Relative Expression Software Tool Research Articles

A CONSORT-guided, randomized controlled clinical trial of nebulized administration of dexamethasone and saline on lower airway cytokine mRNA expression in horses with moderate asthma.

Nebulized administration of dexamethasone on cytokine regulation in horses with moderate asthma has not been investigated. To investigate the changes in expression of inflammatory cytokine mRNA after nebulized administration of dexamethasone treatment of horses with moderate asthma. Horses with naturally occurring moderate asthma (n = 16) and healthy control horses (n = 4). All horses were kept in a dusty environment during the study. Prospective, parallel, randomized, controlled, blinded clinical trial. Blood endogenous cortisol, tracheal mucus, and bronchoalveolar lavage (BAL) were sampled before and after 13 days treatment with either nebulized administration of dexamethasone (15 mg once daily) or 0.9% saline (3 mL). Treatment groups were randomly allocated via randomization function (Microsoft Excel). Amplification of target mRNA in BAL fluid (IL-1β, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-17, IL-23, IFN-γ, Eotaxin-2, and TNF-α) was achieved by qPCR, and the relative expression software tool was used to analyze BAL inflammatory cytokine mRNA. Horses treated with nebulized administration of dexamethasone had increased relative expression of IL-5 (1.70-fold), IL-6 (1.71-fold), IL-17 (3.25-fold), IL-12 (1.66-fold), and TNF-α (1.94-fold), and decreased relative expression of IL-23 (1.76-fold; P = .04) in samples collected on Day 14, in comparison to samples collected on Day 0 (all P < .05). Horses treated with nebulized administration of saline had no significant difference in the relative expression of any gene (all P > .05). Nebulized administration of dexamethasone was associated with increased expression of inflammatory cytokine mRNA. There was no improvement in inflammatory airway cytology associated with either dexamethasone or saline treatment.

In Silico and Experimental Outcomes of the Expression of miR508-5p and miR-635 in Tumor Tissues of Patients with Breast Cancer

Background: Breast cancer (BC) is a malignant tumor that occurs in the epithelial tissue of the breast gland and has become the most common malignancy in women. Various studies have reported the effect of epigenetic changes, including DNA methylation and microRNAs, on breast carcinogenesis. microRNAs play an important role in the post-transcriptional regulation of genes and are important regulators of oncogenic pathways. Studying microRNAs in BC facilitates the development of targeted therapies and early detection of this cancer. Objectives: This study aimed to evaluate the expression level of miR-508-5p and miR-635 in BC tumor tissues compared to healthy marginal tissues. Methods: In silico analysis confirmed microarray datasets (GSE40525, GSE44124 and GSE45666) downloaded from the GEO database. The analysis was defined using the Affy packages in R software to screen remarkably dysregulated miRNAs attended by utilized to predict the potential biological processes and molecular pathways of miR-508-5p and miR-635. Experimental statistical significance of differences in miRNA relative expression results was analyzed by pair-wise fixed reallocation randomization test as a statistical model included in the REST (relative expression software tool). Results: GEO microarray data set, similar to qPCR results, showed that miR-508-5p was downregulated in the sample group by a mean factor of 0.327 (S.E.M range is 0.031-2.000). Moreover, miR-635 was upregulated in the sample group by a mean factor of 2.361 (S.E.M range is 0.250-16.000). Conclusion: miR-508-5p was downregulated, while miR-635 was upregulated in BC tissues. They may be proposed as diagnostic and therapeutic biomarkers for patients with BC.

The effect of trehalose administration on miRNA-10a expression in patients with history of myocardial infarction (MI) and systemic inflammation

Abstract Background MicroRNAs (miRNAs) are small non-coding RNAs involved in the regulation of endothelial function, inflammatory cells, and cholesterol homeostasis, may cause the onset of vascular inflammation which plays an important role in the development of cardiovascular disease. Trehalose is a nonreducing disaccharide which anti-inflammatory properties have been indicated in different experimental models. Purpose This study aimed to evaluate the effectiveness of intravenous (IV) trehalose administration on the circulating level of miRNA-10a as a biomarker of coronary inflammation in patients with history of myocardial infarction (MI) and elevated C-reactive protein (CRP). Methods This was a randomized, double-blind trial comprised 15 men (aged 18–80) with history of MI and evidence of systemic inflammation. The patients were randomly allocated to 2:1 ratio and respectively underwent the injection of either IV trehalose (15 g/week) or placebo for 12 weeks. At baseline and at the end of study, the serum level of miRNA-10a was measured by SYBR Green qPCR, quantified by the comparative method, and normalized to U6 expression. Relative expression software tool (REST) was used to analyze the miRNA-10a fold change (FC) expression level. Results At the baseline, patients in trehalose group showed slightly lower level of miRNA-10a relative to the placebo group (FC: 0.272, P=0.052), while it was not statistically significant. Within-group analysis showed that miRNA-10a had a significantly lower level in placebo group at the end of the study in comparison with the baseline (FC; 0.19, P=0.029). Albeit, miRNA-10a level increased after trehalose administration in relation to the baseline, while it was not statistically significant (FC: 1.963, P=0.114), Moreover, these changes in miRNA-10a levels were statistically significant in trehalose group related to the placebo group (P=0.047). Conclusions Together these findings demonstrate that trehalose administration could effectively increase the circulating level of miRNA-10a and may contribute to the regulation of coronary inflammation in patients with a history of MI and elevated CRP levels. This anti-inflammatory effect of trehalose can be confirmed in the large-scale studies or by evaluating other miRNAs related to the vascular inflammatory processes. Funding Acknowledgement Type of funding sources: None.

Evaluation of the Hypothalamic Kisspeptin System during the Attainment of Puberty in Gilts

Background: Kisspeptin has been demonstrated to affect the attainment of puberty in multiple species, presumably through its actions on GnRH and LH. It has previously been found there is an increase in expression of hypothalamic in the rat and the monkey coincident with puberty. Whether a similar phenomenon occurs in the pig remains to be determined. The objectives of the current experiments were to determine 1) Plasma concentrations of estradiol-17β; 2) Anterior pituitary gland concentrations of LH, IGF-I, kisspeptin, and anterior pituitary gland expression of LH-β and GnRH receptor; 3) Mediobasal hypothalamus expression of Kiss1 and concentrations of kisspeptin during the peripubertal period in the gilt. Methods: Two experiments were performed, each with 25 crossbred gilts (151 d, 105 kg). Gilts were relocated and exposed to a mature boar beginning on d 1 and continuing throughout the experiments to naturally induce puberty. Gilts that stood immobile within 24 hours of slaughter were considered to have attained puberty. Plasma samples were collected on d 1, 3, and 7 of the first experiment and d 2, 4, 6, and 8 of the second experiment. Gilts were slaughtered on d 7 (experiment 1) or d 8 (experiment 2), when mediobasal hypothalamus (MBH), anterior pituitary glands (AP), and blood were collected. Relative expression of MBH Kiss1 and β-actin and AP GnRH receptor, LH-β, was determined using real-time reverse transcriptase PCR. Fold changes in relative expression were determined using the Relative Expression Software Tool. Hypothalamic and AP content of kisspeptin were determined by RIA and differences were determined using the GLIMMIX procedure of SAS. Results: Relative expression of Kiss1 was increased (P = 0.005) 2.2 fold in the gilts that had attained puberty in the first experiment, however, those that had attained puberty in the second were not different (P > 0.05) from gilts that had not. Relative expression of GnRH receptor was not different (P > 0.05) between treatments in both experiments. Relative expression of LH-β tended to be decreased (P = 0.09) 0.80 fold in gilts that attained puberty in the first experiment but was not different (P > 0.05) in gilts that attained puberty in the second experiment. AP concentrations of LH were not different (P > 0.05) between treatments in the first experiment and were decreased (P = 0.01) in gilts that attained puberty in the second experiment. AP concentrations of kisspeptin were not different (P > 0.05) in the first experiment but were increased (P = 0.04) in gilts that had attained puberty in the second experiment. MBH concentrations of kisspeptin were increased (P = 0.03) in gilts that had attained puberty in the first experiment but were not different (P > 0.05) between treatments in the second experiment. Conclusions: These data further support the role that MBH expression of Kiss1 and concentrations of kisspeptin and AP concentrations of kisspeptin fluctuate during the peripubertal period and may play a role in the attainment of puberty in the gilt.

A simple spreadsheet-based method for relative quantification using quantitative real-time PCR.

Relative quantification is a popular analysis in gene expression studies using quantitative real-time PCR (qPCR). However, the calculation steps using the major algorithms for this analysis are rather complicated. In this study, we developed an easy-to-use spreadsheet-based method for relative quantification. The inputs from end-users are the efficiencies of both target and reference genes and the Cq values of those genes from cases and controls. This method performed normalization (with one or more reference genes), calculation of fold change of gene expression, and statistical analysis to analyze the difference between the groups in a step-by-step manner, which would allow the end-users to understand how the analysis arrived at the conclusion. Four previously published data sets with different experimental designs were used as examples. The calculated results were concordant with the results computed by the Relative Expression Software Tool (REST) 2009, a popular tool for relative quantification. Altogether, our method, which offers easy-to-understand calculation steps and does not require specialized instruments, software, or expertise to operate, would be a useful tool for students, educators, and scientists in the field of molecular biology.

Evaluation of the Hypothalamic Kisspeptin System throughout the Estrous Cycle in Gilts

Kisspeptin has been demonstrated to affect reproductive cyclicity and the attainment of puberty in multiple species, presumably through its actions on gonadotropin releasing hormone and luteinizing hormone. Kisspeptin administration causes increased plasma concentrations of LH in pigs, sheep, and rats. The objective of this experiment was to evaluate changes in the hypothalamic kisspeptin system throughout the estrous cycle in gilts. Estrus was synchronized in forty crossbred gilts (191 d, 121 kg) and estrus detection was performed by exposing gilts to a mature boar. The first day gilts stood immobile was denoted d 1 of the estrous cycle. Blood samples were collected via jugular venipuncture on d 1, 4, 7, 9, 14, 16, and 19 of the estrous cycle. Ten animals were slaughtered on d 1, 9, 14, and 21 of the estrous cycle when medial basal hypothalami, anterior pituitary glands, and blood were collected. Relative expression of hypothalamic kisspeptin (KISS1), kisspeptin receptor (KISS1R), estrogen receptors-a, anterior pituitary gland GnRH receptor, β-actin, and GAPDH was determined using real-time reverse transcriptase PCR. Fold changes in relative expression were determined using the Relative Expression Software Tool. Relative expression of KISS1 was increased (P = 0.006) 3.2 fold on d 1 versus d 21 and 2.3 fold (P = 0.003) on d 9 versus d 21 of the estrous cycle, but was not different (P > 0.05) among the remaining days of the estrous cycle. Relative expression of estrogen receptor-b was decreased (P = 0.05) 0.8 fold on d 9 versus d 21 and (P = 0.005) 0.7 fold on d 14 versus d 21, but was not different (P > 0.05) among the remaining days. Relative expression of anterior pituitary gland GnRH receptor was increased (P

Plasma miR-126 levels and its genomic polymorphism SNP rs4636297 in Type 2 diabetes

Since the variation of microRNAs expression has been described in type2 diabetes, we aimed to evaluate the plasma levels of miR-126 with known roles in the angiogenesis. Genomic polymorphism of miR-126 (SNP rs4636297) was also assessed as it is involved in the processing of pri-miR-126 to mature microRNA.Genotyping of the SNP rs4636297 was carried out by PCR-RFLP using HaeII enzyme. Real-time PCR assay was applied to assess miR-126 expression, which the fold change in gene expression was calculated by the Relative Expression Software Tool (REST). Data analysis was performed using exact-like logistic regression, Fisher exact test and the elrm package with the R software. Our data indicated that the group with BMI greater than 30 was at greater risk of diabetes (odds ratio=14.4, p value=0.00), compared with the BMI=19-25. The mean fold decrease in miR-126 gene expression in diabetic samples relative to normal samples was 0.653 (95% confidence interval: 0.012 - 18.765). All patients with the lowest levels of miR-126, had experienced diabetic complications. Considering the AA genotype as the reference, the odds ratio of diabetic complications for the GG and AG genotype were 1.2 and 1.43, respectively. miR-126 is one of the key factors in predisposition to diabetes and diabetic complication. Since the lowest expression of miR-126 leads to the diabetic complications it can be concluded that genetic predisposing factors should be considered in the management and treatment of Type 2 diabetes.

Catechol-O-methyltransferase gene expression in stress-induced and non-stress induced schizophrenia.

As schizophrenia is a complex mental disorder and the outcome of gene-gene-environmental interactions, there are different possible pathophysiological mechanisms in different schizophrenia subtypes corresponding to various risk factors. This study was aimed at examining the impact of one of the most likely interactions, that is, 'dopamine and stress', in schizophrenia pathogenesis. Here, we investigated the interaction between 'war-related psychological trauma' without brain trauma and catechol-O-methyltransferase gene. Using real-time PCR analysis we measured catechol-O-methyltransferase gene expression level in the blood cells of 66 male subjects in four groups, namely veteran schizophrenia patients as 'stress-exposed schizophrenia' (S-schizophrenia), their healthy brothers as 'their genetically closest relatives' (S-siblings), schizophrenia patients without any history of significant stress as 'non-stress-exposed schizophrenia' (NoS-schizophrenia), and the control group. The results were analyzed by Relative Expression Software Tool 2009 software. The catechol-O-methyltransferase gene expression was not significantly different between the S-schizophrenia and NoS-schizophrenia groups. However, compared to the control group, the catechol-O-methyltransferase expression was significantly decreased in three groups of S-schizophrenia, their healthy siblings, and NoS-schizophrenia patients. This data supports that reduced blood catechol-O-methyltransferase expression, which may be associated with higher dopamine level, is involved both in stress-induced and non-stress-induced schizophrenia.

Homeobox B4 gene expression is upregulated by ghrelin through PI3-kinase signaling pathway in rat's bone marrow stromal cells.

Ghrelin, a 28 amino acid peptide, has diverse physiological roles. Phosphatidylino-sitol-bisphosphate 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) are involved in some of the recognized actions of ghrelin. It has been shown that ghrelin upregulates HOXB4 gene expression but the real mechanism of this effect is not clear. Rat bone marrow stromal cells (BMSCs) were cultured in DMEM. BMSCs were treated with ghrelin (100 μM) for 48 h. Real-time PCR for HOXB4 was performed from Control (untreated BMSCs), BG (BMSCs treated with 100 µM ghrelin), PD (BMSCs treated with 10 µM PD98059, a potent inhibitor of mitogen-activated protein kinase, and 100 µM ghrelin), LY (BM-SCs treated with 10 µM LY294002, a strong inhibitor of phosphoinositide 3-kinase, and 100 µM ghrelin) and SY (BMSCs treated with 10 µM LY294002 plus 10 µM PD98059, and 100 µM ghrelin) groups. Relative gene expression changes were determined using Relative expression software tool 9 (REST 9). HOXB4 gene has been overexpressed in ghrelin-treated BMSCs (p<0.05). PI3K inhi-bition by LY294002 significantly downregulated the ghrelin-induced overexpression of HOXB4 (p<0.05). We can conclude that ghrelin, through PI3K/Akt pathway, may improve BMSC transplantation potency by reducing its apoptosis. Moreover, upregulating HOXB4 in BMSC and its possible differentiation to HSCs might in the future open the doors to new treatment for hematologic disorders. Therefore, activating the PI3K/Akt pathway, instead of using a non-specific inducer, could be the principal point to increase the efficiency of BMSC-based cell therapies in the future.

Adenosine receptor distribution in Rhesus monkey ocular tissue

Adenosine receptor (ADOR) antagonists, such as 7-methylxanthine (7-MX), have been shown to slow myopia progression in humans and animal models. Adenosine receptors are found throughout the body, and regulate the release of neurotransmitters such as dopamine and glutamate. However, the role of adenosine in eye growth is unclear. Evidence suggests that 7-MX increases scleral collagen fibril diameter, hence preventing axial elongation. This study used immunohistochemistry (IHC) and reverse-transcription quantitative polymerase chain reaction (RT-qPCR) to examine the distribution of the four ADORs in the normal monkey eye to help elucidate potential mechanisms of action. Eyes were enucleated from six Rhesus monkeys. Anterior segments and eyecups were separated into components and flash-frozen for RNA extraction or fixed in 4% paraformaldehyde and processed for immunohistochemistry against ADORA1, ADORA2a, ADORA2b, and ADORA3. RNA was reverse-transcribed, and qPCR was performed using custom primers. Relative gene expression was calculated using the ΔΔCt method normalizing to liver expression, and statistical analysis was performed using Relative Expression Software Tool. ADORA1 immunostaining was highest in the iris sphincter muscle, trabecular meshwork, ciliary epithelium, and retinal nerve fiber layer. ADORA2a immunostaining was highest in the corneal epithelium, trabecular meshwork, ciliary epithelium, retinal nerve fiber layer, and scleral fibroblasts. ADORA2b immunostaining was highest in corneal basal epithelium, limbal stem cells, iris sphincter, ciliary muscle, ciliary epithelium, choroid, isolated retinal ganglion cells and scattered scleral fibroblasts. ADORA3 immunostaining was highest in the iris sphincter, ciliary muscle, ciliary epithelium, choroid, isolated retinal ganglion cells, and scleral fibroblasts. Compared to liver mRNA, ADORA1 mRNA was significantly higher in the brain, retina and choroid, and significantly lower in the iris/ciliary body. ADORA2a expression was higher in brain and retina, ADORA2b expression was higher in retina, and ADORA3 was higher in the choroid. In conclusion, immunohistochemistry and RT-qPCR indicated differential patterns of expression of the four adenosine receptors in the ocular tissues of the normal non-human primate. The presence of ADORs in scleral fibroblasts and the choroid may support mechanisms by which ADOR antagonists prevent myopia. The potential effects of ADOR inhibition on both anterior and posterior ocular structures warrant investigation.

Identification of Differentially Expressed K-Ras Transcript Variants in Patients With Leiomyoma.

Molecular studies have demonstrated a wide range of gene expression variations in uterine leiomyoma. The rat sarcoma virus/rapidly accelerated fibrosarcoma/mitogen-activated protein kinase (RAS/RAF/MAPK) is the crucial cellular pathway in transmitting external signals into nucleus. Deregulation of this pathway contributes to excessive cell proliferation and tumorigenesis. The present study aims to investigate the expression profile of the K-Ras transcripts in tissue samples from patients with leiomyoma. The patients were leiomyoma cases who had no mutation in mediator complex subunit 12 ( MED12) gene. A quantitative approach has been applied to determine the difference in the expression of the 2 main K-Ras messenger RNA (mRNA) variants. The comparison between gene expression levels in leiomyoma and normal myometrium group was performed using relative expression software tool. The expression of K-Ras4B gene was upregulated in leiomyoma group ( P = .016), suggesting the involvement of K-Ras4B in the disease pathogenesis. Pairwise comparison of the K-Ras4B expression between each leiomyoma tissue and its matched adjacent normal myometrium revealed gene upregulation in 68% of the cases. The expression of K-Ras4A mRNA was relatively upregulated in leiomyoma group ( P = .030). In addition, the mean expression of K-Ras4A gene in leiomyoma tissues relative to normal samples was 4.475 (95% confidence interval: 0.10-20.42; standard error: 0.53-12.67). In total, 58% of the cases showed more than 2-fold increase in K-Ras4A gene expression. Our results demonstrated increased expression of both K-Ras mRNA splicing variants in leiomyoma tissue. However, the ultimate result of KRAS expression on leiomyoma development depends on the overall KRAS isoform balance and, consequently, on activated signaling pathways.

Gastrokine mRNA expression in gastric tissue from dogs with helicobacter colonisation but without inflammatory change during treatment

Gastrokines (GKNs) are bioactive substances secreted by gastric cells. Evidence supports functional roles for GKNs in gastric homeostasis, immune responses and tumour suppression. Down-regulation has been reported in Helicobacter pylori associated gastritis and other inflammatory gastrointestinal conditions in mice and people. The aim of this study was to evaluate GKN gene expression in dogs positive for other Helicobacter spp. both before and after treatment.Expression of Gkn-1 and Gkn-2 mRNA was studied in endoscopic biopsy samples collected from seven healthy dogs over three time-points pre- (T0) and at 1 and 18 weeks post-treatment for Helicobacter spp. colonisation (T1 & T2). The relative expression software tool (REST) was used to provide efficiency corrected expression ratios for comparisons between groups and these results were compared to a standard 2ΔΔCT methodology.Compared with T1 Gkn1 and Gkn2 mRNA expression was greater at T0 by a mean factor of 2.53 (SE=1.83–3.54) for Gkn1 (P=0.000) and 2.85 (SE=2.23–3.75) for Gkn2 (P=0.000). This difference was attenuated when comparisons were made between T0 and T2. Histopathological evidence of gastritis was not present in any Helicobacter spp. positive sample.When compared to post-eradication samples Gkn gene expression is increased in the presence of Helicobacter spp. in dogs without evidence for concurrent inflammation. Further evaluation is required to determine the relevance of this finding, however given a suspected role in gastric homeostasis, up-regulation of GKN1 and GKN2 could limit development of gastritis in Helicobacter spp. positive dogs.

Early pregnancy-related changes in toll-like receptors expression in ovine trophoblasts and peripheral blood leukocytes

In the present study, we aimed to 1) demonstrate the presence of all 10 toll-like receptors (TLRs) in ovine trophoblasts, and 2) investigate the expression profiles of TLR1–10 mRNAs in peripheral blood leukocytes (PBLs) in ewes during early pregnancy. For those purposes, ovine trophoblasts (n = 6) were collected from pregnant ewes on day 13. PBLs were collected from non-pregnant (n = 6) and pregnant ewes (n = 17) on days of mating (d) 0 and 18. TLR mRNAs in ovine trophoblasts were visualized by free-floating in situ hybridization (ISH). To assess the expression profiles of TLR1–10 in PBLs, total RNA was isolated and transcribed to cDNA. TLR1–10 mRNA levels were determined by real-time PCR in triplicate. The Relative Expression Software Tool (REST 2009) was used for statistical analysis. We detected mRNAs for TLR2, TLR4, TLR5, TLR6, TLR7, TLR8, and TLR10 but not for TLR1, TLR3, and TLR9 in trophoblasts. TLR2, TLR5, TLR6, TLR7, TLR8, and TLR10 mRNAs were expressed by all trophoblasts, whereas TLR4 mRNA and protein in trophoblasts were more limited. In PBLs, TLR expression did not differ between day 0 and day 18 in non-pregnant ewes; however, ewes in early pregnancy exhibited significantly upregulated expression of TLR2 (2.3-fold), TLR4 (3.1-fold), TLR6 (1.7-fold), and TLR8 (2.2-fold) on day 18 compared with day 0. In contrast, TLR10 was downregulated (2-fold) on day 18 by pregnancy. Similar results were also obtained for TLR2, TLR4, TLR6, TLR8 and TLR10 from the comparison between day 18 non –pregnant and day 18 pregnant groups. According to these results, the presence of TLRs in early ovine trophoblasts suggests that these cells play an immunological role at the maternal–fetal interface. The results also suggest that tight regulation of some components of TLRs in PBLs due to embryo- and/or pregnancy-related factors is necessary for successful establishment of early pregnancy in ewes.

Pseudo-continuous arterial spin labeling imaging of cerebral blood perfusion asymmetry in drug-naïve patients with first-episode major depression.

Many previous studies have reported that regional cerebral blood flow (rCBF) aberrations may be one of the pathological characteristics of depression and rCBF has demonstrated a certain degree of asymmetry. However, studies investigating the cerebral blood perfusion asymmetry changes of drug-naïve patients experiencing their first episode of major depression using pseudo-continuous arterial spin labeling (pCASL) are rare. Ten drug-naïve patients experiencing their first major depression episode and 15 healthy volunteers were enrolled in the current study. A novel pCASL method was applied to whole brain MRI scans of all of the samples. The Statistics Parameter Mapping and Relative Expression Software Tool software packages were used for the pre-processing and statistical analysis of the two sets of images, and the differences in the cerebral blood perfusion at the whole brain level were compared between the two groups. Compared with the healthy control group, the cerebral perfusion of the depression patients showed an asymmetric pattern. Decreased cerebral blood perfusion regions were primarily located in the left hemisphere, specifically in the left temporal lobe, frontal lobe and cingulate cortex [P<0.05 and cluster size ≥30 with false discovery rate (FDR) correction]. Simultaneously, increased perfusion regions were predominantly located in the right hemisphere, specifically in the right cerebellum, thalamus, frontal lobe and anterior cingulate cortex (P<0.05 and cluster size ≥30, with FDR correction). Thus, pCASL may characterize the alterations in cerebral blood perfusion of patients with depression.

Determination of PFOR gene expression in strains of G. intestinalis with different inhibitory concentrations of metronidazole.

Giardia intestinalis is the most important and common diarrhea-causing parasitic protozoa worldwide with growing clinical relevance in public health. There are many documented cases of G. intestinalis resistance to metronidazole (MZ). Pyruvate: ferredoxin oxidoreductase (PFOR), the membrane-localized enzyme, plays a key role in the development of resistance to drugs. The aim of the present study was to evaluate the difference in the levels of PFOR gene expression between MZ-resistant and MZ-susceptible strains of G. intestinatlis. From 159 samples with G. intestinalis cysts, 48 strains were successfully cultivated. Using specific pair primers, PFOR gene expressions were estimated in different groups of Giardia. The polymerase chain reaction (PCR) data were analyzed with Bayesian analysis of qRT-PCR data using MCMC.qpcr package, with relative expression software tool (REST) and quantitative PCR CopyCount web source. In the group of Giardia with minimum inhibitory concentration (MIC) of 6.3 µM, the level of PFOR gene expression was downregulated and compared with controls, differed by 1.5 to 2.8 times. At the same time, there was no significant difference in PFOR gene expression between the control (susceptible) group and the group with MIC of 3.2 µM. Though there is association between PFOR gene expression and metronidazole resistance of Giardia intestinalis, the level of PFOR gene expression cannot be a strong genetic marker to predict level of resistance to metronidazole based on MICs.

Fas –FasL genotype and phenotype in preeclampsia

Fas –FasL genotype and phenotype in preeclampsia

Cytotoxic effect of fluvastatin on MCF-7 cells possibly through a reduction of the mRNA expression levels of SGK1 and CAV1.

Fluvastatin (FLU) prevents the conversion of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonic acid by inhibiting HMG-CoA reductase and decreases cholesterol level. Although the effects of FLU treatment on several cancer types through many mechanisms have been identified, its relationship with unfolded protein response and apoptosis has not been clearly understood. In this recent study, we aimed to investigate the cytotoxic effect of Fluvastatin on MCF-7 cells and define the transcriptional regulation of specific genes during the occurrence of this cytotoxic effect. We administered 0.62, 2.5, 5, and 40 μM FLU on MCF-7 cells singly and in combination with 2-deoxyglucose (2-DG), and we monitored cell viability and proliferation for 48 hours using real-time cell analyzer system (xCELLigence). At the same time, we measured the mRNA expression levels of glucose-regulated protein 78 (GRP78), CCAAT/enhancer binding protein, homologous protein (CHOP), caveolin-1 (CAV1), NDRG1 Variant 1 and Variant 2, HMOX1, SGK1, and prostate apoptosis response-4 (PAR4) genes using quantitative real-time polymerase chain reaction (LightCycler 480 II). We accepted GAPDH gene and control groups as the reference gene and calibrator, respectively. We performed relative gene expression analyses of the study groups using the QIAGEN 2009 Relative Expression Software Tool (REST). FLU revealed an antiproliferative and cytotoxic effect on MCF-7 cells, while causing the transcriptional regulation of many genes. Of these genes, the mRNA expressions of CHOP, heme oxygenase 1 (HMOX1), N-myc downstream-regulated gene 1 (NDRG1) V1, and NDRG1 V2 increased. On the other hand, the mRNA expression levels of SGK1 and CAV1 decreased. The antiproliferative effects of FLU may be related to the decreased expression levels of SGK1 and CAV1.

HOXD10 expression in human breast cancer

Breast cancer is the most frequent malignancy among females. In this study, we analyzed the expression pattern of a homeobox gene (HOXD10) in human invasive ductal breast cancer tissues and normal tissues. With the ACTB (β-actin) gene as a reference, HOXD10 was detected in 60 breast cancer tissues by using the quantitative real-time PCR (qPCR) method with the Relative Expression Software Tool (REST). We found that the HOXD10 expression level was significantly different between cancerous and normal tissues. Downregulation of the HOXD10 gene expression was examined in high-grade samples. Low-grade tissue showed no difference from the control group. HOXD10 expression was reduced in grade II breast carcinoma tissues. This data reveal that misexpression of the HOXD10 gene supports the development and involvement in breast cancer and may serve as a potential biomarker for the diagnosis of human ductal invasive breast carcinoma.

Immunomodulatory activity of two potential probiotic strains in LPS-stimulated HT-29 cells

The relative expression of mucin, pro- and anti-inflammatory genes besides other signaling molecules in HT-29 cells by two test probiotic strains of Lactobacillus plantarum Lp9 and Lp91 and the reference strain L. plantarum 5276 was evaluated by RT-qPCR using Relative Expression Software Tool qBase-Plus under in vitro simulated gut conditions. Ten house keeping genes were evaluated by using geNorm 3.4 excel based application. The most stable genes were RPL27, ACTB and B2M which were subsequently used for calculating the normalization factor. Under pretreatment conditions (4h probiotic treatment, followed by lipopolysaccharide challenge for 3h), all the three strains evoked downregulation of IL-8 expression by ~100%, while in case of TNF-α, the downregulation of the relative gene expression was at the rate of 98.2, 93.8 and 98.0% with Lp5276, Lp9 and Lp91, respectively, under the same set of conditions. Lp91 evoked maximum downregulation of IL12p35 and IFN-γ with corresponding fold reduction in relative expression of the two genes by 96.5 and 96.7% during pre-treatment conditions. However, IL-10 and IFN-α were significantly upregulated to the extent of 8.13±0.36 and 2.62±0.14 fold by Lp91 under the same conditions. Lp9 and Lp91 were also quite effective in inducing the expression of Cox-1 and Cox-2 in HT-29 cells as can be reflected from their ratios, i.e., 5.90 and 6.50 (under pretreatment conditions); 3.79 and 4.36 (under co-culture conditions). Thus, the two putative indigenous L. plantarum strains Lp9 and Lp91 demonstrated immunomodulating functions in HT-29 cells at significant levels under different experimental conditions.

Searching for circulating microRNAs in genitourinary tumors.

468 Background: Detection of circulating tumor cells (CTC) may provide diagnostic and prognostic information in genitourinary tumors (GT). The aim of this work was identify aberrantly expressed miRNAs potentially useful for CTC detection in blood samples from patients with GT to assess their potential clinical significance, and to gain a greater understanding of the mechanisms driving tumor progression. Methods: We examined blood levels of 92 microRNAs in 113 metastatic patients: prostate (mP), renal cell carcinoma (mRCC), bladder tumors (mB) and healthy volunteers (HV) (N=18) using SYBR-green-based microRNA RT-qPCR arrays (Exiqon). Array design was made by literature review and bioinformatics approach using free databases. Relative Expression Software Tool (REST) and SPPS 21.0 were used to data processing and analysis. Results: microRNAs differential expressed between tumors and HV (only up-regulated miRNAs are shown in Table). Conclusions: microRNAs in the circulation are relatively stable, very accessible, low invasive and easily testable biomarkers. These results suggest that our bioinformatic approach is an useful high-throughput method to identified tumors-associated miRNAs. The selected miRNAs should be further evaluated for their potential as markers for CTC detection, prognosis and therapeutic outcome. Further studies of precision and sensitivity on these markers in this GT population will clarify its role as novel stable blood-based markers. [Table: see text]