative PCR (qRT-PCR). Inappropriate reference genes may lead to inaccurate results or even wrong conclusions. This study aims to identify stable reference genes for analyzing the expression of proliferation-related and differentiation-inducing genes in bovine primary preadipocytes (BPPs) in vitro. In this study, the stability of 16 candidate internal reference genes (GAPDH, ACTB, PPIA, LRP10, HPRT1, YWHAZ, B2M, TBP, EIF3K, RPS9, UXT, 18S rRNA, RPLP0, MARVELD, EMD and RPS15A) for qRT-PCR at proliferation and differentiation stages of BPPs was investigated by three different algorithms (geNorm, NormFinder and BestKeeper). The expression of two marker genes, PCNA and LPL, was used to determine the validity of the candidate reference genes (RGs) at the proliferation and differentiation stages, respectively. The results showed that GAPDH and RPS15A were the most stable RGs in the proliferation of bovine primary preadipocyte, while PPIA was the least stable internal reference gene. RPLP0 and EIF3K were the most stable RGs in the differentiation induction of bovine primary preadipocyte, while GAPDH was the least stable internal reference gene. This study of RGs laid the foundation for subsequent research into the mechanism of proliferation and differentiation of BPPs in vitro using qRT-PCR.

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Housekeeping genes (HKGs) are constitutively expressed with low variation across tissues/conditions. They are thought to be highly conserved and fundamental to cellular maintenance, with distinctive genomic features. Here, we identify 1505 HKGs in the unicellular marine diatom Thalassiosira pseudonana based on an RNA-seq analysis of 232 samples taken under 12 experimental conditions over 0-72 h. We identify promising internal reference genes (IRGs) for T. pseudonana from the most stably expressed HKGs. A comparative analysis indicates < 18% of HKGs in T. pseudonana have orthologs in other eukaryotes, including other diatom species. Contrary to work on human tissues, T. pseudonana HKGs are longer than non-HKGs, due to elongated introns. More ancient HKGs tend to be shorter than more recent HKGs, and expression levels of HKGs decrease more rapidly with gene length relative to non-HKGs. Our results indicate that HKGs are highly variable across the tree of life and thus unlikely to be universally fundamental for cellular maintenance. We hypothesize that the distinct genomic features of HKGs of T. pseudonana may be a consequence of selection pressures associated with high expression and low variance across conditions.

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ObjectiveTo screen the appropriate reference genes for real-time fluorescence-based quantitative polymerase chain reaction（Real-time PCR）analysis of the Andrographis paniculata under methyl jasmonate（MeJA）and various abiotic stresses. MethodThe actin 1（ACT1），actin 2（ACT2），elongation factor（EF-1α），glyceraldehyde-3-phosphate dehydrogenase（GAPDH），tubulin（TUB），polyubiquitin（UBQ）， and 18S rRNA（18S）gene were selected as candidate reference genes based on the RNA-seq data of high temperature，drought， UV， and MeJA. The expression of seven candidate reference genes in the A. paniculata leaves was assessed by Real-time PCR，and the stability was analyzed by geNorm，NormFinder，BestKeeper， and Refinder. ResultThe results of stability evaluated by geNorm，NormFinder， and BestKeeper were not the same due to different indicators. As analyzed by Refinder， for the stability of the expression， the genes were ranked as UBQ>18S>EF-1α>ACT2>ACT1>GAPDH>TUB under high temperature stress， ACT1>UBQ>EF-1α>18S>ACT2>GAPDH>TUB under drought stress， EF-1α>TUB>ACT2>UBQ>18S>GAPDH>ACT1 under UV stress， and ACT1>EF-1α>UBQ>ACT2>18S>TUB>GAPDH under MeJA stress. Among them，18S gene was not suitable as an internal reference gene duo to its high expressive abundance. This study also verified the relative expression level of andrographolide synthesis-related gene hydroxy-methylglutaryl-CoA synthase （HMGS） in the four stresses on the basis of transcriptome data，and found that the Real-time PCR results of appropriate internal reference genes were accurate and reliable. ConclusionUBQ-ACT1-UBQ，EF-1α-TUB，and ACT1-EF-1α were the suitable combinations under stresses of high temperature，drought，UV， and MeJA. This study is expected to provide references for the research on function regulation and expression of genes in A. paniculata under high temperature，drought，UV， and MeJA stresses.

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Real-time quantitative polymerase chain reaction is the most commonly used method to accurately detect gene expression patterns. The method requires stable internal reference genes to standardize the data. However, studies have shown that there is no stable expression of internal reference genes in different tissues and under different treatments. Therefore, in order to study the optimal reference genes of quinoa under different hormones and abiotic stress, leaves and stems from quinoa seedlings treated with low temperature (4 °C), salt (200 mmol/L) and abscisic acid (200 mmol/L) were used as experimental materials. Using ACT-1, eIF, EF1α, GAPDH, TUA, TUB-9, TUB-1, H2A and L8-1 as candidate reference genes, the expression stability of these 9 quinoa candidate reference genes under different hormone treatment and abiotic stress was evaluated by using geNorm, NormFinder and BestKeeper software. The results showed that TUB-1 gene under salt stress, L8-1 gene under low temperature stress, EF-1α gene induced by ABA. PLIM2c WLIM1and WLIM2b were selected to verify the candidate internal reference genes, and finally the expression of GAPDH was most unstable under the three treatments, which was not suitable to be the internal reference gene of quinoa under specific conditions, while EF1α showed good stability under the three different treatments and was suitable to be used as the internal reference gene. In conclusion, the results of this study could provide an important reference for quantifying the expression level of reference genes in quinoa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01094-z.