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Because of low sensitivity and specificity of the currently available urine biomarkers of bladder cancer (BC) detection and painful cystoscopy procedure. Our study aimed to evaluate expression of urinary exosomal miR-96-5p and miR-183-5p as probable non-invasive and accurate biomarkers for the diagnosis and follow up of BC. Using quantitative real-time polymerase chain reaction; expression of exosomal microRNA (miR)-96-5p and miR- 183-5p in the urine samples of 51 patients with BC, 21 patients with benign urinary bladder lesions and in 24 normal individuals as control group was done. Our study results showed higher expressions of both miR-96-5p and miR-183-5p in urine of BC patients in comparison with control group (P < 0.001 for each). Receiver operating characteristic curve (ROC) analysis showed that each microRNA had good sensitivity and specificity to differentiate BC from non-BC patients miR-96-5p 80.4% and 91.8% and miR-183-5p 78.4% and 81.6% respectively compared to cytology (37.3% and 100%). In addition, it was obvious that the sensitivity of combined miR-96-5p and miR-183-5p for the diagnosis of BC reached 88.2%% and specificity reached 87.8%, which were higher than each one alone. We also found that expression of miR-96-5p and miR-183-5p with high grade, and pathological stage was significantly increased. After surgery, collected urine samples showed significantly lower expression of miR-96-5p-: P < 0.001; and miR-183-5p: P = 0.002. In conclusion, urine miR-96-5p and miR-183-5p are promising tumor biomarkers of BC diagnosis; particularly, when they combined with each other or with urinary cytology.

Diabetes mellitus (DM) is a metabolic disease characterized by hyperglycemia and abnormal insulin secretion. MicroRNAs are small, non-coding RNAs that are able to affect cell biological functions and act as biomarkers for some diseases such as DM. In current study, we measured serum miR-33 in three groups (n = 15) as follows; non-diabetic control, pre-diabetic, and DM patients. Real-time PCR method was used to quantify miR-33 expression. miR-33 expression was significantly increased in pre-diabetic subjects compared to other two groups (p < 0.001). FBS (p < 0.001), insulin (p < 0.001), HOMA-IR (p < 0.001), and TG (p = 0.026) were higher in diabetic subjects than the other two groups. In people that had high physical activity, the number of diabetic subjects were zero and most of them were in pre-diabetic group (p = 0.019). Serum miR-33 level significantly and positively correlated with pre-diabetic state (B = 2.67, p = 0.000), Sex (B = 1.03, p = 0.025), and FBS (B = 0.04, p = 0.036) and also miR-33 was significantly and negatively correlated with HOMA-IR (B = - 1.58, p = 0.04). These findings support the possible role of miR-33 to monitor pre-diabetes onset and progression. It needs to be evaluated in future studies with high number of participants to clarify its mechanism and diagnostic viability.

The present study was conducted to investigate the effects of colloidal nanoparticles of silver (Nano-Ag) on the expression of myogenesis-related genes in chicken embryos. The investigated genes included the members of the myogenic regulatory factors family ( MRFs ) and myocyte enhancer factor 2A ( MEF2A ) genes. A total of 200 fertilized broiler eggs (Indian River) were randomly distributed into four groups; non-injected control, injected control with placebo, treatment I in ovo injected with 20 ppm Nano-Ag, and treatment II in ovo injected with 40 ppm Nano-Ag. The eggs were then incubated for 21 days at the optimum temperature and humidity conditions. Breast muscle tissues were collected at the 5th, 8th, and 18th days of the incubation period. The mRNA expression of myogenic determination factor 1 ( MYOD1 ), myogenic factor 5 ( MYF5 ), myogenic factor 6 ( MYF6 ), myogenin ( MYOG ), and MEF2A was measured at the three sampling points using real-time quantitative PCR, while MYOD1 protein expression was evaluated on day 18 using western blot. Breast muscle tissues were histologically examined on day 18 to detect the changes at the cellular level. Our results indicate that myogenesis was enhanced with the low concentration (20 ppm) of Nano-Ag due to the higher expression of MYOD1 , MYF5 , and MYF6 at the transcriptional level and MYOD1 at the translational level. Moreover, histological analysis revealed the presence of hyperplasia (31.4% more muscle fibers) in treatment I (injected with 20 ppm). Our findings indicate that in ovo injection of 20 ppm Nano-Ag enhances the development of muscles in chicken embryos compared with the 40-ppm dosage and provide crucial information for the use of silver nanoparticles in poultry production.

Long noncoding RNAs are defined as transcripts longer than 200 nt with no protein coding potential. Most lncRNAs are expressed in a tissue-specific manner and barring a few, their absolute expression is lower compared to most coding transcripts. Differential expression studies have contributed the most to the functional characterisation of the lncRNAs we know. Sensitive and specific quantification of lncRNA expression is crucial for such studies. SYBR Green dye based real time quantitative PCR is a simple and affordable method of quantitative PCR, wherein the specific binding of the dye to double stranded DNA amplicon emits fluorescence proportionate to the amount of PCR products. Here we describe a detailed protocol for successful lncRNA quantitation by reverse transcription followed by SYBR Green chemistry-based real-time PCR.

Kawasaki disease (KD) has been declared a rare idiopathic condition for a long time. The children age less than five years, as the most susceptible group, are at risk of this disease. Since the cause of the disease is unknown, this study was designed to investigate the cause of KD. We applied metaDE and WGCNA packages in order to perform a meta-analysis and identify network modules of co-expressed genes, respectively, on three expression array datasets and also CEMiTool package to confirm detected modules by WGCNA. Using the Pearson correlation coefficient, the resemblance of KD to other symptomatic-similar diseases, including bacterial infections, viral infections, JIA (juvenile idiopathic arthritis), HSP (Henoch-Schönlein purpura), GAS (group A streptococcal), and HAdV (adenovirus) was accurately estimated. In addition to validation by more three expression array datasets, serum samples of 16 patients and eight control participants have undergone the Real-Time PCR assay so as to evaluate produced bioinformatic results. WGCNA showed 3840 differentially expressed genes (DEGs) in KD in comparison with other diseases accompanying resembling clinical manifestations. Through further bioinformatic analysis and validation, 42 out of DEGs were introduced as hub genes, which the results of Real-Time PCR assay subsequently attested to the majority of them. The DEGs possessed a remarkable commonality with those of bacterial conditions. According to our exhaustive results, the origin of KD has been revealed pertinent to bacterial infections. Another interesting finding in this study is introducing IVIG in combination with particular antibiotics as a novel therapeutic approach, which supported by a score of authentic research studies to overcome KD., Competing Interests: Declaration of Competing Interest The authors have indicated that they have no conflicts of interest regarding the content of this article., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Bladder cancer is one of the most predominant tumors of the genitourinary tract. In addition to pathological findings, the molecular modifications that might affect tumorigenesis and tumor outcome should be considered when treating bladder cancer. Accordingly, we aimed to investigate the expression levels of both the ASPM and TEF genes in bladder cancer tissues and their value in disease prognosis. The expression levels of the ASPM and TEF genes were analyzed by quantitative real-time PCR (qRT-PCR) in 90 bladder cancer tissue specimens and 90 specimens of normal urinary bladder tissue taken away from the tumor site. The upregulation of ASPM expression and the downregulation of TEF expression were observed in bladder cancer tissues compared to adjacent normal tissues, and these levels were correlated with high-grade tumors, advanced stage disease and the presence of metastasis. Both genes had the ability to predict metastatic association with sensitivity (84.62%) and specificity (68.42%; *P < 0.001) for the ASPM gene and for the TEF gene with sensitivity (80.77%) and specificity (78.95%; *P < 0.001). Additionally, Kaplan-Meier survival analysis indicated that elevated ASPM expression levels and reduced TEF expression levels significantly correlated with decreased overall survival and progression-free survival. The current analysis concludes that ASPM and TEF expressions might be used as potential biomarkers in bladder cancer patients.

Gastric cancer is one of the most common worldwide types of cancer. It is a multifactorial disease and both environmental and genetic factors play an important role in its etiology. Evaluation of the relative expression level of NFKB2 gene in two groups of patients: peptic ulcer and gastric cancer and its role in the pathomechanism of these diseases was the aim of this study. RNA was isolated from: 79 samples of peptic ulcer, 22 gastric cancer and 11 control tissue. The real-time PCR technique was used to study the expression of NFKB2 gene. The relative expression level of NFKB2 gene was a variable in all three studied groups. The relative NFKB2 gene expression depends on the type of a disease. Peptic ulcer cases showed the increased relative NFKB2 gene expression to control group (p = 0.0000). Cancer cases presented decreased relative NFKB2 gene expression to normal stomach tissue (p = 0.0183). There are statistically important differences in the investigated gene expression between peptic ulcer, where the expression level is higher comparing to gastric cancer and control tissue which confirmed that such an activation is connected with an inflammatory process. The relative expression level of NFKB2 is decreased in cancer cases as opposed to control tissue and peptic ulcer cases which could suggest that during carcinogenesis of gastric cancer inhibition of NF-kB pathway takes place which could be a promising factor for patients.

Polymerase chain reaction (PCR) plays significant roles in modern molecular biology. However, it is relatively cumbersome and less accurate to use the traditional PCR method in quantifying gene expression because it requires first generating a standard curve with multiple input controls showing linearity with amplified control PCR products on a electrophoresis gel to compare with the abundance of the to-be-determined gene transcript PCR amplicons. Quantitative real-time PCR (qRT-PCR) is a time-efficient and reliable tool for accurate quantification and comparison of gene (RNA transcript) expression from various biological samples. Current technology has simplified and expedited the qPCR process significantly. However, proper techniques and standard protocols are required in eliminating potentially erroneous experimental outcome. Here, we provide an example from a drug-treated bacterial gene expression study with detailed protocols to demonstrate real-time qPCR with SYBR ™ Green and TaqMan ® , two of the most adapted and well-established qPCR technologies. Relative quantification of gene (RNA transcript) expression using qRT-PCR is demonstrated in detail from sample preparations to data analysis.

Although many time-dependent parameters involved in wound healing have been exhaustively investigated, establishing an objective and reliable means for estimating wound age remains a challenge. In this study, 78 Sprague-Dawley rats were divided randomly into a control group and contusion groups at 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, and 48 h post-injury (n = 6 per group). The expression of 35 wound healing-related genes was explored in contused skeletal muscle by real-time polymerase chain reaction. Differences between the groups were assessed by partial least squares discriminant analysis (PLS-DA). The results show that the samples were classified into three groups by wound age (4-12, 16-24, and 28-48 h). A Fisher discriminant analysis model of 14 selected genes was constructed, and 94.9% cross-validated grouped cases were correctly classified. A PLS regression analysis using 14 genes showed reasonable internal predictive validity, with a root mean squared error of cross-validation of approximately 8 h. To examine whether the prediction models were capable of analyzing new (ungrouped) cases, an external validation was carried out using the expression data from an additional 30 rats. Approximately 76.7% of ungrouped cases were correctly classified, which was a lower proportion than that for cross-validation. Similarly, the prediction results of the PLS model showed lower relatively external predictive validity (root mean squared error of prediction = 11 h) than internal predictive validity. Although the prediction results were less accurate than expected, the gene expression modeling and multivariate analyses showed great potential for estimating injury time. These multivariate methods may be valuable when devising future wound time estimation strategies.

Polybrominated diphenyl ethers (PBDEs) are brominated flame retardants. Biomonitoring studies have shown widespread presence of PBDEs in humans and their accumulation in food chain cause concern to human health, especially for foetus and infant development. The early-life stages are generally considered more sensitive to exposure to toxic compounds than juvenile or adults. For this reason the aim of this study was to evaluate the effects of the three most environmentally relevant BDE (BDE- 47, 99 and 209) on zebrafish embryos. The fish embryo toxicity (FET) OECD tests on zebrafish were performed followed by histopathogical examination to assess morphological changes. The gene expression of the thyroid stimulating hormone β (Tshβ), the transport proteins transthyretin (Ttr) and thyroxine-binding globulin (Tbg) as well as the enzyme iodothyronine deiodinase 1 (Dio1) was also assessed by Real-time PCR. BDE-47 and BDE-99 showed an increase of the severity of the effects at the lower concentrations while for the BDE-209 the effects were higher to the high concentrations. Although all compounds did not show any acute toxicity for none of the concentrations tested, they reported interesting sub-acute lesions, including yolk and pericardial edema, tail and head malformation, reduced and extremely reduced heart beat rate, blood stasis and spinal curvature, with the highest percentage recorded for BDE-209. Cardiac edema, damage of eye structure and hydrocephaly were confirmed also by histophatological examination. Furthermore, a toxic and dose-dependent liver vacuolization in BDE-209 was observed in all experimental groups. Although no statistically significant difference in gene expression was observed, BDE-209 up-regulated only Dio1 while the other congeners induced Tshβ, Ttr, Tbg and Dio1. Overall, this research highlighted that exposure to BDE-47, BDE-99 and BDE-209 at realistic concentrations caused lethal and sub-lethal alterations and impaired genes involved in thyroid hormones homeostasis leading to abnormal development of zebrafish embryos., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem-loop reverse transcriptase-PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.

Background and objectives: Human gastric adenocarcinoma (AGS) is one of the most common malignant cancers worldwide. The present study aimed to transfer oleuropein into cancer cells using synthetic paramagnetic nanoparticles and study their effect on the AGS (ATCC ® CRL1739™) cell line. Materials and Methods: Paramagnetic nano-oleuropein was synthesized using four-stage co-precipitation by developing NH-connected bridges and was evaluated by EDS, SEM and FTIR methods. Different concentrations of magnetic oleuropein (0, 0.15, 0.45, 1.37, 4.12, 12.35, 37.04, 111.11, 333.33, 1000 µg/mL) were used to treat the AGS cell line in a completely randomized design using a statistical framework with three replicates. The relative expression rate of miR-200 and KRAS oncogenes was evaluated using real-time PCR. The inhibition rate of the AGS cells was assessed using the MTT test at 24, 48 and 72 h intervals. Results: The results showed that there was a significant difference between the inhibition rates of magnetic nano-oleuropein at IC50-24h (23.6 µg/mL), IC50-48h (15.2 µg/mL) and IC50-72h (9.2 µg/mL). Real-time PCR indicated that the relative expression of KRAS and miR-200 genes was highest at IC50 at these intervals. Conclusions: Magnetic nano-oleuropein can be subjected to objective testing and clinical evaluations as a natural antioxidant to prevent and treat gastric adenocarcinoma.

Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful tool to evaluate gene expression, but its accuracy depends on the choice and stability of the reference genes used for normalization. In this study, we aimed to identify reference genes for studies on osteoblasts derived from rat bone marrow mesenchymal stem cells (bone marrow osteoblasts), osteoblasts derived from newborn rat calvarial (calvarial osteoblasts), and rat osteosarcoma cell line UMR-106. The osteoblast phenotype was characterized by ALP activity and extracellular matrix mineralization. Thirty-one candidates for reference genes from a Taqman ® array were assessed by qRT-PCR, and their expressions were analyzed by five different approaches. The data showed that several of the most traditional reference genes, such as Actb and Gapdh, were inadequate for normalization and that the experimental conditions may affect gene stability. Eif2b1 was frequently identified among the best reference genes in bone marrow osteoblasts, calvarial osteoblasts, and UMR-106 osteoblasts. Selected stable and unstable reference genes were used to normalize the gene expression of Runx2, Alp, and Oc. The data showed statistically significant differences in the expression of these genes depending on the stability of the reference gene used for normalization, creating a bias that may induce incorrect assumptions in terms of osteoblast characterization of these cells. In conclusion, our study indicates that a rigorous selection of reference genes is a key step in qRT-PCR studies in osteoblasts to generate precise and reliable data., (© 2018 Wiley Periodicals, Inc.)

Although not fully recognized, the neurotoxic effects of silver nanoparticles (Ag-NPs) are thought to occur through induction of oxidative stress and apoptosis. To investigate the exact underlying molecular mechanism, we aimed to explore the apoptotic effects of intraperitoneal injection of Ag-NPs and investigated the possible attributed changes in the mRNA expression of Bcl-2 and Bax genes in the rat hippocampus. Two in vivo sets of experiments, one to demonstrate apoptosis and the other to assess gene expression, were conducted on male Wistar rats. In each set, the first group, acting as control, received saline and the other three groups received Ag-NP at doses of 100, 200, and 400 ppm for five successive days. Ten days after the last injection, hippocampal tissue of the first set of rats was assessed for apoptosis using terminal deoxynucleotidyl transferase-mediated deoxy uridine triphosphate nick-end labeling staining. In the second set of experiments, mRNA expression of Bcl-2 and Bax genes was evaluated using real-time polymerase chain reaction. Ag-NP treatment was shown to induce apoptosis in a dose-dependent manner. Furthermore, Ag-NP reduced mRNA level of Bcl-2 in the rat hippocampal cells at all investigated doses compared to the control group ( p < 0.001). The mRNA level of Bax, on the other hand, was increased in these cells. The increase was significant compared to the control group at the doses of 200 ppm ( p < 0.05) and 400 ppm ( p < 0.001). Our results show that Ag-NPs reduce Bcl-2 and increase Bax genes expression, resulting in increased Bax/Bcl-2 ratios in rat hippocampal cells. This altered gene expression induces cell apoptosis and contributes to the neurotoxicity of Ag-NPs.

The quantitative reverse transcription polymerase chain reaction or real-time PCR has become a routine technique for the detection and comparison of amounts of specific mRNA transcripts, done by measuring amplified levels of specific cDNAs. In this chapter, we provide our real-time RT-PCR experimental procedure using SYBR Green I for the quantitative analysis of CCN family gene expression. Especially, we describe the extraction and purification steps for RNA derived from mesenchymal cells, such as chondrocytes and osteoblasts that produce a large amount of extracellular matrix in detail.

Endocannabinoids are derived from phospholipids and reduce fertility by interfering with implantation. Identification of changes in the expression of genes of the endocannabinoid system as a result of dietary inclusion of conjugated linoleic acid (CLA) is critical to the advancement of our understanding of the nutritional regulation of uterine function. An experiment was conducted on transition cows to evaluate the expression of key endocannabinoid genes in bovine endometrium in response to dietary supplementation with CLA. A total of 16 cows were randomly assigned to two treatments: (1) control (75 g/day palm oil) and (2) CLA (75 g/day CLA) from 21 days prepartum to Day 42 postpartum. Cows underwent uterine biopsy on days 21 and 42 postpartum. The abundance of mRNA encoding endocannabinoid receptor (CNR2), N-acyl phosphatidylethanolamine phospholipase D (NAPEPLD), fatty acid amide hydrolase (FAAH), N-acylethanolamine acid amidase (NAAA), and monoglyceride lipase (MGLL) was measured by real-time PCR. Results reported that relative levels of mRNA encoding CNR2 and NAPEPLD were decreased (P < 0.05) compared with control cows between Days 21 and 42 postpartum. Relative levels of mRNA coding for NAAA and MGLL were not different (P > 0.05) in the same situation. Mean plasma progesterone concentrations were higher in CLA-fed cows compared with control cows at Day 42 postpartum (3.51 and 1.42 ng/mL, respectively, P < 0.05). In conclusion, we suggest that the beneficial effects of a diet enriched with CLA are the result of a decrease in relative gene expression of the endocannabinoid receptor (CNR2) and enzymes that synthesize fatty acid amides (NAPEPLD) and of an increase in the expression of PTGS2 that in turn can oxidate endocannabinoids and consequently resulted in increased plasma progesterone concentrations during early lactation., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Objective: Quantitative real-time PCR (qPCR) is routinely performed for experiments designed to identify the molecular mechanisms involved in the pathogenesis of dental fluorosis. Expression of reference gene(s) is expected to remain unchanged in fluoride-treated cells or in rodents relative to the corresponding untreated controls. The aim of this study was to select optimal reference genes for fluoride experiments performed in vitro and in vivo., Design: Five candidate genes were evaluated: B2m, Eef1a1, Gapdh, Hprt and Tbp. For in vitro experiments, LS8 cells derived from mouse enamel organ were treated with 0, 1, 3 and/or 5mM sodium fluoride (NaF) for 6 or 18 h followed by RNA isolation. For in vivo experiments, six-week old rats were treated with 0 or 100 ppm fluoride as NaF for six weeks at which time RNA was isolated from enamel organs. RNA from cells and enamel organs were reverse-transcribed and stability of gene expression for the candidate reference genes was evaluated by qPCR in treated versus non-treated samples., Results: The most stably expressed genes in vitro according to geNorm were B2m and Tbp, and according to Normfinder were Hprt and Gapdh. The most stable genes in vivo were Eef1a1 and Gapdh. Expression of Ddit3, a gene previously shown to be induced by fluoride, was demonstrated to be accurately calculated only when using an optimal reference gene., Conclusions: This study identifies suitable reference genes for relative quantification of gene expression by qPCR after fluoride treatment both in cultured cells and in the rodent enamel organ., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

In order to reveal the inhibitory effects of cinnamaldehyde, citral, and eugenol on aflatoxin biosynthesis, the expression levels of 5 key aflatoxin biosynthetic genes were evaluated by real-time PCR. Aspergillus flavus growth and AFB1 production were completely inhibited by 0.80 mmol/L of cinnamaldehyde and 2.80 mmol/L of citral. However, at lower concentration, cinnamaldehyde (0.40 mmol/L), eugenol (0.80 mmol/L), and citral (0.56 mmol/L) significantly reduced AFB1 production with inhibition rate of 68.9%, 95.4%, and 41.8%, respectively, while no effect on fungal growth. Real-time PCR showed that the expressions of aflR, aflT, aflD, aflM, and aflP were down-regulated by cinnamaldehyde (0.40 mmol/L), eugenol (0.80 mmol/L), and citral (0.56 mmol/L). In the presence of cinnamaldehyde, AflM was highly down-regulated (average of 5963 folds), followed by aflP, aflR, aflD, and aflT with the average folds of 55, 18, 6.5, and 5.8, respectively. With 0.80 mmol/L of eugenol, aflP was highly down-regulated (average of 2061-folds), followed by aflM, aflR, aflD, and aflT with average of 138-, 15-, 5.2-, and 4.8-folds reduction, respectively. With 0.56 mmol/L of citral, aflT was completely inhibited, followed by aflM, aflP, aflR, and aflD with average of 257-, 29-, 3.5-, and 2.5-folds reduction, respectively. These results suggest that the reduction in AFB1 production by cinnamaldehyde, eugenol, and citral at low concentration may be due to the down-regulations of the transcription level of aflatoxin biosynthetic genes. Cinnamaldehyde and eugenol may be employed successfully as a good candidate in controlling of toxigenic fungi and subsequently contamination with aflatoxins in practice., (© 2015 Institute of Food Technologists®)

Hepatic gene expression studies are vital for identification of molecular factors involved in insulin resistance. However, the need of normalized gene expression data has led to the search of stable genes which are useful as a reference in specific experimental conditions. The aim of this study was to evaluate expression stability of potential reference genes for real-time PCR gene expression studies, in rats with insulin resistance, early programmed in intrauterine environment of maternal insulin resistance and triggered by exposure to a high sucrose and fat diet in adult life. Male rats coming from insulin resistant (F1IR) mothers or normal (F1N) mothers were fed a standard rodent diet from postnatal day 21 to day 56, and then divided in two groups each. One of each subgroups were fed a high sucrose and fat diet (groups F1IR + HSFD and F1N + HSFD respectively), the rest were fed a control diet (groups F1IR + CD and F1N + CD) for 14 days. Glucose metabolism related tests were later performed. After liver extraction, RNA was isolated and gene expression analyzes of seven potential reference genes (Actb, Gapdh, Gusb, Hprt1, Ldha, Rpl13a and Rplp1) were carried out. LinRegPCR software was used to analyze raw data and determinate baseline corrections, threshold lines, efficiency of PCR reactions and corrected Cq values. Evaluations of gene expression stabilities as well as the number of necessary genes for normalization were assessed with geNorm tool. All samples from all groups showed acceptable PCR amplification efficiencies. The most stable genes were Rplp1, Ldha, Hprt1 and Rpl13a and the less stable was Gapdh. For all groups, just 2 to 3 of the most stable genes were necessary for optimal gene expression data normalization in rat liver. Genes encoding ribosomal proteins are the most appropriated for normalization of expression data in the presented animal model. By contrast, Gapdh, one of the most used genes in normalization, is not recommendable due to its high intergroup variation.

Feeding n-6 polyunsaturated fatty acids (PUFA) increases the endometrial percentages of linoleic and arachidonic acids (AA), enhances the synthesis of prostaglandin F2α (PGF2α), and improves uterine health. In contrary, the n-3 PUFA, eicosapentaenoic acid, and docosahexaenoic acid may play pivotal roles by suppressing the synthesis of uterine PGF2α, a component being centrally involved in the control of the bovine estrous cycle and in early embryo survival. The objectives of the present study were to determine the effect of feeding a diet enriched in either α-linolenic acid (n-3) or linolenic acid (n-6) on the uterine expression of genes related to prostaglandin cascade and uterine release of PGF2α (measured as 13, 14-dihydro-15-keto PGF2α [PGFM]). From calving to 60 days in milk, cows (n = 24) were fed isonitrogenous, isocaloric, and isolipidic diets that differed in the ratio of n-3/n-6 PUFA. Treatments including palm oil ([PLM]; saturated FA, n = 8), soybean whole roast ([SOY]; n-6, n = 8), and linseed extruded ([LIN]; n-3, n = 8). At 30 days in milk, the ovulatory cycles of cows were synchronized using 2 injections of PGF2α with a 14-day interval. On day 15 postovulation, cows were injected with oxytocin and blood samples were collected to monitor the uterine release of PGF2α (measured as PGFM) and uterine endometrial biopsies were prepared to evaluate the expression of genes related to prostaglandin cascade (prostaglandin F synthase [PGFS], prostaglandin E synthase [PGES], prostaglandin endoperoxide synthase-2 [PGHS-2]), phospholipase A2 (PLA2), peroxisome proliferator-activated receptors [PPAR]). Results showed that uterine endometrial PPAR-δ genes were higher in cows fed LIN (3.17-fold) compared with cows fed PLM or SOY (P < 0.05). The messenger RNA (mRNA) level of PGES in the LIN group was threefold as high as those found in SOY and PLM diets (P < 0.05). The mean relative gene expression of PLA2 and PGFS was increased in animals fed the SOY diet (2.4- and 1.7-fold, respectively) compared with LIN and PLM diets (P < 0.05). The expression of mRNA for the PGHS-2, PPAR-α, and PPAR-γ was not influenced by the diet effect. Dietary inclusion of soy FAs was associated with an increase in the PGFM concentration, possibly through an increase in the expression of genes involved in prostaglandin cascade. The uterine concentration of PGFM, however, was decreased in cows fed diets containing n-3 FAs., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Okadaic acid (OA), a main component of diarrheic shellfish poisoning (DSP) toxins, is a strong and specific inhibitor of the serine/threonine protein phosphatases PP1 and PP2A. However, not all of the OA-induced effects can be explained by this phosphatase inhibition, and controversial results on OA are increasing. To provide clues on potential mechanisms of OA other than phosphatase inhibition, here, acute toxicity of OA was evaluated in zebrafish, and changes in gene expression in zebrafish liver tissues upon exposure to OA were observed by microarray. The i.p. ED50 (6 h) of OA on zebrafish was 1.54 μg OA/g body weight (bw). Among the genes analyzed on the zebrafish array, 55 genes were significantly up-regulated and 36 down-regulated in the fish liver tissue upon exposure to 0.176 μg OA/g bw (low-dose group, LD) compared with the low ethanol control (LE). However, there were no obvious functional clusters for them. On the contrary, fish exposure to 1.760 μg OA/g bw (high-dose group, HD) yielded a great number of differential expressed genes (700 up and 285 down) compared with high ethanol control (HE), which clustered in several functional terms such as p53 signaling pathway, Wnt signaling pathway, glutathione metabolism and protein processing in endoplasmic reticulum, etc. These genes were involved in protein phosphatase activity, translation factor activity, heat shock protein binding, as well as transmembrane transporter activity. Our findings may give some useful information on the pathways of OA-induced injury in fish., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Relative quantification is the strategy of choice for processing real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) data in microRNA (miRNA) expression studies. Normalization of relative quantification data is performed by comparison to reference genes. In teleost species, such as grass carp (Ctenopharyngodon idella), the determination of reference miRNAs and the optimal numbers of these that should be used has not been widely studied. In the present study, the stability of seven miRNAs (miR-126-3p, miR-101a, miR-451, miR-22a, miR-146, miR-142a-5p and miR-192) was investigated by RT-qPCR in different tissues and in different development stages of grass carp. Stability values were calculated with geNorm, NormFinder, BestKeeper and Delta CT algorithms. The results showed that tissue type is an important variability factor for miRNA expression stability. All seven miRNAs had good stability values and, therefore, could be used as reference miRNAs. When all tissues and developmental stages were considered, miR-101a was the most stable miRNA. When each tissue type was considered separately, the most stable miRNAs were 126-3p in blood and liver, 101a in the gills, 192 in the kidney, 451 in the intestine and 22a in the brain, head kidney, spleen, heart, muscle, skin and fin. 126-3p was the most stable reference miRNA gene during developmental stages 1-5, while 22a was the most stable during developmental stages 6-18. Overall, this study provides valuable information about the reference miRNAs that can be used to perform appropriate normalizations when undertaking relative quantification in RT-qPCR studies of grass carp., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Chronic arsenic exposure results in higher risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. The purpose of this study was to investigate the effects on expression of selected genes in the blood lymphocytes from 159 people exposed chronically to arsenic in their drinking water using a novel RT-PCR TaqMan low-density array (TLDA). We found that expression of tumor necrosis factor-α (TNF-α), which activates both inflammation and NF-κB-dependent survival pathways, was strongly associated with water and urinary arsenic levels. Expression of KCNA5, which encodes a potassium ion channel protein, was positively associated with water and toe nail arsenic levels. Expression of 2 and 11 genes were positively associated with nail and urinary arsenic, respectively. Because arsenic exposure has been reported to be associated with long QT intervals and vascular disease in humans, we also used this TLDA for analysis of gene expression in human cardiomyocytes exposed to arsenic in vitro. Expression of the ion-channel genes CACNA1, KCNH2, KCNQ1 and KCNE1 were down-regulated by 1-μM arsenic. Alteration of some common pathways, including those involved in oxidative stress, inflammatory signaling, and ion-channel function, may underlay the seemingly disparate array of arsenic-associated diseases, such as cancer, cardiovascular disease, and diabetes.

Physical exercise has been demonstrated to be neuroprotective in both clinical and laboratory settings. However, the exact mechanism underlying this effect is unclear. Our study aimed to investigate whether pre-ischemic treadmill training could serve as a form of ischemic preconditioning in a rat model undergoing middle cerebral artery occlusion (MCAO). Thirty-six rats were divided into three groups: a sham control group, a non-exercise with operation group and an exercise with operation group. After treadmill training, ischemia was induced by occluding the MCA for 2 h, followed by reperfusion. Half of the rats in each group were sacrificed for mRNA detection of mGluR5 and NR2B 80 min after occlusion. The remaining animals were evaluated for neurological deficits by behavioral scoring and then decapitated to assess the infarct volume. The mRNA expression of mGluR5 and NR2B was detected by real-time PCR. The results suggest that pre-ischemic treadmill training may induce brain ischemic tolerance by reducing the mRNA levels of mGluR5 and NR2B, and thus, the results indicate that physical exercise might be an effective method to establish ischemic preconditioning.

Background: Sepsis is a serious worldwide health concern, and Escherichia coli (E. coli) is the main cause. This study investigates the co-expression of blaCTX-M1 and iutA, csgA, and kpsMII genes in E. coli isolated from septicemic patients, aiming to clarify the interaction between virulence and resistance. Methods: This study evaluated 100 E. coli isolates from septicemic patients. With the disc diffusion method, antibiotic susceptibility was confirmed. The use of ceftazidime–clavulanic acid allowed for the confirmation of ESBL. PCR and real-time PCR were used to detect virulence and beta-lactamase genes. The expression levels of important genes were compared between isolates in LB and blood. Results: Antibiotic resistance was common in isolates carrying blaCTX-M1, including tetracycline (93%) and erythromycin (99%). Instead, there was no resistance to fosfomycin and 3% resistance to carbapenems. Real-time PCR revealed more expression levels in blood for the virulence genes kpsMII and csgA. Pathogenicity and resistance increased with blaCTX-M1 co-expression with the kpsMII and csgA genes. Conclusions: The coexistence of ESBL and virulence genes in E. coli isolates significantly increases antibiotic resistance and infection severity. Monitoring of these genes is critical for developing effective therapeutic strategies. The key to treating these diseases is having sophisticated diagnostic tools and using antibiotics cautiously. [ABSTRACT FROM AUTHOR]

Objectives: Irisin has emerged as a potential cardiovascular biomarker with protective effects. This study aimed to evaluate serum irisin levels and FNDC5 gene expression in obese individuals undergoing bariatric surgery and to assess irisin's role as a cardiovascular biomarker in obesity and post-surgery. Method: Forty severely obese participants and 40 healthy, normal-weight controls were evaluated at baseline, 6 months and 12 months after surgery. Serum irisin was measured using ELISA and FNDC5 gene expression was assessed via Real-Time PCR. Various biochemical, anthropometric and clinical parameters were also measured. Results: Serum irisin levels decreased significantly from 10.45±2.49 ng/mL at baseline to 7.66±1.49 ng/mL at 12 months post-surgery (p = 0.000). FNDC5 gene expression also significantly declined (p = 0.000). Irisin levels were positively correlated with BMI and FNDC5 expression and inversely correlated with cholesterol, LDL, triglycerides, CRP, MDA and hs-Tn. Higher irisin levels were associated with lower cholesterol, LDL, CRP and MDA levels. At 12 months, irisin was negatively correlated with cholesterol, ApoB/ApoA ratio and hs-Tn. Conclusion: Irisin may serve as a cardiovascular biomarker in obese individuals both before and after bariatric surgery. Elevated irisin levels are associated with obesity but decrease following surgery, correlating with inflammatory markers and cardiovascular risk factors. These results suggest that higher irisin levels could be linked to a lower cardiovascular risk in obese patients. [ABSTRACT FROM AUTHOR]

Background and Objectives During chronic hepatitis B virus infection, the dynamic balance between virus replication and the host immune response is crucial in developing liver disease. In this study, the level of expression of programmed death type 1 in asymptomatic donors infected with hepatitis B during the natural course of the infection was investigated. Materials and Methods In this case-control study, 120 blood donors were divided into two groups. The first control group included 60 healthy individuals who tested negative for HBsAg and anti-HBc. The second group, known as the case group, comprised 60 asymptomatic HBV-infected blood donors who tested positive for HBsAg and anti-HBc. All participants were entered from the Tehran Blood Center in 2018. To check gene expression after RNA extraction and cDNA synthesis, a Real-Time PCR test was performed for the PD-1 gene and β-actin reference gene, then using REST software, gene expression changes compared to the healthy group were checked Results All the samples of asymptomatic HBV-infected blood donors were 100% positive for total anti-HBc, anti-HBe, and negative for HBe Ag. The gene expression levels were analyzed using REST software, utilizing Cycle Threshold values obtained from Real-Time PCR tests for the PD-1 gene and a reference gene. The analysis revealed 1.5 times increase in PD-1 gene expression in asymptomatic HBV-infected donors compared to healthy donors. However, this increase was not found to be statistically significant Conclusions PD-1 gene expression does not change during the normal course of chronic HBV infection in asymptomatic HBV-infected donors and is similar to healthy individuals. [ABSTRACT FROM AUTHOR]

Given the rising population and food demand, it is imperative to devise solutions to enhance plant resilience against abiotic stresses. Salinity stress impacts plant growth but also hampers plant performance and productivity. Plant hormones have emerged as a viable remedy to mitigate the detrimental effects of salinity stress on plants. This study delved into the molecular investigation of the impact of 24-Epibrassinolide (EBL) on Okra plants (Abelmoschus esculentus L.) under two levels of salinity stress (75 and 150 mM), scrutinizing morphological, biochemical, and physiological parameters. Salinity stress led to a decline in growth, pigment and protein content, with EBL application ameliorating these indicators, albeit insignificantly impacting protein levels. Salinity triggered an upsurge in soluble sugars, proline, antioxidant enzymes (CAT, SOD, GP, and APX), and sodium levels, while reducing potassium and micronutrient concentrations (copper, iron, zinc). It downregulated the expression of NHX1, NHX4, SOS1, SOS2, and SOS3 genes. EBL treatment bolstered potassium and micronutrient uptake, upregulated gene expression and enzymatic antioxidants, and elevated soluble sugar and proline levels. Analysis of the outcomes across these parameters suggests that EBL holds promise as an effective agent in mitigating salinity stress in Okra plants. [ABSTRACT FROM AUTHOR]

Background: Acute myeloid leukemia (AML) has a heterogeneous molecular profile, clinical presentations, and response to treatments and outcomes. DNA methylation is conducted by DNA methyltransferases including DNMT3B. Poly ADP-ribose polymerase 1 belongs to a family of enzymes that mediate important cellular processes including DNA repair, transcription, and cell death/cell proliferation, and it is involved in the development, spread, treatment, and prognosis of some cancers. The objective of this study is to assess the impact of PARP1 and DNMT3B genes expression on laboratory characteristics, response to treatment and survival in Egyptian cytogenetically normal AML patients. Methods: This study included 67 Egyptian CN-AML patients in addition to 8 healthy bone marrow donors. Measurement of DNMT3B and PARP1 gene expression was done on bone marrow samples via real-time semiquantitative polymerase chain reaction. Result: Expression of both DNMT3B and PARP1 genes was significantly upregulated in AML (P =.001, P =.036, respectively). Upregulated DNMT3B was associated with higher total leukocyte count (TLC), PB, and BM blast cell%. Also, upregulated PARP1 correlated with higher TLC, PB, and BM blast cell%. High expression of both DNMT3B and PARP1 correlated with greater frequencies of FLT3-ITD. High DNMT3B expression, and combined upregulation of both PARP1 and DNMT3B genes associated significantly with ELN stratification. But no correlation was found with response (CR), overall survival (OS), disease-free survival (DFS), or event-free survival (EFS). Conclusion: Our findings highlight the importance of considering DNMT3B and PARP1 expression levels as potential prognostic biomarkers for progression and aggressiveness of CN-AML patients in AML. Assessing their expression levels could be an indicator to guide treatment decisions and potentially improve patient outcomes. [ABSTRACT FROM AUTHOR]

The expression of the LYST and SLFN12L genes in peripheral blood leukocytes (PBL) in patients with pulmonary sarcoidosis with a chronic course of the disease and in healthy people was studied. Patients with chronic pulmonary sarcoidosis, on the second stage of the disease (20 people without therapy, average age of whom was 41.00 ± 12.56 years) and 25 healthy people (average age was 45.86 ± 2.13 years) were enrolled in this study. The level of gene expression was determined by real-time PCR. A significant decrease in the transcripts of the SLFN12L gene (p = 0.002) and a low content of mRNA of the LYST gene (p = 0.09) in the PBL of patients with pulmonary sarcoidosis compared to healthy people was established. Differential expression of LYST and SLFN12L may indicate the involvement of these genes in the pathogenesis of this disease, and it is possible they participate in the modulation of immune reactions during the development of inflammatory processes in pulmonary sarcoidosis. [ABSTRACT FROM AUTHOR]

Bipolar disorder (BD) is a psychiatric condition that is frequently misdiagnosed and linked to inadequate treatment. Long non‐coding RNAs (lncRNAs) have lately gained recognition as crucial genetic elements and are now regarded as regulatory mechanisms in the neurological system. Our objective was to measure the quantities of HOXA‐AS2 and MEG3 ncRNA transcripts. HOXA‐AS2 and MEG3 ncRNA levels were checked in the peripheral blood of 50 type I BD and 50 control samples by real‐time PCR. Furthermore, we conducted ROC curve analysis and correlation analysis to examine the association between gene expression and specific clinical characteristics in instances with BD. Additionally, a computational study was performed to investigate the binding sites of miRNAs on the HOXA‐AS2 and MEG3 lncRNAs. BD subjects showed a significant increase in the expression of HOXA‐AS2 and MEG3 compared to controls. The lncRNAs HOXA‐AS2 and MEG3 have an area under the ROC curve (AUC) values of 0.70 and 0.71, respectively. There was a significant correlation between the expression levels of ncRNAs HOXA‐AS2 and MEG3 in the peripheral blood of patients with BD and occupation scores. The data presented indicate a potential correlation between the expression of HOXA‐AS2 and MEG3 lncRNAs with an elevated risk of BD. Furthermore, these lncRNAs may be linked to several molecular pathways. Our findings indicate that the amounts of lncRNAs HOXA‐AS2 and MEG3 in transcripts might be a promising potential biomarker for patients with BD. [ABSTRACT FROM AUTHOR]

Objective Potato (Solanum tuberosum. L.) belongs to the Solanaceae family. It is the third important crop plant as human food source after wheat and rice. Several biotic and abiotic stresses affect potato production and reduce its potential yield. In the drought stress and dehydration, the expression level of many genes changes and the accumulation of stress-related proteins is affected. Chitinases are proteins that show a basic level of expression in normal conditions, but their expression increases dramatically in disease conditions and some abiotic stresses. The existence of great diversity in plant chitinases and its induction by a wide range of biotic and abiotic factors indicates their important role in the functions related to defense and stress. According to the Economic importance and Limiting effects of drought stress for plant growth in this research, the effect of drought stress on the expression level of different classes of chitinase gene was investigated. Materials and methods In this research, the members of chitinase gene family were identified in potato genome by bioinformatics and computational methods. Then, one gene was selected from each class of chitinase gene based on RNA-Seq data analysis in drought stress, and their expression level was evaluated following a water deficit treatment (50% field capacity) by Real-time PCR analysis. The expression level of genes was measured using the Livak and Schmittgen method using the 2-ΔΔct formula. Results Under drought stress conditions, the majority of chitinase gene classes exhibited distinct expression patterns. Notably, among the four classes of identified chitinase genes in potato, class I exhibited up-regulation, whereas class V displayed a down-regulated trend. Conclusions In conclusion, our findings suggest a significant role for chitinases in potato's response to drought stress. The outcomes of this study offer valuable insights for screening potato cultivars/genotypes for drought tolerance and provide a foundation for molecular genetic strategies aimed at engineering drought-resistant potatoes. [ABSTRACT FROM AUTHOR]

Background: Selective breeding in pigs based on a higher potential of disease resistance can be achieved by studying the association between immune responsiveness and susceptibility to infectious diseases. The early immune responsiveness of pigs assessed in a quantifiable scale for different determinant cytokine genes' expression involved in regulation of immune response can be a major determinant for evaluating the immune responsiveness. Methods: In this study, we carried out the quantitative relative expression of candidate cytokine genes [Interleukin-1 beta-(IL1β), IL6, IL10 and tumor necrosis factor-alpha (TNFβ) and toll-like receptor-4 (TLR4) gene expression in the lipopolysaccharide (LPS) stimulated peripheral blood mononuclear cells (PBMCs) of Zovawk (indigenous) and Large White Yorkshire (LWY-exotic) pig breeds using real-time PCR to understand the differences in swift immune responsiveness against gram-negative bacteria. Results: Zovawk PBMCs' pro-inflammatory cytokines IL1β and IL6 expression increased rapidly with LPS stimulation up to 12 h, being significantly higher as early as 4 h compared to that of the LWY PBMCs. In Zovawk pigs, the pro-inflammatory cytokine genes' expression was found to be quick and high; whereas, in LWY pigs the response was slow and low. Interestingly, the expression of IL10 was not detected in LPS-stimulated PBMCs of Zovawk pigs indicating that the remarkably higher expressions of IL6 and IL1β in response to LPS are within the threshold of the Zovawk pigs which have evolved through generations. Our findings clearly indicate the sturdy and early immune responsiveness of indigenous pigs against gram-negative bacteria over the exotic pigs. [ABSTRACT FROM AUTHOR]

Background: Bread Wheat is the most extensively cultivated wheat and one of the four major crops in the world that constitutes the principal food of more than 30% of the world population. Biotic and abiotic environmental stressors are major factors limiting plant growth and productivity, which play a significant role in determining the yield and production potential of plants by affecting morphological, physiological, biochemical, and molecular processes. Among the abiotic stresses, the deficiency of micronutrients in the soil is important. Micronutrients regulate food metabolism in humans, and their deficiency endangers human health. Iron and zinc are essential micronutrients for human health and cofactors of many vital enzymes involved in many human metabolic processes. In plants, iron is the most required element among all micronutrients. It is a part of the catalytic group of many oxidation and reduction enzymes and is required for chlorophyll synthesis. To facilitate the adequate uptake and prevent excessive absorption of iron, plants have developed a balanced network to regulate the uptake, use, and storage of ions. In fact, such adjustment processes depend on genes that regulate ion homeostasis in plants. Due to the existence of a large allohexaploid genome and technical challenges in wheat transformation, few genes involved in iron and zinc uptake, transfer, and storage have been characterized functionally. Considering the important role of ZIP proteins in iron uptake efficiency, investigating the expression of the ZIP genes in Fe-efficient and - inefficient bread wheat cultivars can be effective in improving Fe-efficient cultivars in this valuable crop. Therefore, this research aimed to evaluate the expression of ZIP3, ZIP6, and ZIP7 genes in the leaves and roots of two Fe-efficient and -inefficient bread wheat cultivars at different growth stages under iron deficiency stress. Methods: This research was carried out in a completely randomized design (CRD) based on a factorial experiment with three replications in the research greenhouse of the Faculty of Agriculture, Urmia University. The first factor was two Fe-efficient (Pishtaz) and -inefficient (Flat) bread wheat cultivars, the second factor was two soil iron levels (iron deficiency and sufficiency, respectively, 1.4 and 10 mg/kg of soil), and the third factor was two sampling stages (vegetative and reproductive, respectively, one month after planting and 30% heading). To evaluate the expression of genes, the roots and leaves of the plants were sampled at each growth stage. The seeds were obtained from the Iranian Seed and Plant Improvement Institute, disinfected with 1% hydrogen peroxide, and planted at a depth of 4 cm in the soil. The plants were irrigated using distilled water to the extent of field capacity during the growing period. Results: The results of variance analysis of the relative expression of all three studied genes showed that the interaction effect of cultivar × organ × sampling stage was significant at the probability level of 1%. The comparison of the means for the cultivar × organ × sampling stage interaction effect revealed the highest ZIP3 expression in the roots of the Fe-efficient cultivar (Pishtaz) in the vegetative and reproductive stages. The relative expression of this gene was higher in the roots of the Fe-inefficient cultivar (Falat) than that of the Fe-efficient cultivar (Pishtaz). However, the Fe-inefficient cultivar (Falat) showed the highest relative expression increase in the leaf in both reproductive and vegetative stages, but the difference in the gene expression level in the leaf between the two growth stages was not statistically significant. The lowest gene expression level in the leaf belonged to the Pishtaz cultivar. The comparison of the means of cultivar × organ × sampling stage for the ZIP6 gene indicated an increase in the relative expression of this gene in the roots of the Fe-efficient (Pishtaz) and -inefficient (Falat) varieties in the vegetative and reproductive stages, respectively. The comparison of the means of cultivar × organ × sampling stage for the ZIP7 gene indicated the highest relative expression of this gene in the roots of the Fe-efficient cultivar (Pishtaz) at the vegetative stage. The relative expression level of this gene in the root of the Fe-efficient variety in the vegetative stage was significantly higher than that in the reproductive stage. In both vegetative and reproductive stages in the leaf, the increase in gene expression was higher in the Fe-inefficient cultivar. Conclusion: The increased ZIP3 expression in iron deficiency conditions in the roots of the Feefficient cultivar at the vegetative stage demonstrates the possible role of this gene in Fe uptake from the soil and its transfer to the aerial parts of the plant in the early growth phase. The ZIP6 gene was expressed in both roots and leaves throughout the entire growth period of the plant. However, the expression level of this gene increased with the age of the plant. Therefore, the ZIP6 gene is probably responsible for Fe uptake and transport to different organs throughout the entire growth period of the plant and plays an important role in preserving iron in iron deficiency conditions. The ZIP7 gene is expressed in both leaves and roots in iron deficiency conditions, but the level of expression is higher in the roots of the Fe-efficient variety during the vegetative stage. This gene may be involved in iron uptake from the soil and its transfer to aerial organs. [ABSTRACT FROM AUTHOR]

Background: MS (Multiple sclerosis) is a progressive neurologic disorder often appearing in the third decade of life. MS is the most frequent demyelinating disease of the central nervous system. The development of MS is influenced by environmental, genetic, and epigenetic factors. The bulk of the human transcriptome comprises lncRNAs, which play crucial regulatory roles. We aimed to assess the SNHG3 and BCYRN1 lncRNA expression in blood samples from MS patients and how these lncRNAs and disease activity are related. Methods: A total of 100 MS patients, including 8 primary progressive (PP), 82 relapsing-remitting (RR), and 10 secondary progressive (SP) MS, as well as 100 healthy controls, had their blood samples taken. Gene expression was assessed using quantitative real-time PCR. Recognizing the receiver operating characteristic (ROC) curve analysis, the diagnostic potential of lncRNA levels was evaluated. Results: Expressions of SNHG3 and BCYRN1 were found to have significantly increased (p < 0.0001). SNHG3 expression level showed significant differences compared to age groups and MS subtypes (p value = 0.001 and p value = 0.02). Furthermore, patients with a family history showed elevated BCYRN1 expression with a p value of 0.01. Considering the age factor, BCYRN1 exhibits altered expression levels in patient groups compared to healthy controls (p value 0.04). Additionally, the novel biomarkers SNHG3 and BCYRN1 can be used to diagnose MS (AUC = 0.97 and AUC = 0.88, respectively). Discussion: Increased levels of SNHG3 and BCYRN1 in the serum may serve as potential molecular biomarkers for the MS diagnosis. [ABSTRACT FROM AUTHOR]

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The collective involvement of virulence markers of Escherichia coli as an emerging pathogen associated with periodontitis remains unexplained. This study aimed to implement an in vitro model of infection using a human epithelial cell line to determine the virulome expression related to the antibiotic and disinfectant resistance genotype and pulse field gel electrophoresis (PFGE) type in E. coli strains isolated from patients with periodontal diseases. We studied 100 strains of E. coli isolated from patients with gingivitis (n = 12), moderate periodontitis (n = 59), and chronic periodontitis (n = 29). The identification of E. coli and antibiotic and disinfectant resistance genes was performed through PCR. To promote the expression of virulence genes in the strains, an in vitro infection model was used in the human epithelial cell line A549. RNA was extracted using the QIAcube robotic equipment and reverse transcription to cDNA was performed using the QuantiTect reverse transcription kit (Qiagen). The determination of virulence gene expression was performed through real-time PCR. Overall, the most frequently expressed adhesion genes among the isolated strains of gingivitis, moderate periodontitis, and chronic periodontitis were fimH (48%), iha (37%), and papA (18%); those for toxins were usp (33%); those for iron acquisition were feoB (84%), fyuA (62%), irp-2 (61%), and iroN (35%); those for protectins were traT (50%), KpsMT (35%), and ompT (28%); and those for pathogenicity islands were malX (45%). The most common antibiotic and disinfectant resistance genes among gingivitis, moderate periodontitis, and chronic periodontitis strains were sul-2 (43%), blaSHV (47%), blaTEM (45%), tet(A) (41%), dfrA1 (32%), marR-marO (57%), and qacEA1 (79%). The findings revealed the existence of a wide distribution of virulome expression profiles related to the antibiotic and disinfectant resistance genotype and PFGE type in periodontal strains of E. coli. These findings may contribute toward improving the prevention and treatment measures for periodontal diseases associated with E. coli. [ABSTRACT FROM AUTHOR]

The annual killifish Austrolebias charrua is an endangered species, endemic to the southern region of South America, which inhabits temporary ponds that emerges in the rainy season. The main anthropogenic threat driving the extinction of A. charrua stems from extensive agriculture, primarily due to the widrespread use of glyphosate-based herbicides near their habitats. Annual killifishes have been used as models for ecotoxicological studies but, up to now, there are no studies about reference genes in any Austrolebias species. This represents an obstacle to the use of qPCR-based technologies, the standard method for gene expression quantification. The present study aimed to select and validate potential reference genes for qPCR normalization in the annual killifish Austrolebias charrua considering different tissues, gender and environmental conditions. The candidate reference genes 18 s, actb, gapdh, ef1a, shox, eif3g, and the control gene atp1a1 were evaluated in male and female individuals in three different tissues (brain, liver, and gills) under two experimental conditions (control and acute exposition to Roundup Transorb®). The collected tissues were submitted to RNA extraction, followed by cDNA synthesis, cloning, sequencing, and qPCR. Overall, 18 s was the most stable reference gene, and 18 s and ef1a were the most stable combination. Otherwise, considering all variables, gapdh and shox were the least stable candidate genes. Foremost, suitable reference genes were validated in A. charrua, facilitating accurate mRNA quantification in this species, which might be useful for developing molecular tools of ecotoxicological assessment based on gene expression analysis for environmental monitoring of annual killifish. [ABSTRACT FROM AUTHOR]

Short-chain chlorinated paraffins (SCCPs) are ubiquitous, persistent chemicals whose toxicity and potential impacts on aquatic ecosystems have been overlooked for many years. This study aims to determine the impact of these chemicals on rotifers. As sexual reproduction is often more sensitive to toxicants than amictic reproduction, this study focuses on endpoints describing sexual reproduction and on the impact on the gene expression of three receptors associated with reproduction: retinoid-x-receptor (rxr), retinoid activated receptor (rar) and membrane-associated progesterone receptor (mapr). Brachionus calyciflorus was exposed to environmental concentrations of SCCPs (10,100 and 1000 ng/L) and the impact on sexual reproduction (mixis rate, fertilization rate, resting egg production and viability, inter-generational effects) was assessed. Variations in the gene expressions of rxr, rar and mapr were also studied through RT-qPCR analysis. Our results show that SCCPs increase the mixis rate but decrease the fertilization rate, leading to unaltered resting egg production. Exposure to SCCPs also affected the mRNA levels of the studied receptors in ways which could be linked to observed changes in mixis and fertilization rates. [ABSTRACT FROM AUTHOR]

As sturgeon breeding has proliferated, there has been a heightened demand for growth stimulators in their diets. This study aimed to determine the impact of dietary chitosan on growth performance, whole‐body proximate composition, growth‐related gene expression, and intestinal histology in juvenile Acipenser stellatus. A total of 180 A. stellatus juveniles with an average weight of 31.90 ± 0.73 g were fed with diets containing 0 (control), 1.5, 3.0, 4.5, and 6.0 g chitosan.kg−1 basic diet for eight weeks. The findings revealed a significant enhancement in growth performance with rising chitosan concentrations. Furthermore, chitosan supplementation upregulated the expression of the growth hormone gene in both brain and liver tissues. In liver samples, the most pronounced expression of the insulin‐like growth factor‐1 gene was noted at 6.0 g chitosan.kg−1, while in brain samples, peak expressions were observed in both the 4.5 and 6.0 g chitosan.kg−1 treatments. While the whole‐body proximate composition remained relatively stable, there was a notable decrease in whole‐body lipids with the escalation of chitosan dosage. Intestinal villi dimensions, both height and width, were amplified in the chitosan‐supplemented groups compared to controls. In summation, chitosan supplementation showed promise in bolstering growth performance, refining intestinal morphology, and enhancing growth‐related gene expression. Analysis of the polynomial regression of weight gain and specific growth rate revealed that the optimum dietary chitosan requirements in A. stellatus were 5.32 and 5.21 g chitosan.kg−1, respectively. [ABSTRACT FROM AUTHOR]

Aim: This study aimed to evaluate the expression of tcdA, tcdB, and binary toxin genes (cdtA and cdtB) by Real-Time PCR and molecular typing of Clostridioides difficile isolated from patient diarrhea samples from Hamadan Hospitals, west of Iran. Background: The concentration of C. difficile toxins (CDTs) is associated with the severity of the disease and the mortality rate. Measuring CDT levels could provide a reliable and objective means of determining the severity of C. difficile infection (CDI). Methods: From November 2018 to September 2019, 130 diarrhea samples were collected from hospitalized patients in three hospitals in Hamadan. C. difficle isolates were detected by culture and PCR. The presence of the genes encoding the toxin was identified by PCR, whereas the measurement of toxin expression was conducted using a relative Real-Time PCR technique. Genetic linkage of the isolates was also assessed by Ribotyping and Repetitive Extragenic Palindromic (rep-PCR) methods. Results: Among 130 diarrhea samples, 16 (12.3%) were positive for C. difficile. Genes encoding cdtA and tcdB were detected in all isolates, and 8 (50%) and 6 (37.5%) isolates were positive for the cdtA and cdtB genes. Real-time PCR results showed different expression levels of the toxin genes. A significant increase in the expression of the tcdA gene was observed compared with the control strain (P<0.05). Besides, more expression of cdtA gene was observed in the strains compared with cdtB gene. Ribotyping and rep-PCR results showed high genetic diversity of C. difficile among hospitals investigated. Conclusion: We encountered toxigenic C. difficile strains with various toxin expression levels, ribotypes, and rep types based on the findings of this study. This indicated that various clones from various sources circulate in the hospitals and among patients. [ABSTRACT FROM AUTHOR]

Background and purpose: Breast cancer is the 1st most common cancer in the female population and the third leading cause of cancer mortality in Ladies. Given the importance of early detection of cancer, it is necessary to find biomarkers related to this disease that are essential for the prognosis and early diagnosis of breast cancer. The estrogen receptor gene for beta, whose full name is Estrogen Receptor-β (ESRβ). Our main aim in this study was to investigate the expression changes of this gene in cancer tissue tumor samples compared to normal tissue samples to obtain a biomarker to predict the risk of cancer. Materials and methods: In this research, in 2023 samples were obtained from 30 patients diagnosed with breast cancer who underwent surgery at Omid Hospital in Mashhad. Both tumor tissue and adjacent healthy tissue were collected from each patient. The diagnosis of breast cancer was confirmed by a specialist doctor, and none of the patients had received any prior treatment such as chemotherapy or radiation therapy. Tissue samples were collected immediately after surgery and stored at -70°C. RNA extraction and synthesis were performed, followed by analysis of the expression of the ESR gene along with the GAPDH gene as an internal control, using real-time PCR. Results: In this study, 30 cancer patients were examined, with ages ranging from 32 to 62 years old and a mean age of 47.5 ± 9.38. Among them, one person had tumor grade 1, 16 had grade 2 tumors, and 8 had grade 3 tumors. Metastasis was observed in 11 patients (36.7%), while 19 patients (63.3%) had no metastasis. Regarding tumor size distribution, 5 patients (16.7%) had tumors smaller than 1 cm, and 25 patients (83.3%) had tumors sized between 1 and 2 cm. The study focused on changes in the expression of the ESRβ gene in both tumor and adjacent healthy tissues of breast cancer patients. It was found that the gene expression was higher in tumor samples compared to the adjacent healthy tissues. Using SPSS software, the analysis revealed a significant relationship between gene expression intensity and tumor grade across all three groups. Additionally, a significant difference was observed between patients with and without tumor metastasis. Conclusion: Overall, the findings of this study indicate a significant correlation between gene expression intensity and tumor grade across all three groups. Moreover, there is a significant distinction between patients with and without tumor metastasis. Notably, a considerable expression difference was observed between healthy and tumor samples. Hence, this gene could serve as a potential biomarker for cancer diagnosis.

Pr1A a subtilisin-like protease was generated by Metarhizium is known to involved in the early stages of fungal invasion of arthropod hosts. Current intended to establish a link between cotton bollworm mortality H. armigera expression on levels of the conidial pr1A gene in Metarhizium. Intriguingly, subtilisin-like proteases were emitted by defensive metabolism on volatile organic compounds in H. armigera products. Fifth day after treatment, conidial of M. anisopliae, M. robertsii, M. majus (6.59, 4.65, and 4.65 × 105 conidia/ml) respectively, resulted in greater than 95% mortality rates. We used particular primers were existence of pr1A genes in M. anisopliae, M. robertsii, M. majus through the pr1A expression was confirmed. Subsequently, investigated Pr1A expression using RT-qPCR and discovered that the Pr1A gene was strongly expressed for conidiogenesis or pathogenesis at 72 h, showing that gene expression is time-dependent. The time pr1A gene expression is critical to understanding its role in disease or fungal development. Finally, secondary metabolic were playing a significant role in VOCs compounds by beta-caryophyllene, octanonene, 1-octadecene, benzene, 1,2-dimethoxy, methylheptenone, benzaldehyde, 9-octadecenoic acid (E), and methyl salicylate though the microbe defence signals by H. armigera interactions Therefore, our research haven been showed, it can be helpful to examine the expression of genes related to conidiogenesis or pathogenesis in M. anisopliae, M. robertsii, M. majus their pathogenic with saprophytic life phases. In the creation techniques to detecting and deploying pathogenic biological control agents. [ABSTRACT FROM AUTHOR]

Several crustaceans including shrimps change the amount of specific free amino acids to regulate the osmotic pressure in their bodies. Kuruma shrimp Penaeus japonicus also increases the concentration of alanine (Ala) in the abdominal muscle following the increase of environmental salinity. In the present study, to elucidate the mechanisms of changes in Ala accumulation of kuruma shrimp depending on salinity, we cloned the gene encoding alanine aminotransferase (ALT), an enzyme involved in Ala biosynthesis, and examined its expression profile. It was found that the full‐length kuruma shrimp ALT1 cDNA consisted of 3,301 bp, encoding 514 amino acids, and that all amino acid residues important for ALT activity were conserved. Phylogenetic analysis also indicated that the ALT gene cloned in this study was classified as ALT1. Moreover, we examined the expression levels of the ALT1 gene in the abdominal muscle and the hepatopancreas of kuruma shrimp acclimated at 17‰, 34‰, and 40‰ salinities, resulting that the mRNA levels of the ALT1 genes in both tissues of the shrimp acclimated at 40‰ were significantly higher than those at 17‰ for 12 h (p < 0.05). The mRNA levels of the ALT1 gene in the abdominal muscle of the shrimp acclimated for more than 24 h tended to increase following the increase of environmental salinity. These results indicate that ALT1 is responsible for the increase of free Ala concentration in the abdominal muscle of kuruma shrimp to regulate osmotic pressure at high salinity. [ABSTRACT FROM AUTHOR]

Importance: Haemaphysalis longicornis is an obligate blood-sucking ectoparasite that has gained attention due its role of transmitting medically and veterinary significant pathogens and it is the most common tick species in Republic of Korea. The preferred strategy for controlling ticks is a multi-antigenic vaccination. Testing the efficiency of a combination antigen is a promising method for creating a tick vaccine. Objective: The aim of the current research was to analyze the role of subolesin and enolase in feeding and reproduction of H. longicornis by gene silencing. Methods: In this study, we used RNA interference to silence salivary enolase and subolesin in H. longicornis. Unfed female ticks injected with double-stranded RNA targeting subolesin and enolase were attached and fed normally on the rabbit's ear. Real-time polymerase chain reaction was used to confirm the extent of knockdown. Results: Ticks in the subolesin or enolase dsRNA groups showed knockdown rates of 80% and 60% respectively. Ticks in the combination dsRNA (subolesin and enolase) group showed an 80% knockdown. Knockdown of subolesin and enolase resulted in significant depletion in feeding, blood engorgement weight, attachment rate, and egg laying. Silencing of both resulted in a significant (p < 0.05) reduction in tick engorgement, egg laying, egg hatching (15%), and reproduction. Conclusions and Relevance: Our results suggest that subolesin and enolase are an exciting target for future tick control strategies. [ABSTRACT FROM AUTHOR]

The administration route affects the biodistribution of a gene transfer vector and the expression of a transgene. A simian adenovirus 1 vector carrying firefly luciferase and GFP reporter genes (SAdV1-GFluc) were constructed, and its biodistribution was investigated in a mouse model by bioluminescence imaging and virus DNA tracking with real-time PCR. Luciferase activity and virus DNA were mainly found in the liver and spleen after the intravenous administration of SAdV1-GFluc. The results of flow cytometry illustrated that macrophages in the liver and spleen as well as hepatocytes were the target cells. Repeated inoculation was noneffective because of the stimulated serum neutralizing antibodies (NAbs) against SAdV-1. A transient, local expression of low-level luciferase was detected after intragastric administration, and the administration could be repeated without compromising the expression of the reporter gene. Intranasal administration led to a moderate, constant expression of a transgene in the whole respiratory tract and could be repeated one more time without a significant increase in the NAb titer. An immunohistochemistry assay showed that respiratory epithelial cells and macrophages in the lungs were transduced. High luciferase activity was restricted at the injection site and sustained for a week after intramuscular administration. A compromised transgene expression was observed after a repeated injection. When these mice were intramuscularly injected for a third time with the human adenovirus 5 (HAdV-5) vector carrying a luciferase gene, the luciferase activity recovered and reached the initial level, suggesting that the sequential use of SAdV-1 and HAdV-5 vectors was practicable. In short, the intranasal inoculation or intramuscular injection may be the preferred administration routes for the novel SAdV-1 vector in vaccine development. [ABSTRACT FROM AUTHOR]

Background: Quantifying gene expression is a critical aspect of applied genomics research across all organisms, and real-time PCR has emerged as a powerful tool for this purpose. However, selecting appropriate internal control genes for data normalization presents specific challenges. This study aimed to identify suitable reference genes for gene expression analysis under various conditions, encompassing salinity, low and high-temperature stresses, and different elicitor treatments. These treatments included titanium dioxide, cold plasma, 24-epibrassinolide, and melatonin, resulting in a total of 13 unique treatments and 148 treatment combinations applied to fenugreek plants. Results: As per the analysis performed with the BestKeeper tool, EEF-1α, and GAPDH were recognized as the most stable reference genes under the majority of conditions. Furthermore, the GeNorm and NormFinder tools identified β-tubulin and EEF-1α as the most stable reference genes. The findings of this research demonstrated that, although the stability of three reference genes expression was acceptable in almost all evaluated treatments, fluctuations in their expression were observed under the treatments of cold stress with TiO2 NPs application, cold plasma application with salinity stress, and cold plasma application with high-temperature stress compared to others. Simultaneously, the GeNorm analysis results demonstrated that in the mentioned treatments, relying on only one reference gene is inadequate. To corroborate the results, we examined the expression profile of the SSR gene, a pivotal gene in diosgenin biosynthesis, under all investigated treatments and treatment combinations. The outcomes suggested that employing stable reference genes yielded highly consistent results. Conclusions: The varying expression patterns of the target genes emphasize the crucial need for precise optimization of experimental conditions and selecting stable reference genes to achieve accurate results in gene expression studies utilizing real-time PCR. These findings offer valuable insights into the selection of appropriate reference genes for gene expression analysis under diverse conditions using real-time PCR. [ABSTRACT FROM AUTHOR]

Apocynum venetum L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves as a high-quality fiber material. To gain insights into the gene expression patterns of A. venetum using quantitative real-time PCR (qRT-PCR), it is crucial to identify appropriate reference genes. This study selected nine candidate genes, including α-tubulin (TUA), β-tubulin (TUB), actin (ACT), cyclophilin (CYP), elongation factor-1α (EF-1α), the B family of regulatory subunits of protein phosphatase (PPP2R2, PPP2R3, and PPP2R5), and phosphoglycerate kinase (PGK), to determine the most appropriate reference genes in the leaf, stem, and root tissues of A. venetum. A comprehensive ranking by geNorm, NormFinder, BestKeeper, and RefFinder software and Venn diagrams was used to screen more stable reference genes in different tissues. The two most stable reference genes were CYP and TUA in leaves, PGK and PPP2R3 in stems, and TUA and EF-1α in roots, respectively. The relative expression values of the four genes involved in proline metabolism under polyethylene glycol treatment were used to validate the screened reference genes, and they exhibited highly stable expression levels. These findings represent the first set of stable reference genes for future gene expression studies in A. venetum. They significantly contribute to enhancing the accuracy and reliability of gene expression analyses in this economically important plant species. [ABSTRACT FROM AUTHOR]

HLA-G is the checkpoint molecule involved in the suppression of the immune response. Increased expression of HLA-G and its ILTs receptors have been correlated with tumor progression in various cancer types. In head and neck squamous cell carcinoma (HNSCC) tumors, the effect of HLA-G, ILT2 and ILT4 expression on cancer development has to be explained. The 34 HNSCC patients and 98 controls were genotyped for the HLA-G 14 bp ins/del polymorphism. In HNSCC lesions, HLA-G, ILT2 and ILT4 mRNA expression was analysed using real-time PCR. The association between HLA-G, ILT2 and ILT4 mRNA expression and clinical variables (age at onset, TNM staging system and p16 positivity) was also evaluated. No genetic association between the HLA-G 14 bp ins/del and HNSCC risk was detected (p > 0.05). However, in the non-metastatic HNSCC group, a significantly higher HLA-G mRNA expression was noted in tumors in the T4 stage compared to those in the T1 and T2 stages (p = 0.0289). ILT2 mRNA expression was significantly increased in non-metastatic vs. metastatic tumors (p = 0.0269). Furthermore, a significantly higher ILT4 mRNA expression was noted in tumors in the T1+T2 stage compared to those in the T3 stage (p = 0.0495). Our results suggest that the HLA-G molecule creates an immunological microenvironment involved in HNSCC development. [ABSTRACT FROM AUTHOR]

Background: qPCR is a widely used technique in scientific research as a basic tool in gene expression analysis. Classically, the quantitative endpoint of qPCR is the threshold cycle (CT) that ignores differences in amplification efficiency among many other drawbacks. While other methods have been developed to analyze qPCR results, none has statistically proven to perform better than the CT method. Therefore, we aimed to develop a new qPCR analysis method that overcomes the limitations of the CT method. Our f0% [eff naught percent] method depends on a modified flexible sigmoid function to fit the amplification curve with a linear part to subtract the background noise. Then, the initial fluorescence is estimated and reported as a percentage of the predicted maximum fluorescence (f0%). Results: The performance of the new f0% method was compared against the CT method along with another two outstanding methods—LinRegPCR and Cy0. The comparison regarded absolute and relative quantifications and used 20 dilution curves obtained from 7 different datasets that utilize different DNA-binding dyes. In the case of absolute quantification, f0% reduced CV%, variance, and absolute relative error by 1.66, 2.78, and 1.8 folds relative to CT; and by 1.65, 2.61, and 1.71 folds relative to LinRegPCR, respectively. While, regarding relative quantification, f0% reduced CV% by 1.76, 1.55, and 1.25 folds and variance by 3.13, 2.31, and 1.57 folds regarding CT, LinRegPCR, and Cy0, respectively. Finally, f0% reduced the absolute relative error caused by LinRegPCR by 1.83 folds. Conclusions: We recommend using the f0% method to analyze and report qPCR results based on its reported advantages. Finally, to simplify the usage of the f0% method, it was implemented in a macro-enabled Excel file with a user manual located on https://github.com/Mahmoud0Gamal/F0-perc/releases. [ABSTRACT FROM AUTHOR]