Transformation of real-time PCR fluorescence data to target gene quantity

Interrogating nitritation at a molecular level: Understanding the potential influence of Nitrobacter spp

Water resource recovery facilities (WRRFs) increasingly must maximize nitrogen and phosphorus removal, but concurrently face challenges to reduce their energy usage and environmental footprint. In particular, biological nutrient removal (BNR), which targets removal of phosphorus and nitrogen, exhibits a large energy demand. However, a BNR process achieving partial oxidation of NH₃ to NO₂ (nitritation) could reduce energy demands, with secondary environmental emission benefits. Research was conducted on bench-scale systems performing nitritation and nitrification to better understand how mixed microbial consortia, cultured on real wastewater, can sustain nitritation. BNR configurations achieved nitrite accumulation ratios of 64-82%, with excellent overall effluent quality. Applying phylogenetic, transcriptomic, and metabolomic methods, coupled with process monitoring, results indicate that partial nitritation may be induced through a combination of: (1) Employing ammonia-based aeration control, with an ammonia setpoint of 2, 3 mgN/L; (2) Maintaining an aerobic period DO of 1.0-2.0 mg/L; and (3) Operating BNR post-anoxically, integrated within enhanced biological phosphorus removal (EBPR). Significant nitritation was achieved despite the presence Nitrobacter spp., but nitrite oxidoreductase must be functionally impaired or structurally incomplete. Overall, this research demonstrated the value of interrogating a mixed microbial consortia at a macro and molecular level to explore unique metabolic responses such as nitritation.

Multiple Compact Camera Fluorescence Detector for Real-Time PCR Devices

The polymerase chain reaction is an important technique in biological research because it tests for diseases with a small amount of DNA. However, this process is time consuming and can lead to sample contamination. Recently, real-time PCR techniques have emerged which make it possible to monitor the amplification process for each cycle in real time. Existing camera-based systems that measure fluorescence after DNA amplification simultaneously process fluorescence excitation and emission for dozens of tubes. Therefore, there is a limit to the size, cost, and assembly of the optical element. In recent years, imaging devices for high-performance, open platforms have benefitted from significant innovations. In this paper, we propose a fluorescence detector for real-time PCR devices using an open platform camera. This system can reduce the cost, and can be miniaturized. To simplify the optical system, four low-cost, compact cameras were used. In addition, the field of view of the entire tube was minimized by dividing it into quadrants. An effective image processing method was used to compensate for the reduction in the signal-to-noise ratio. Using a reference fluorescence material, it was confirmed that the proposed system enables stable fluorescence detection according to the amount of DNA.

Apoptotic cells in mouse blastocysts are eliminated by neighbouring blastomeres

Apoptosis is a physiological process that occurs commonly during the development of the preimplantation embryo. The present work examines the ability of apoptotic embryonic cells to express a signal promoting their phagocytosis, and quantifies the ability of neighbouring, normal embryonic cells to perform that task. Microscopic analysis of mouse blastocysts revealed phosphatidylserine externalization to be 10 times less common than incidence of apoptotic cells (as detected by TUNEL). In spite of the low frequency of phosphatidylserine-flipping (in inner cell mass, no annexin V staining was recorded), fluorescence staining of the plasma membrane showed more than 20% of apoptotic cells to have been engulfed by neighbouring blastomeres. The mean frequency of apoptotic cells escaping phagocytosis by their extrusion into blastocyst cavities did not exceed 10%. Immunochemically visualised RAC1 (an enzyme important in actin cytoskeleton rearrangement) was seen in phagosome-like structures containing a nucleus with a condensed morphology. Gene transcript analysis showed that the embryonic cells expressed 12 receptors likely involved in phagocytic process (Scarf1, Msr1, Cd36, Itgav, Itgb3, Cd14, Scarb1, Cd44, Stab1, Adgrb1, Cd300lf, Cd93). In conclusion, embryonic cells possess all the necessary mechanisms for recognising, engulfing and digesting apoptotic cells, ensuring the clearance of most dying blastomeres.

Different response of embryos originating from control and obese mice to insulin in vitro

The aim of the present work was to investigate the impact of maternal obesity on DNA methylation in ovulated oocytes, and to compare the response of in vitro-developing preimplantation embryos originating from control and obese mice to insulin. An intergenerational, diet-induced obesity model was used to produce outbred mice with an increased body weight and body fat. Two-cell and eight-cell embryos recovered from obese and control mice were cultured in a medium supplemented with 1 or 10 ng/ml insulin until blastocyst formation. In the derived blastocysts, cell proliferation, differentiation, and death rates were determined. The results of immunochemical visualization of 5-methylcytosine indicated a slightly higher DNA methylation in ovulated metaphase II oocytes recovered from obese females; however, the difference between groups did not reach statistical significance. Expanded blastocysts developed from embryos provided by control dams showed increased mean cell numbers (two and eight-cell embryos exposed to 10 ng/ml), an increased inner-cell-mass/trophectoderm ratio (two-cell embryos exposed to 1 ng/ml and eight-cell embryos exposed to 10 ng/ml), and a reduced level of apoptosis (two and eight-cell embryos exposed to 10 ng/ml). In contrast, embryos originating from obese mice were significantly less sensitive to insulin; indeed, no difference was recorded in any tested variable between the embryos exposed to insulin and those cultured in insulin-free medium. Real-time RT-PCR analysis showed a significant increase in the amount of insulin receptor transcripts in blastocysts recovered from obese dams. These results suggest that maternal obesity might modulate the mitogenic and antiapoptotic responses of preimplantation embryos to insulin.

Glucocorticoid receptor isoforms and effects of glucocorticoids in ovulated mouse oocytes and preimplantation embryos†

To investigate possible involvement of glucocorticoid receptor (GR) in mediating effects of maternal stress or therapeutically administered glucocorticoids on early embryo, we analyzed the expression of GR subtypes in ovulated mouse oocytes and preimplantation embryos. RT-PCR analysis results showed that GRα and GRγ transcripts are relatively highly expressed in mouse oocytes, and both transcripts are present at lower amounts in preimplantation embryos. We also detected low expression of two other splice variants, GRβ and a transcript orthologous to the human GR-P subtype, mainly at the blastocyst stage. Using western blot analysis, we detected several GR protein bands that differed in size between oocytes and preimplantation embryos. To compare the effects of corticosterone (a major endogenous glucocorticoid in rodents) and dexamethasone (a synthetic glucocorticoid) on early embryos, we cultured mouse preimplantation embryos in the presence of these glucocorticoids. Corticosterone showed a strong inhibitory effect on embryo development (starting from a 50 μM concentration), without a significant influence on apoptosis incidence. On the other hand, dexamethasone induced apoptosis in early embryo cells (starting from a 1.5 μM concentration), and its effect on embryo development was less detrimental than that found with the same dose of corticosterone. In summary, our results showed that different GR subtypes are expressed in ovulated mouse oocytes and preimplantation embryos and that the composition of GR subtypes changes during early embryo development. Moreover, we found significant differences in the effects of the two glucocorticoids on early embryo development, which might be associated with activation of different GR subtypes.

Intrafollicular paraoxonase 1 activity and the steroidogenic potential of the first post-partum dominant follicle in dairy cows

Cows experiencing high levels of inflammation and specific metabolic conditions tend to have slower follicular growth and lower serum and follicular concentrations of oestradiol (E2). Paraoxonase1 (PON1) activity decreases during inflammatory processes. Therefore, the aim of this study was to evaluate the association between serum and intrafollicular (FF) PON1 activity and the serum and intrafollicular levels of E2 and progesterone (P4), as well as the mRNA expression of genes related to steroidogenesis, metabolism and inflammation in the first post-partum dominant follicle of Holstein cows. No correlation was found between PON1 activity, the expression of the analysed genes and levels of follicular E2 and P4, except for a negative correlation between serum E2 and follicular PO1 activity. Also, no correlation was found between serum and follicular PON1 during the first post-partum follicular wave.

Evaluation-independent system for DNA section amplification

Background

In general, the image analysis of nucleic acid for detecting DNA is dependent on the gel documentation system. These experiments may deal with harmful staining agents and are time consuming. To address these issues, real-time polymerase chain reaction (PCR) devices have been developed. The advantages of real-time PCR are its capabilities for real-time diagnosis, improved sensitivity, and digitization of measurement results. However, real-time PCR equipment is still too bulky and expensive for use in small hospitals and laboratories.

Methods

This paper describes an evaluation-independent real-time PCR system that differs from conventional systems in that it uses a side-illumination optical detection system and a temperature adjustment coefficient for DNA detection. The overall configuration of the evaluation-independent system includes the PCR chip and system hardware and software. The use of the side-illumination method for detection enables the system size to be reduced compared to systems using a typical illumination method. Furthermore, the results of a PCR test are strongly affected by the reaction temperature. Thus, extremely precise control of the temperature of the reaction is needed to obtain accurate results and good reliability. We derived a temperature compensation coefficient that allows us to compensate for the differences between the measured temperature of the negative temperature coefficient (NTC) thermistor sensor and the real temperature of the thermocouple.

Results

Applying the temperature compensation coefficient parameter using the NTC thermistor and using the side-illumination method resulted in an increase in the initial sensor value. The occurrence of the DNA section amplification decreased to 22 cycles from 24 cycles.

Conclusions

The proposed system showed comparable performance to that of an existing real-time PCR, even with the use of simpler and smaller optical devices.

Analysis and Normalization of Real-Time Polymerase Chain Reaction (PCR) Experimental Data

In real-time polymerase chain reaction (PCR), also called quantitative real-time PCR [or simply quantitative PCR (qPCR)] or kinetic PCR, the amplification of DNA is monitored by the detection and quantitation of a fluorescent reporter signal, which increases in direct proportion to the amount of PCR product in the reaction. The fluorescent reporter is excited by light from the real-time PCR machine, a fluorescence-detecting thermocycler. By recording the amount of fluorescence emission at each cycle, the PCR can be monitored during the exponential phase when the first significant increase in the amount of PCR product correlates with the initial amount of target template. The ability to quantify the amplified DNA during the exponential phase of the PCR, when none of the components of the reaction is limiting, has resulted in dramatically improved precision in the quantitation of target sequences. In addition, because of the high sensitivity of fluorometric detection, real-time PCR is capable of measuring the initial concentration of target DNA over a vast dynamic range (up to eight or nine orders of magnitude) and with a high degree of sensitivity (as little as one copy of template DNA). Although it is a powerful technique, researchers often face challenges in reliability and reproducibility because of the lack of assay standardization. Therefore, it is critical to optimize the reagents and reaction conditions, include proper internal and external controls, and perform rigorous data analysis in order to generate accurate and reproducible results in real-time PCR experiments.

Analysis of menstrual effluent: diagnostic potential for endometriosis

BACKGROUND

Endometriosis is a chronic and underdiagnosed disease which affects 5-10% of women of childbearing age and is characterized by growth of endometrial tissue outside of the uterus, most often in the peritoneal cavity. Delay in diagnosis is a major problem for management of this disorder, and treatment is often not initiated until the disease has progressed for many years. Although the exact etiology of endometriosis remains unknown, retrograde menstruation is recognized as a common underlying factor leading to the deposit of menstrual effluent (ME) into the peritoneal cavity. Differences in the cellular biology and genetics of the cells within ME are therefore likely to explain why endometriosis develops in only a subset of women.

METHODS

Patients with and without endometriosis were consented to provide ME. ME was analyzed by flow cytometry for CD45- and CD45+ cell populations or used to isolate stromal fibroblast cells. ME-derived stromal fibroblast cells were assessed using decidualization assays following the addition of cAMP and IGFBP-1 concentrations in the culture supernatants were measured by ELISA. In addition, RNA was collected and analyzed by RNA-Seq and qPCR for markers of decidualization and to identify differentially expressed genes in ME-derived stromal fibroblast cells obtained from controls and subjects with endometriosis (±cAMP).

RESULTS

Flow cytometry analysis of cell subsets within the CD45+ fraction of ME revealed a significant decrease in the number of uterine NK cells in endometriosis patients compared with controls (p < 0.01). No other significant differences within either the CD45+ or CD45- cell populations were observed. Most strikingly, ME-derived stromal fibroblast cells cultured from endometriosis subjects showed impaired decidualization potential compared with controls. Highly significant differences in decidualization response were detected by measuring IGFBP-1 production at multiple time points after cAMP stimulation (p = 0.0025 at 6 h; p = 0.0045 at 24 h; p = 0.0125 at 48 h). RNA-Seq and qPCR analyses were used to identify genes differentially expressed by ME-derived stromal fibroblast cells obtained from endometriosis and control subjects.

CONCLUSIONS

Menstrual effluent can be useful for investigating the pathobiology of endometriosis and for developing a non-invasive diagnostic for endometriosis which may lead to earlier and more effective treatments for this common disorder.

Comparative transcriptome analysis of the calcium signaling and expression analysis of sodium/calcium exchanger in Aspergillus cristatus

Aspergillus cristatus develops into various stages under different Na concentrations: the sexual stage in 0.5 M NaCl and asexual development stage in 3 M NaCl. In order to explore whether the Ca²⁺ signaling pathway in A. cristatus responded to the changes in the salt stress, we analyzed the gene expression levels in A. cristatus respectively cultured in 0.5 M NaCl and 3 M NaCl. According to the BLAST analysis results, we identified 25 Ca²⁺ -signaling proteins in A. cristatus. The expression levels of most genes involved in the Ca²⁺ -signaling pathway in A. cristatus cultured in different salt concentrations showed significant differences, indicating that the Ca²⁺ signaling pathway was involved in the response to the changes in the salt stress. In yeasts, only calcium ion influx proteins were reported to be involved in the response to the changes in the salt stress. So far, the protein for the exchanger of calcium/sodium ions has not been reported. Therefore, we obtained the sodium/calcium exchanger (termed NCX) proteins from the KEGG Database. The ncx gene of A. cristatus was cloned and characterized. The full length of ncx gene is 3055 bp, including a 2994-bp open reading frame encoding 994 amino acids. The expression levels of ncx in the sexual development stage and asexual development stage were respectively ∼8.94 times and ∼2.57 times of that in the hyphal formation stage. Therefore, we suggested that ncx gene was up-regulated to resist the sodium stress. The study results provide the basis for further exploring the Ca²⁺ -signaling mechanism and ion exchanger mechanism.

Effect of bovine somatotropin injection in late pregnant Holstein heifers on metabolic parameters and steroidogenic potential of the first postpartum dominant follicle

The aim of this study was to determine the effect of pre-partum injections of bovine somatotropin (bST) in dairy heifers on metabolic markers and the steroidogenic potential of the first postpartum dominant follicle. Heifers were assigned to two groups: bST (ST; n = 29), that received two doses of bST (500 mg/dose) at -28 and -14 days relative to calving; and control (CTL; n = 30), that did not received bST. Follicular development was monitored via ultrasound every 3 days starting at 8 days in milk (DIM) in a subset of 20 heifers until the day the first large follicle reached a diameter of 16 mm. From these cows follicular fluid was aspirated and the follicular cells recovered (ST; n = 8 and CTL; n = 10). Blood samples were collected weekly for all heifers. Follicular fluid IGF-I concentrations of the first postpartum dominant follicle was higher (P = 0.05) in ST (87.1 ± 7.7 mg/mL) than CTL cows (64.3 ± 6.8 mg/mL). Also, E2 concentration in the follicular fluid was higher (P = 0.02) for ST (199.7 ± 55.9 ng/mL) than CTL cows (74.5 ± 37.7 ng/mL). The expression of LHCGR and STAR mRNA in follicular cells was higher (P < 0.05) in ST than CTL cows. Nonetheless, HSD3B, P450scc, P450c17, IGFr and CYP19A1 mRNA expression was not different between groups (P > 0.05). Serum IGF-I concentration was higher in ST treated heifers during the pre-partum period (P = 0.01) and no difference was observed in the postpartum period (P = 0.19). In conclusion, pre-partum bST treatment in dairy heifers increased intrafollicular IGF-I and expression of LHCGR and STAR mRNA in follicular cells of the first postpartum dominant follicle. These changes were associated to increased intrafollicular and serum E2 concentration, which can potentially increase the chance of ovulation of the first follicular wave.

Dairy manure resource recovery utilizing two-stage anaerobic digestion - Implications of solids fractionation

Dairy manure management is increasingly becoming an environmental challenge. In this regard, manure anaerobic digestion (AD) can be applied to address environmental concerns; however, dairy manure AD remains economically uncompetitive. Ongoing research is focused on enhanced resource recovery from manure, including maximizing AD methane yield through a novel multi-stage AD configuration. Research presented herein centered on the hypothesis that separately digesting fine and coarse solids from fermented dairy manure would improve methane production; the hypothesis was disproven. While maximum methane concentration was realized on fine solids, combined solids AD yielded enhanced VS destruction. The diverse combined-solids substrate enriched for a more heterogeneous bacterial/archaeal consortium that balanced fermentation and methanogenesis to yield maximum product (methane). However, results suggest that targeted AD of the fat-rich fine solids could be a more optimal approach for processing manure; alternate (non-AD) methods could then be applied to extract value from the fibrous fraction.

Diurnal Variation Has Effect on Differential Gene Expression Analysis in the Hippocampus of the Pilocarpine-Induced Model of Mesial Temporal Lobe Epilepsy

The molecular mechanisms underlying epileptogenesis have been widely investigated by differential gene expression approach, especially RT-qPCR methodology. However, controversial findings highlight the occurrence of unpredictable sources of variance in the experimental designs. Here, we investigated if diurnal rhythms of transcript's levels may impact on differential gene expression analysis in hippocampus of rats with experimental epilepsy. For this, we have selected six core clock genes (Per1, Per3, Bmal1, Clock, Cry1 and Cry2), whose rhythmic expression pattern in hippocampus had been previously reported. Initially, we identified Tubb2a/Rplp1 and Tubb2a/Ppia as suitable normalizers for circadian studies in hippocampus of rats maintained to 12:12 hour light:dark (LD) cycle. Next, we confirmed the temporal profiling of Per1, Per3, Bmal1, Cry1 and Cry2 mRNA levels in the hippocampus of naive rats by both Acrophase and CircWave statistical tests for circadian analysis. Finally, we showed that temporal differences of sampling can change experimental results for Per1, Per3, Bmal1, Cry1 and Cry2, but not for Clock, which was consistently decreased in rats with epilepsy in all comparison to the naive group. In conclusion, our study demonstrates it is mandatory to consider diurnal oscillations, in order to avoid erroneous conclusions in gene expression analysis in hippocampus of rats with epilepsy. Investigators, therefore, should be aware that genes with circadian expression could be out of phase in different animals of experimental and control groups. Moreover, our results indicate that a sub-expression of Clock may be involved in epileptogenicity, although the functional significance of this remains to be investigated.

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay

BACKGROUND

The community structure of bacteria in aged and aging pit mud, which was judged according to their sensory and physicochemical characteristics, was analysed using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR).

RESULTS

The phyla Firmicutes, Actinobacteria, Proteobacteria, Synergistetes and Unclassified Bacteria were detected and the fermentative Firmicutes was predominant in both types of pit mud in the PCR-DGGE analysis. Among Firmicutes, Clostridiales was dominant in aged pit mud while Bacillales and Lactobacillales were dominant in aging pit mud. The diversity of bacterial communities in aged pit mud was higher than that in aging pit mud. In the qPCR analysis the abundance of Clostridium IV in aged pit mud was higher than that in aging pit mud and there were significant differences in the quantity of Clostridium IV between aged and aging pit mud of the same cellar (P < 0.05).

CONCLUSION

There were some significant differences in the microbial community structure between aged and aging pit mud. The differences in the quantity of Clostridium IV might be involved in the distinction that the aged pit mud has a strong aroma while the aging pit mud does not.

Evaluation of eight reference genes for quantitative polymerase chain reaction analysis in human T lymphocytes co‑cultured with mesenchymal stem cells

Accurate gene expression analysis relies on the selection of a stable reference gene, as unstable reference genes can alter experimental results and conclusions. It is widely‑accepted that reference genes exhibit different expression levels in different types of tissues and cells. Therefore, it is essential to screen for stably‑expressed reference genes in the cells and tissues used for experimental analysis prior to performing reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). In the present study, eight reference genes were screened for their suitability for RT‑qPCR in five T lymphocytes co‑cultured with mesenchymal stem cells from different sources. Using NormFinder, geNorm, and BestKeeper algorithms consistently demonstrated that RPL13A and B2M were the optimal reference genes for the normalization of RT‑qPCR data obtained from T lymphocytes, whereas glyceraldehyde 3‑phosphate dehydrogenase was not a suitable reference gene due to its extensive variability in expression. These findings highlight the importance of evaluating reference genes for RT‑qPCR.

miR-21 promotes renal fibrosis in diabetic nephropathy by targeting PTEN and SMAD7

The cytokine transforming growth factor (TGF)-β1 plays a central role in diabetic nephropathy (DN) with data implicating the miRNA (miR) miR-21 as a key modulator of its prosclerotic actions. In the present study, we demonstrate data indicating that miR-21 up-regulation positively correlates with the severity of fibrosis and rate of decline in renal function in human DN. Furthermore, concomitant analyses of various models of fibrotic renal disease and experimental DN, confirm tubular miR-21 up-regulation. The fibrotic changes associated with increased miR-21 levels are proposed to include the regulation of TGF-β1-mediated mothers against decapentaplegic homolog 3 (SMAD3)- and phosphoinositide 3-kinase (PI3K)-dependent signalling pathways via co-ordinated repression of mothers against decapentaplegic homolog 7 (SMAD7) and phosphatase and tensin homologue (PTEN) respectively. This represents a previously uncharacterized interaction axis between miR-21 and PTEN-SMAD7. Targeting of these proteins by miR-21 resulted in de-repression of the respective pathways as reflected by increases in SMAD3 and V-Akt murine thymoma viral oncogene homolog 1 (AKT) phosphorylation. Many of the changes typically induced by TGF-β1, including phosphorylation of signalling mediators, were further enhanced by miR-21. Collectively, these data present a unified model for a key role for miR-21 in the regulation of renal tubular extracellular matrix (ECM) synthesis and accumulation and provide important insights into the molecular pathways implicated in the progression of DN.

Identification of endogenous reference genes for the analysis of microRNA expression in the hippocampus of the pilocarpine-induced model of mesial temporal lobe epilepsy

Real-time quantitative RT-PCR (qPCR) is one of the most powerful techniques for analyzing miRNA expression because of its sensitivity and specificity. However, in this type of analysis, a suitable normalizer is required to ensure that gene expression is unaffected by the experimental condition. To the best of our knowledge, there are no reported studies that performed a detailed identification and validation of suitable reference genes for miRNA qPCR during the epileptogenic process. Here, using a pilocarpine (PILO) model of mesial temporal lobe epilepsy (MTLE), we investigated five potential reference genes, performing a stability expression analysis using geNorm and NormFinder softwares. As a validation strategy, we used each one of the candidate reference genes to measure PILO-induced changes in microRNA-146a levels, a gene whose expression pattern variation in the PILO injected model is known. Our results indicated U6SnRNA and SnoRNA as the most stable candidate reference genes. By geNorm analysis, the normalization factor should preferably contain at least two of the best candidate reference genes (snoRNA and U6SnRNA). In fact, when normalized using the best combination of reference genes, microRNA-146a transcripts were found to be significantly increased in chronic stage, which is consistent with the pattern reported in different models. Conversely, when reference genes were individually employed for normalization, we failed to detect up-regulation of the microRNA-146a gene in the hippocampus of epileptic rats. The data presented here support that the combination of snoRNA and U6SnRNA was the minimum necessary for an accurate normalization of gene expression at the different stages of epileptogenesis that we tested.

Comparing real-time quantitative polymerase chain reaction analysis methods for precision, linearity, and accuracy of estimating amplification efficiency

New methods are used to compare seven qPCR analysis methods for their performance in estimating the quantification cycle (Cq) and amplification efficiency (E) for a large test data set (94 samples for each of 4 dilutions) from a recent study. Precision and linearity are assessed using chi-square (χ(2)), which is the minimized quantity in least-squares (LS) fitting, equivalent to the variance in unweighted LS, and commonly used to define statistical efficiency. All methods yield Cqs that vary strongly in precision with the starting concentration N0, requiring weighted LS for proper calibration fitting of Cq vs log(N0). Then χ(2) for cubic calibration fits compares the inherent precision of the Cqs, while increases in χ(2) for quadratic and linear fits show the significance of nonlinearity. Nonlinearity is further manifested in unphysical estimates of E from the same Cq data, results which also challenge a tenet of all qPCR analysis methods - that E is constant throughout the baseline region. Constant-threshold (Ct) methods underperform the other methods when the data vary considerably in scale, as these data do.

Validation of suitable reference genes for expression studies in different pilocarpine-induced models of mesial temporal lobe epilepsy

It is well recognized that the reference gene in a RT-qPCR should be properly validated to ensure that gene expression is unaffected by the experimental condition. We investigated eight potential reference genes in two different pilocarpine PILO-models of mesial temporal lobe epilepsy (MTLE) performing a stability expression analysis using geNorm, NormFinder and BestKepeer softwares. Then, as a validation strategy, we conducted a relative expression analysis of the Gfap gene. Our results indicate that in the systemic PILO-model Actb, Gapdh, Rplp1, Tubb2a and Polr1a mRNAs were highly stable in hippocampus of rats from all experimental and control groups, whereas Gusb revealed to be the most variable one. In fact, we observed that using Gusb for normalization, the relative mRNA levels of the Gfap gene differed from those obtained with stable genes. On the contrary, in the intrahippocampal PILO-model, all softwares included Gusb as a stable gene, whereas B2m was indicated as the worst candidate gene. The results obtained for the other reference genes were comparable to those observed for the systemic Pilo-model. The validation of these data by the analysis of the relative expression of Gfap showed that the upregulation of the Gfap gene in the hippocampus of rats sacrificed 24 hours after status epilepticus (SE) was undetected only when B2m was used as the normalizer. These findings emphasize that a gene that is stable in one pathology model may not be stable in a different experimental condition related to the same pathology and therefore, the choice of reference genes depends on study design.

Occurrence and genetic diversity of Arcobacter spp. in a spinach-processing plant and evaluation of two Arcobacter-specific quantitative PCR assays

Some species of the genus Arcobacter are considered to be emerging food pathogens. With respect to recent vegetable-borne outbreaks, the aim of this work was to investigate the occurrence and diversity of Arcobacter within the production chain of a spinach-processing plant by a combination of cultivation and molecular methods. Samples including spinach, water, and surface biofilm were taken over a period of three years from the entire processing line. Ten 16S rRNA (rrs) gene clone libraries were constructed and analysed using amplified rRNA gene restriction analysis (ARDRA). Approximately 1200 clones were studied that resulted in 44 operational taxonomic units (OTUs). Sequences with high similarities to Arcobacter cryaerophilus (13% of clones, 3 OTUs), A. ellisii (4%, 6 OTUs), A. suis (15%, 3 OTUs), and the type strain of A. nitrofigilis (1%, 7 OTUs) were identified. This represents the first report of the detection of the recently described species A. ellisii, A. suis and, in addition, A. venerupis from alternative habitats. A total of 67% of the clones (22 OTUs) could not be assigned to a genus, which indicated the presence of uncharacterised Arcobacter species. For the cultivation-independent detection of Arcobacter, two genus-specific quantitative PCR (qPCR) assays were developed and tested on 15 Arcobacter species. When these assays were applied to samples from the spinach-processing plant, they showed positive results for up to 35% of the samples and supported the conclusion that there is a considerable risk for the transfer of pathogenic Arcobacter species on vegetables, which was also verified by a cultivation approach.

Prevalence and burden of two rickettsial phylotypes (G021 and G022) in Ixodes pacificus from California by real-time quantitative PCR

The western black-legged tick, Ixodes pacificus Cooley and Kohls, commonly bites humans in the far western U.S. In addition to transmitting Lyme borreliosis and anaplasmosis, it is a host of nonpathogenic bacteria as well as some of unknown pathogenicity. In this study, we report the detection, prevalence, and burden of 2 rickettsial phylotypes with unknown pathogenicity in I. pacificus ticks from 6 California counties using real-time quantitative PCR with phylotype-specific primers and probes. Prevalence of rickettsial phylotypes G021 and G022 from 247 I. pacificus ticks was 100% and 2.0%, respectively. The median burden of phylotype G021 was 7.3 per tick cell, whereas the burden of phylotype G022 was 0.8 per tick cell. The burden of phylotype G021 significantly differed between collection sites and between vegetation habitats. Ticks collected from the coastal sage scrub habitat of southern California had a lower burden of phylotype G021 when compared to central California oak woodland, northern California oak woodland, and mixed evergreen and ponderosa pine-oak habitats of northern California. No significant correlation was found between the burden of the phylotype G021 in the presence and absence of the phylotype G022 in I. pacificus, suggesting that the presence of these Rickettsia species do not interfere with each other in I. pacificus.

Effect of exogenous insulin and fasting on growth hormone receptor and IGF-I expression in the pre-ovulatory follicle of ewes

The aim of this study was to investigate the effect of fasting and exogenous insulin administration on the expression of growth hormone receptor (GHR) and IGF-I mRNA in the pre-ovulatory follicle of ewes. Fifteen ewes received an intravaginal progesterone releasing device that was removed 6 days later (day of removal = day 0). On day -2, the ewes were divided into three groups: (i) fasting group (n = 5) that was fasted from day -2 to day 2; (ii) control group (n = 5) that received a maintenance diet; and (iii) insulin group (n = 5) that received insulin injections (0.25 IU/kg) every 12 h from day -2 to day 2 under the same diet as the control group. Follicular samples were obtained on day 2. Fasting increased plasma non-esterified fatty acids concentrations from day -1 to day 2 (P < 0.001). There was no difference (P > 0.05) in the number of follicles, although there was a tendency for an increase in the pre-ovulatory follicle diameter for the insulin group in comparison to the control group (P = 0.12). Thecal GHR mRNA expression was very low and was considered insignificant. Moreover, granulosa cells GHR mRNA expression increased (P < 0.05) in the insulin group. Expression of IGF-I mRNA was not different among groups in both tissues. In conclusion, insulin administration increases GHR mRNA but not IGF-I mRNA expression in granulosa cells of the pre-ovulatory follicle. However, fasting did not change the pattern of GHR/IGF-I mRNA expression in the pre-ovulatory follicle.

Adiponectin and its receptors in preimplantation embryo development

Adiponectin can play an important role in regulating the female reproductive function and embryo development and can affect the embryo at very early stages of pregnancy--during the preimplantation period. Disturbances in the maternal adiponectin system are associated with several diseases, including diabetes type 2, obesity, and some female reproductive disorders. Adiponectin receptors are expressed in oocytes and preimplantation embryos and can be activated by adiponectin produced by maternal adipose tissue or organs of the female reproductive tract. Adiponectin can affect proliferation and survival of cells in preimplantation embryos, and these effects are isoform dependent. Experimental results suggest involvement of various protein kinases, including mitogen-activated protein kinases, in the regulation of these processes by adiponectin. Actions of adiponectin on lipid and glucose metabolism can increase the energy supply to the embryo, and final targets of adiponectin signaling are metabolic enzymes, glucose transporters, and fatty acid transporters. The involvement of several signaling molecules, such as AMPK/PRKA, PI3K, or AKT/PKB, in the regulation of metabolic processes by adiponectin has been demonstrated in preimplantation embryos. In summary, adiponectin produced in an endocrine/paracrine/autocrine manner can significantly influence preimplantation embryo development, uterine receptivity, and embryo implantation.

Quantification of trace-level DNA by real-time whole genome amplification

Quantification of trace amounts of DNA is a challenge in analytical applications where the concentration of a target DNA is very low or only limited amounts of samples are available for analysis. PCR-based methods including real-time PCR are highly sensitive and widely used for quantification of low-level DNA samples. However, ordinary PCR methods require at least one copy of a specific gene sequence for amplification and may not work for a sub-genomic amount of DNA. We suggest a real-time whole genome amplification method adopting the degenerate oligonucleotide primed PCR (DOP-PCR) for quantification of sub-genomic amounts of DNA. This approach enabled quantification of sub-picogram amounts of DNA independently of their sequences. When the method was applied to the human placental DNA of which amount was accurately determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES), an accurate and stable quantification capability for DNA samples ranging from 80 fg to 8 ng was obtained. In blind tests of laboratory-prepared DNA samples, measurement accuracies of 7.4%, -2.1%, and -13.9% with analytical precisions around 15% were achieved for 400-pg, 4-pg, and 400-fg DNA samples, respectively. A similar quantification capability was also observed for other DNA species from calf, E. coli, and lambda phage. Therefore, when provided with an appropriate standard DNA, the suggested real-time DOP-PCR method can be used as a universal method for quantification of trace amounts of DNA.

1-Million droplet array with wide-field fluorescence imaging for digital PCR

Digital droplet reactors are useful as chemical and biological containers to discretize reagents into picolitre or nanolitre volumes for analysis of single cells, organisms, or molecules. However, most DNA based assays require processing of samples on the order of tens of microlitres and contain as few as one to as many as millions of fragments to be detected. Presented in this work is a droplet microfluidic platform and fluorescence imaging setup designed to better meet the needs of the high-throughput and high-dynamic-range by integrating multiple high-throughput droplet processing schemes on the chip. The design is capable of generating over 1-million, monodisperse, 50 picolitre droplets in 2-7 minutes that then self-assemble into high density 3-dimensional sphere packing configurations in a large viewing chamber for visualization and analysis. This device then undergoes on-chip polymerase chain reaction (PCR) amplification and fluorescence detection to digitally quantify the sample's nucleic acid contents. Wide-field fluorescence images are captured using a low cost 21-megapixel digital camera and macro-lens with an 8-12 cm(2) field-of-view at 1× to 0.85× magnification, respectively. We demonstrate both end-point and real-time imaging ability to perform on-chip quantitative digital PCR analysis of the entire droplet array. Compared to previous work, this highly integrated design yields a 100-fold increase in the number of on-chip digitized reactors with simultaneous fluorescence imaging for digital PCR based assays.

Selection of reference genes for qRT-PCR in high fat diet-induced hepatic steatosis mice model

With the epidemic proportions of obesity worldwide and the concurrent prevalence of hepatic steatosis, there is an urgent need for better understanding the intrinsic mechanism of hepatic steatosis, especially the changes of gene expression underlying the development of hepatic steatosis and its associated abnormal liver function. Quantitative real-time PCR (qRT-PCR) is a sensitive and highly reproducible technique of gene expression analysis. However, for accurate and reliable gene expression results, it is vital to have an internal control gene expressed at constant levels under all the experimental conditions being analyzed for. In this study, the authors validated candidate reference genes suitable for qRT-PCR profiling experiments using livers from control mice and high fat diet-induced obese mice. Cross-validation of expression stability of ten selected reference genes using three popular algorithms, GeNorm, NormFinder, and BestKeeper found HPRT1 and GAPDH as most stable reference genes. Thus, HPRT1 and GAPDH are recommended as stable reference genes most suitable for gene expression studies in the development of hepatic steatosis.

A mechanistic model of PCR for accurate quantification of quantitative PCR data

BACKGROUND

Quantitative PCR (qPCR) is a workhorse laboratory technique for measuring the concentration of a target DNA sequence with high accuracy over a wide dynamic range. The gold standard method for estimating DNA concentrations via qPCR is quantification cycle () standard curve quantification, which requires the time- and labor-intensive construction of a standard curve. In theory, the shape of a qPCR data curve can be used to directly quantify DNA concentration by fitting a model to data; however, current empirical model-based quantification methods are not as reliable as standard curve quantification.

PRINCIPAL FINDINGS

We have developed a two-parameter mass action kinetic model of PCR (MAK2) that can be fitted to qPCR data in order to quantify target concentration from a single qPCR assay. To compare the accuracy of MAK2-fitting to other qPCR quantification methods, we have applied quantification methods to qPCR dilution series data generated in three independent laboratories using different target sequences. Quantification accuracy was assessed by analyzing the reliability of concentration predictions for targets at known concentrations. Our results indicate that quantification by MAK2-fitting is as reliable as standard curve quantification for a variety of DNA targets and a wide range of concentrations.

SIGNIFICANCE

We anticipate that MAK2 quantification will have a profound effect on the way qPCR experiments are designed and analyzed. In particular, MAK2 enables accurate quantification of portable qPCR assays with limited sample throughput, where construction of a standard curve is impractical.

Expression of adiponectin receptors and effects of adiponectin isoforms in mouse preimplantation embryos

BACKGROUND

Adiponectin, a pleiotropic hormone secreted from adipose tissue, can mediate some negative effects of obesity on female health, and can participate in the impaired reproductive performance of obese women. Using a mouse model, we investigated expression of adiponectin receptors in ovulated oocytes and in vivo derived preimplantation embryos, and tested effects of different adiponectin isoforms on development of preimplantation embryos in vitro.

METHODS AND RESULTS

Using RT-PCR and immunohistochemistry, we found expression of adiponectin receptors AdipoR1 and AdipoR2, at the mRNA and protein level, in mouse ovulated oocytes and preimplantation embryos. Quantitative real-time RT-PCR analysis showed a decrease in the amount of AdipoR1 and AdipoR2 mRNA after fertilization, which was followed by an increase in mRNA at the morula and blastocyst stage; mRNA for adiponectin was detected only at the blastocyst stage. Administration of full-length adiponectin significantly changed the distribution in numbers of cells of cultured preimplantation embryos, increasing the proportion of embryos with high cell numbers (>128 cells) and decreasing the proportion of embryos with lower cell numbers (<65 cells). Blastocysts possessed significantly higher cell numbers after full-length adiponectin treatment. Mutated trimeric adiponectin had the opposite effect, a significant decrease in the proportion of embryos with higher cell numbers (>96 cells) and increase in the proportion of embryos with lower cell numbers (<65 cells). Trimeric adiponectin also significantly decreased the cell number and increased cell death in blastocysts. Truncated globular adiponectin had no significant effect on development of mouse preimplantation embryos.

CONCLUSIONS

Our results indicate that adiponectin can directly influence the development of the preimplantation embryo, and the effects are isoform dependent.

Quantitative polymerase chain reaction analysis by deconvolution of internal standard

Background

Quantitative Polymerase Chain Reaction (qPCR) is a collection of methods for estimating the number of copies of a specific DNA template in a sample, but one that is not universally accepted because it can lead to highly inaccurate (albeit precise) results. The fundamental problem is that qPCR methods use mathematical models that explicitly or implicitly apply an estimate of amplification efficiency, the error of which is compounded in the analysis to unacceptable levels.

Results

We present a new method of qPCR analysis that is efficiency-independent and yields accurate and precise results in controlled experiments. The method depends on a computer-assisted deconvolution that finds the point of concordant amplification behavior between the "unknown" template and an admixed amplicon standard. We apply the method to demonstrate dexamethasone-induced changes in gene expression in lymphoblastic leukemia cell lines.

Conclusions

This method of qPCR analysis does not use any explicit or implicit measure of efficiency, and may therefore be immune to problems inherent in other qPCR approaches. It yields an estimate of absolute initial copy number of template, and controlled tests show it generates accurate results.