Real-time Quantitative RT-PCR Results Research Articles

β-glucan and anisodamine can enhance the immersion immune efficacy of inactivated cyprinid herpesvirus 2 vaccine in Carassius auratus gibelio

As one of the most important fish in freshwater aquaculture, gibel carp (Carassius auratus gibelio) is easily susceptible to Cyprinid herpesvirus 2 (CyHV-2). Immersion vaccination has attracted many researchers due to its simple operation in preventing infectious diseases. However, the unavoidable disadvantage is that the immersion vaccine must be used with adjuvants to get a better performance. In this study, gibel carps were vaccinated by a 60 min bath in a β-propiolactone-inactivated Cyprinid herpesvirus 2, mixed with DTT, β-glucan, anisodamine and scopolamine, respectively. After immunization, the fishs were challenged by CyHV-2 in 2 weeks. By analyzing pathological section, we found that β-glucan, anisodamine and scopolamine groups protected the gibel carp compared to the control group, which was consistent with the trend of survival rate. Specifically, β-glucan group in serum appeared best on lysozyme, TSOD and complement C3. Real time quantitative RT-PCR results demonstrated that in both spleen and head kidney tissues, mRNA expressions of typical Th1 immune response cytokines IL-2 and IFN-γ2 in β-glucan group and anisodamine group were significantly higher than other groups and the level of immunoglobulins related to systemic immunity (IgM) and mucosal immunity (IgZ) were also enhanced in the immune period. DTT group slightly affected immune gene and serum enzyme activity, while did not show an adjuvant effect on survival rate. In addition, four adjuvant groups could obviously inhibit CyHV-2 replication. This study explored and proved the good efficiency of β-glucan or anisodamine as immersion immune adjuvant and also provided reference for improving the efficiency of immersion immunity.

Nobiletin Reduces Intracellular and Extracellular β-Amyloid in iPS Cell-Derived Alzheimer's Disease Model Neurons.

Alzheimer's disease (AD) is the most common cause of dementia, with progressive memory impairment. Recently, neprilysin, a β-amyloid (Aβ)-degrading enzyme has become featured as a drug target for AD. Previously, we identified nobiletin from citrus peels as a natural compound possessing anti-dementia activity. In addition, we demonstrated that nobiletin improved memory in memory-impaired animals and, further, that Aβ levels were markedly decreased in the brains of these animals. We demonstrated in vitro that nobiletin up-regulates neprilysin expression and activity in human neuroblastoma cells. However, the action of nobiletin with regard to Aβ degradation under in vitro AD pathological conditions remains unclear. In this study, we examined whether nobiletin could enhance the degradation of intra- and extracellular Aβ using human induced pluripotent stem cell-derived AD model neurons, which generate an excess of Aβ1-42 due to the familial AD presenilin-1 mutation. The neurons were treated in the presence or absence of nobiletin. The results of real-time quantitative RT-PCR indicated that neprilysin mRNA levels were significantly up-regulated by nobiletin. Furthermore, immunostaining with an anti-Aβ antibody revealed that nobiletin substantially reduced the intraneuronal content of Aβ. Interestingly, the results of Aβ1-42 immunoassays confirmed that nobiletin also significantly decreased the levels of Aβ1-42 released into the cellular medium. These results suggest that nobiletin enhanced the reduction of intra- and that extracellular Aβ levels under AD pathologic conditions, and this is associated with the up-regulation of neprilysin expression. Collectively, nobiletin appears to be a promising novel prophylactic seed drug or functional food for AD.

Type VIII Collagen Mediates Vessel Wall Remodeling after Arterial Injury and Fibrous Cap Formation in Atherosclerosis

Collagens in the atherosclerotic plaque signal regulation of cell behavior and provide tensile strength to the fibrous cap. Type VIII collagen, a short-chain collagen, is up-regulated in atherosclerosis; however, little is known about its functions invivo. We studied the response to arterial injury and the development of atherosclerosis in type VIII collagen knockout mice (Col8(-/-) mice). After wire injury of the femoral artery, Col8(-/-) mice had decreased vessel wall thickening and outward remodeling when compared with Col8(+/+) mice. We discovered that apolipoprotein E (ApoE) is an endogenous repressor of the Col8a1 chain, and, therefore, in ApoE knockout mice, type VIII collagen was up-regulated. Deficiency of type VIII collagen in ApoE(-/-) mice (Col8(-/-);ApoE(-/-)) resulted in development of plaques with thin fibrous caps because of decreased smooth muscle cell migration and proliferation and reduced accumulation of fibrillar type I collagen. In contrast, macrophage accumulation was not affected, and the plaques had large lipid-rich necrotic cores. We conclude that in atherosclerosis, type VIII collagen is up-regulated in the absence of ApoE and functions to increase smooth muscle cell proliferation and migration. This is an important mechanism for formation of a thick fibrous cap to protect the atherosclerotic plaque from rupture.

Microarray-based analysis of the gene expression profile in GC-1 spg cells transfected with spermatogenesis associated gene 12

The unique differentiation mechanisms of spermatogenesis suggest the existence of cell type- and stage-specific molecules. Herein, a microarray-based approach was used to identify changes in the gene expression profile in mouse GC-1 spg germ cells transfected with spermatogenesis associated gene 12 (SPATA12). One hundred and eighty-two upregulated genes and 104 downregulated genes with fold changes of ≥2 or ≤0.5 (P≤0.05) in expression were identified. Ten genes were selected for validation of the microarray results using quantitative RT-PCR. The real-time quantitative RT-PCR results were consistent with that of the microarray. The gene ontology (GO) terms for the biological functions of the differentially expressed genes induced by SPATA12 included binding activity and immune response. Biological pathway analysis identified several related pathways which are associated with immune responses, cell adhesion and the developmental process. In addition, we observed that SPATA12 may interact with the β-catenin signaling pathway and that SPATA12 may negatively regulate β-catenin signaling during spermatogenesis.

Imprinting and expression analysis of a non-coding RNA gene in the mouse Dlk1-Dio3 domain

The Dlk1-Dio3 imprinted domain not only is implicated growth and development of the embryo and placenta, but also affects adult metabolism and brain function. In this study, we identified the imprinting status of a mouse non-coding RNA gene, B830012L14Rik, mapped to the Dlk1-Dio3 domain by the polymorphism- and sequencing-based approach. Imprinting analysis showed that the gene was expressed maternally at E15.5, E18.5 and postnatal day 1 mice. Two transcripts of approximately 1.9 and 3.5kb were detected by northern blot. Furthermore, we examined the spatiotemporal expression patterns of the gene during the mouse development. In situ hybridization analysis showed that B830012L14Rik was mainly expressed in forebrain, pituitary, cartilage primordium of spinal column, lung and liver at E13.5 and E15.5. The results of real-time quantitative RT-PCR showed that the B830012L14Rik expression in brain, heart, lung and liver was higher at E15.5 than at E12.5 and E18.5. Furthermore, the gene expression increased progressively in brain from E12.5 to E15.5 whereas decreased from E15.5 to E19.5. This study may provide further insights into the imprinting, genomic features and expression regulation of the Dlk1-Dio3 imprinted cluster.

The regulatory mechanism of neuromedin S on luteinizing hormone in pigs

Neuromedin S (NMS) has been implicated in the regulation of luteinizing hormone (LH) secretion. However, the regulatory mechanism of NMS on LH in pigs remains unexplored. In the present study, we confirmed the hypothesis that the effect of NMS on LH could be mediated via hypothalamic melanocyte-stimulating hormones (MSH) neurons of ovariectomized pigs. In an immunohistological experiment, NMS receptor NMU2R-positive neurons were found in the paraventricular nucleus of hypothalamus, widely distributed in the anterior pituitary, and sparsely observed in the posterior pituitary. We also found that serum LH level was declined at between 12 and 60 min with the lowest level at 24 min after NMS injection. The decreased LH secretion induced by NMS could be completely abolished by pretreatment with melanocortin receptor-4 antagonist SHU9119, while a signal injection of 1.0 nM SHU9119 per se did not affect the serum LH level. Real time quantitative RT-PCR results showed that the expression of GnRH and LH mRNAs were down-regulated by NMS treatment, but their reduction was restored to normal level by SHU9119 treatments. The expression of NMU2R and PR mRNAs were up-regulated by NMS treatment, but their effects were blocked by SHU9119 treatments. The expression of the estrogen receptor mRNA in the pig hypothalamus and pituitary was unchanged under the NMS and SHU9119+NMS treatments. In summary, all results suggest that the inhibitory effect of NMS on LH is at least in part through its receptor NMU2R and mediated via MSH neurons in hypothalamus–pituitary axis of ovariectomized pigs.

SloR modulation of the Streptococcus mutans acid tolerance response involves the GcrR response regulator as an essential intermediary

Streptococcus mutans, the primary causative agent of human dental caries, grows as a biofilm on the tooth surface, where it metabolizes dietary carbohydrates and generates acid byproducts that demineralize tooth enamel. A drop in plaque pH stimulates an adaptive acid-tolerance response (ATR) in this oral pathogen that allows it to survive acid challenge at pHs as low as 3.0. In the present study, we describe the growth of an S. mutans mutant, GMS901, that harbours an insertion-deletion mutation in gcrR, a gene that encodes a transcriptional regulatory protein. The mutant is acid-sensitive and significantly compromised in its ATR relative to the UA159 wild-type progenitor strain. Consistent with these findings are the results of real-time quantitative RT-PCR (qRT-PCR) experiments that support the GcrR-regulated expression of known ATR genes, including atpA/E and ffh. Although we observed gcrR transcription that was not responsive to acidic pH, we did note a significant increase in gcrR expression when S. mutans cells were grown in a manganese-restricted medium. Interestingly, the results of gel mobility shift assays indicate that the S. mutans SloR metalloregulatory protein is a potential regulator of gcrR by virtue of its manganese-dependent binding to the gcrR promoter region, and expression studies support the hypothesis that sloR transcription is responsive to manganese deprivation and acidic pH. Taking these results together, we propose that SloR-Mn modulates S. mutans gcrR expression as part of a general stress response, and that GcrR acts downstream of SloR to control the ATR.

Protection of Angelica sinensis against radiation-induced pulmonary fibrosis in mice

To evaluate the Angelica Sinensis as a protecting agent affecting the radiation-induced pulmonary fibrosis in an animal model, The thoraces of C57BL/6 mice were exposed to either sham irradiation or single fraction of 12 Gy. Four groups were defined: that received neither irradiation nor Angelica Sinensis (N group), that received Angelica Sinensis but no irradiation (A group), that underwent irradiation without Angelica Sinensis (NX group) and that received both Angelica Sinensis and irradiation (AX group). Mice were sacrificed at 1, 24, 72 hours and 1, 2, 4, 8, 16, 24 weeks post-irradiation. The lungs tissue were removed and processed for definitive analysis, including hydroxyproline content, HE and Masson staining, and the TGF-beta1, (Transforming Growth Factor beta1, TGF-beta1) mRNA expressions. Compared with N and A group, there was some differences in the AX group, but a significant histological and pathologic changes in NX group. Non-irradiated groups (N and A group) exhibited low levels of hydroxyproline (0.775 +/- 0.024) microg/mg and (0.751 +/- 0.034) microg/mg, and there was a significantly elevated level of hydroxyproline in NX group (0.875 +/- 0.009) microg/mg (P < 0.05). AX group (0.782 +/- 0.010) microg/mg was in between the non-irradiated groups (N and A group) and the radiation-only group (NX group), and the difference between AX group and NX group was significant (P < 0.01). The results of real-time quantitative RT-PCR showed that the relative mRNA expressions of cytokine TGF-beta1 in NX group(249.655 +/- 16.320) was significantly higher than that in group A (1.254 +/- 0.061) and N (1.324 +/- 0.057) (P < 0.01), and that in AX group (108.076 +/- 9.870) decreased than that of NX group (P < 0.01). An animal model of mice with radiation-induced lung injure was established successfully. This study has demonstrated that Angelica sinensis in Hibits the progress of radiation-induced pulmonary fibrosis, Possibly by down-regulating the expression of the proinflammatory cytokine Tgfb1. These data suggest that Angelica sinensis maybe useful in preventing and/or treating radiation-induced pulmonary fibrosis in the clinic.

Minimal Residual Disease (MRD) and Risk of Relapse in Acute Promyelocytic Leukemia (APL): Insights from the North American Intergroup Phase III Trial C9710.

MRD results during and following treatment (Rx) of APL have become an important predictor of clinical outcome and are beginning to be used to guide Rx for this highly curable leukemia, but important questions remain. Some studies suggest that low/intermediate (LI)-risk patients (pts), as defined by the Sanz criteria, who achieve a negative PCR result after intensive consolidation Rx have a very low risk of relapse and may not require maintenance Rx, while those with MRD might benefit from hematopoietic stem cell transplantation. However, these data are controversial. We studied whether a single quantitative MRD test obtained immediately after completion of C9710 consolidation Rx (with all-trans retinoic acid, daunorubicin, with or without arsenic trioxide) predicted relapse and could be used to guide further Rx. Real-time quantitative RT-PCR( RQ-PCR) was used to measure PML-RARα in bone marrow (BM) and blood (B) of 43 pts treated on C9710. All 43 pts were in first complete remission after completion of consolidation Rx when MRD was measured, but all of them later relapsed during, or after completion of maintenance Rx. By Sanz criteria, 14/43 were high risk and 29/43 LI-risk at diagnosis. 29 had S-isoform, 12 had L-isoform, and 2 had V-isoform. Median time from MRD assessment to relapse was 253 days (range: 44–1231). RQ-PCR results were expressed as a normalized quotient (NQ) of PML-RARα/GAPDH or ABL control. The sensitivity of the assay was 1 in 104–5. A NQ of >10−5 was found in the prior intergroup study, INT0129, to be strongly associated with risk of relapse and was set as the threshold for considering a result “positive”. MRD with NQ >10−5 was detected in only 4 of 43 (9%) pts after completion of consolidation Rx. 8 others had detectable PML-RARα transcript but had NQs < 10−5. The remaining 31 pts had no evidence of MRD. There was excellent concordance between MRD measurements in 26 paired B and BM NQ values and a strong correlation between NQ values in B and BM using either GAPDH or ABL controls (p = 0.0001 and p <0.0001, respectively). To determine whether a more sensitive assay might identify a higher percentage of pts with MRD, we also evaluated the post-consolidation samples in 19 of these pts using a qualitative nested RT-PCR assay with a sensitivity of detection of 1 in 106. We found 13 of 19 (68%) pts had detectable MRD. In conclusion, RQ-PCR analysis of MRD using a threshold NQ of >10−5 at a single post-consolidation Rx timepoint did not predict relapse of APL in pts on C9710. Setting a lower NQ threshold for the RQ-PCR assay or using a more sensitive, but qualitative PCR assay improved the detection rate; however, neither approach identified all pts destined to relapse, nor has the prognostic value of a positive result using the more sensitive assay been determined. Based on these results, we caution against the use of a single MRD test at the end of consolidation Rx to determine further Rx. Ongoing analysis of serial samples obtained during and following completion of Rx might provide further insights into optimal timing and frequency of MRD measurements needed to identify APL pts at high risk of relapse.

Assessment of Minimal Residual Disease (MRD) by Qualitative RT-PCR (Q-PCR) vs Real-Time Quantitative RT-PCR (RQ-PCR) in a Phase II Study of Acute Promyelocytic Leukemia (APL).

Assessment of MRD in APL by Q-PCR analysis for the presence or absence of PML-RARα mRNA after the completion of consolidation therapy in treatment regimens employing all-trans retinoic acid (ATRA) and chemotherapy (CT) has provided a reasonably accurate but not infallible prognostic test for disease recurrence (DR). This assessment has been made at detection sensitivity levels up to 1 in 104, which is considered to have optimal predictive value, since non-quantified lower levels of PML-RARα mRNA may not be relevant to clinical outcome. In the current study, we compared the results of Q-PCR (touchdown PCR for 40 cycles followed by post-PCR blot hybridization with a RARα chemiluminescent probe) to results from RQ-PCR in 15 patients on a Phase II clinical trial designed to eliminate CT (low-risk/LR patients, WBC <10K) or minimize CT (high-risk/HR patients, WBC >10K), using combined ATRA and arsenic trioxide therapy. All patients achieved complete remission (CR) and have been followed for a median of 1.2 years. DR occurred in 0/8 LR, 0/1 unclassified and 2/6 HR patients. At CR, all Q-PCR and RQ-PCR assays were positive. For RQ-PCR, the normalized quotient (NQ) value of PML-RARα, i.e., the PML-RARα copy number divided by the housekeeping gene glyceraldehyde-3′-phosphate dehydrogenase (GAPDH) copy number, ranged widely from 1.5 x 10−6 to 7.0 x 10−3. Post-CR follow-up data were:Patient GroupNumberQ-PCR+RQ-PCR+NQ RangeLR/Unclassified90/2416/249 x 10−9 – 1 x 10−7HR/no DR40/238/232 x 10−9 – 3 x 10−7HR/DR21/75/71 x 10−8 – 5 x 10−5For the 2 HR/DR patients, the last pre-DR results were, respectively: Q-PCR, positive and negative; RQ-PCR, NQ = 5 x 10−5 and NQ = 2.3 x 10−7. In overall comparisons to RQ-PCR results, all Q-PCR assays were positive for NQ >10−5, 3/4 were positive in the NQ 10−6 to 10−5 range, and all were negative for NQ <10−6. Additionally, dilution-reconstruction experiments confirmed the stochastic nature of PCR assays near the detection limit and indicated that RQ-PCR was about 10-fold more sensitive than Q-PCR. Although larger studies are needed, our results suggest that HR patients who are Q-PCR-negative but RQ-PCR-positive in the >10−7 – <10−5 range at a critical post-CR checkpoint may be at increased risk of DR and, more generally, they suggest that the results of RQ-PCR testing at a critical checkpoint can be used in combination with clinical risk assessment to stratify the intensity of subsequent MRD monitoring in individual patients.

CDNA macroarray analysis of gene expression changes in rat brain after a single administration of a 2-aminoadamantane derivative

The Atlas™ Rat cDNA Expression Array (BD Biosciences, United States) has been used to analyze changes in the expression of 588 genes in rat brain cells in response to a single administration of Ladasten, a 2-aminoadamantane derivative that has psychostimulating and anxiolytic effects. The analysis of hybridization on macroarrays, confirmed by the results of real-time quantitative RT-PCR, has demonstrated that Ladasten alters the expression of 12 genes in the rat brain. The GAT3 and CARBH genes are presumed to be pharmacologically important targets of Ladasten. The changes in their activity explain the mechanisms of the anxiolytic and mood-stabilizing effects of the drug. Ladasten has been shown to induce the genes whose products are involved in various signal pathways (APC, Rb, PKCIP, and PMCA), as well as the genes of cytoskeletal proteins (Tubα1 and actin), synaptic proteins (SynIA&IB and PLP), and enzymes (Gapdh and NSE). The proteins encoded by these genes are presumably involved in compensatory and/or neuroplastic adaptation to the effects of Ladasten.

RT-PCR Analysis of RNA Extracted from Bouin-Fixed and Paraffin-Embedded Lymphoid Tissues

In the present study, we have investigated whether RNA can be efficiently isolated from Bouin-fixed or formalin-fixed, paraffin-embedded lymphoid tissue specimens. To this aim, we applied a new and simple method that includes the combination of proteinase K digestion and column purification. By this method, we demonstrated that the amplification of long fragments could be accomplished after a pre-heating step before cDNA synthesis associated with the use of enzymes that work at high temperature. By means of PCR using different primers for two examined genes (glyceraldehyde-3-phosphate dehydrogenase [GAPDH]- and CD40), we amplified segments of cDNA obtained by reverse transcription of the isolated RNA extracted from Bouin-fixed or formalin-fixed paraffin-embedded tissues. Amplified fragments of the expected sizes were obtained for both genes tested indicating that this method is suitable for the isolation of high-quality RNA. To explore the possibility for giving accurate real time quantitative RT-PCR results, cDNA obtained from matched frozen, Bouin-fixed and formalin-fixed neoplastic samples (two diffuse large cell lymphomas, one plasmacytoma) was tested for the following target genes: CD40, Aquaporin-3, BLIMP1, IRF4, Syndecan-1. Delta threshold cycle (DeltaC(T)) values for Bouin-fixed and formalin-fixed paraffin-embedded tissues and their correlation with those for frozen samples showed an extremely high correlation (r > 0.90) for all of the tested genes. These results show that the method of RNA extraction we propose is suitable for giving accurate real time quantitative RT-PCR results.

Detection of BCR-ABL transcripts in chronic myeloid leukemia (CML) using a 'real time' quantitative RT-PCR assay.

Quantitative competitive RT-PCR techniques have been developed to detect BCR-ABL fusion transcripts in CML but they are hardly reproducible. In this work, we have developed BCR-ABL quantification by real time RT-PCR using the ABI PRISM 7700 (Perkin Elmer), a new technique which allows simple and rapid quantification of a target sequence during the extension phase of PCR amplifications. A fluorogenic probe labeled with both a reporter dye at the 5' end and a quencher-dye at the 3' end hybridizes to the target sequence on the third exon of the ABL gene. The exonuclease activity of the Taq DNA polymerase cleaves the probe and releases the reporter dye, resulting in an increase in the fluorescence signal. The absolute copy number of the target sequence (BCR-ABL) or a control gene (ABL) in an unknown sample can then be calculated using a calibration curve prepared from a set of BCR-ABL RNA standards, and results are expressed as a BCR-ABL/ABL ratio. In our hands, the sensitivity of a serial dilution of total RNA from a positive cell line (K562) in a negative cell line (HL60) was 10(-4). Fifteen CML patients in cytogenetic CR, including 11 allografted patients, two autografted patients and two patients treated by IFN were studied sequentially by this new real time quantitative RT-PCR technique in parallel with conventional qualitative two round nested RT-PCR. The two autografted patients showed high BCR-ABL/ABL ratio in all samples. The two patients treated by IFN showed a progressive decrease in the ratio. In the 11 allografted patients, four were sequentially studied 2 years or more after allo-BMT, and all ratios were below 10(-4). The four patients remained in clinical and cytogenetic CR. The seven other allografted patients were studied immediately after the procedure. Three of them showed a progressive decrease in the BCR-ABL/ABL ratio which reached 10(-4) 7 months after allo-BMT. The three patients remained in hematologic and cytogenetic CR. The remaining four allografted patients had progressive increase of BCR-ABL ratio; three developed cytogenetic relapse 9, 11, 28 months after allo-BMT, and the last patient remained in cytogenetic CR in the bone marrow but developed granulocytic sarcoma. Results of real-time quantitative RT-PCR were in agreement with those of qualitative two round nested PCR. However, evolution changes in the results of real-time quantitative RT-PCR often preceded those of the conventional technique: a decrease of the BCR-ABL/ABL ratio preceded progression from first round to second round positivity and then negativity with the classical technique; conversely, an increase in the ratio preceded evolution with the classical technique. Thus, real-time quantitative RT-PCR may show better correlation with clinical and cytogenetic evolution than conventional qualitative techniques and may help in making early therapeutic decisions in CML, especially after molecular relapse.