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Salt stress is a serious environmental threat reducing crop yield. Hence, developing any breeding plan requires an understanding of the basic physiology and cell molecular genetic regulation under salinity stress. In this study, we evaluated the effectiveness of gene expression changes on ion homeostasis comprising salt overly sensitive (SOS1) and vacuolar Na+/H+ antiporter (NHX1) along with ion content measurement and proline content in the rice mutants at Rice Research Institute of Iran in 2018-2019. To survey these realities, tolerant mutant genotypes (em₄hs290 and em₄hs84) along with Hashemi parent cultivar, IR28 (sensitive), and FL478 (tolerant) seedlings were treated with 100 mM NaCl. Based on the results of growth indices, the seedling length of Hashemi cultivar and IR28 decreased considerably about 44.7%, and 44.2% reduction to that of the control, and the leaves progressively yellowed. Results showed that proline content and K⁺ and K⁺/Na⁺ ratio increased about ~2–3-fold higher in the tolerant genotypes than in the susceptible ones. Also, the overall amount of the OsNHX1 and SOS1 expression increased in tolerant genotypes compared to the susceptible ones. Accordingly, the compatible solute accumulation significantly advanced resulting in improvement of ionic homeostasis and probably suppresses the stress. Moreover, the variable pattern of gene expression in the two salt-tolerant mutants (em₄hs290 and em₄hs84) and Hashemi parent showed that the induced mutation could increase the salt-tolerant in mutant genotypes through ionic and osmotic homeostasis. Generally, these tolerant mutant genotypes could be applied to develop salt-tolerant varieties in rice breeding programs which can bring on production sustainability.

 

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The current study evaluated the interactive impacts of water temperature and feeding rate on digestive enzymes, intestine histology, growth and stress-related genes, and cultivable intestinal microbiota of Asian seabass (Lates calcarifer). For this purpose, 180 fish (85.0±3.0 g) were reared at three different temperatures (20, 27, and 33 °C) and two feeding rates (apparent satiation and 2.5% of biomass) with three replications for 6 weeks. The results revealed no significant differences among different treatments regarding the activity of digestive enzymes (P˃0.05) of fish reared under different temperatures and feeding rates. The length, width, and thickness of intestinal villi were unaffected by different temperatures and feeding rates (P˃0.05). In addition, no variations were found in the total aerobic bacterial count of fish gut from different experimental groups (P˃0.05). At the molecular level, IGF-I and HSP70 coding genes were found to be highly expressed in experimental treatments (P<0.05). To conclude, present results showed that temperatures between 27 to 33 °C are more optimal for Asian seabass, and the different temperatures and feeding rates do not affect digestive enzymes, intestine histology, and gut microbiota after 6 weeks. Further molecular research is needed to unravel the complex impact and mechanisms of feeding rate and different rearing temperature on fish physiology.

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Background: Adhesion and biofilm formation are two important steps in Candida pathogenesis. The aim of the current study was to investigate the presence of bcr1 gene in Candida albicans (C. albicans) isolates from women with vaginal candidiasis and its impact on biofilm formation. Methods: We used 50 clinical isolates which confirmed C. albicans by PCR-RFLP. Then total RNA was extracted from C. albicans isolates by glass bead and lysis buffer, and cDNA was synthesized using reverse transcriptase enzyme. RT-PCR (Reverse Transcriptase PCR) was used to evaluate the expression of bcr1 gene. Biofilm formation was evaluated in 96-well microplate and then tetrazolium reduction was assayed. All data were analyzed using t-test by SPSS software. Results: Fifty clinical isolates out of 150 were confirmed as C. albicans by using PCR-RFLP method. All the isolates were resistant to fluconazole, 47/50(94%) isolates had bcr1 gene by using PCR, and 45(95.7%) out of 47 isolates, showed BCR1 expression by the RT-PCR. Isolates which harbored bcr1 gene was succeed to form a dense biofilm on microplate. Comparison of the results of the tetrazolium reduction assay on the two isolates that had BCR1expression and two isolates that had no BCR1 expression showed significant differences (p=0.014). Conclusion: According to our result, all of the isolates that had bcr1 gene expression according to RT-PCR, were also resistant to fluconazole in disk diffusion test and additionally, their adherence was higher compared to the control group. These results indicate that there is a positive relation between expression of bcr1 gene and biofilm formation.

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Morphological changes of the chloride cells and the α_1b subunit gene expression of Na⁺-K⁺-ATPase in triploid rainbow trout (70.6 g average weight) were studied upon direct transferring to 6, 12 and 18 ppt salinities. Changes in abundance, distribution pattern, and the sectioned area of the chloride cells was studied through classic histology and Na⁺ K⁺-ATPase localization was performed through immunofluorescence light microscopy using a mouse monoclonal antibody IgGα5. Gene expression of Na⁺-K⁺-ATPase α_1b subunit was studied by semi-quantitative gene expression methods.No mortality occurred among the fish in all salinities during the 10-days experimental period and treated fish kept their plasma osmolality at standard physiologic levels. All the fish also showed similar distribution pattern in their chloride cells that were distributed on filaments, between and over lamella. Histological studies confirmed some abnormal morphological changes such as lamella interruption. Immunohistochemical studies showed the highest number of the chloride cells on lamella and between lamella in 18 ppt and the maximum sectional area of the chloride cells in freshwater. Gene expression of Na⁺-K⁺-ATPase α_1b subunit had direct correlation with increasing trend of salinity. In conclusions, triploid rainbow trout was found to be adaptable to the various experimented salinities and could be recommended for rearing in brackish water.

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Linum album is an herbaceous and medicinal plant that has important lignan such as podophyllotoxin (PTOX). PTOX has antiviral and anticancer properties. Since the chemical synthesis of PTOX is an expensive process, production of PTOX using cell and cultures of linum species is a cost-effective alternative approach. Various strategies have been employed to increase the production of secondary metabolites in cell cultures. In this study, we have verified the effect of chitosan on cell growth, PTOX production in 1, 2, 3 and 5 days after treatment. Cells elicited with chitosan for 5 days yielded the highest amount of PTOX. To study mechanism of chitosan action, expression of phenylalanine ammonio-lyase (PAL), cinnamoyl-CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD) and pinoresinol lariciresinol reductase (PLR) genes were investigated. The expression of genes were increased, reaching a peak at 3 day after treatment. Chitosan up-regulate the production of PTOX, by effecting on gene expression of PTOX biosynthesis pathway.

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The effect of essential oil (EO) from Carum copticum at concentrations of 0 (control), 0.5%, 0.75% and 1% on Staphylococcus aureus growth and gene expression of enterotoxins (SE) A and C in surimi from kilka (Clupeonella cultriventris caspia) was determined during  0, 5, 10, 15 and 20 days of refrigeration storage (4 °C). The main compounds of EO were thymol (36.4%), p-cymene (31.4%) and γ-terpinen (21.73%). Minimum inhibitory concentration and maximum tolerable concentration of EO against in S. aureus in broth medium were 0.06% and 0.015%, respectively. The growth rate significantly differ between S.aureus population in control (11.31 log CFU/g) and EO-treated samples, 9.76, 7.21 and 6.06 log CFU/g in samples containing 0.5%, 0.75% and 1%, respectively. The highest inhibitory activity against gene transcription of entertoxins was observed at 1% EO; also, the inhibitory effect of EO concentrations against expression of enterotoxin C was higher than enterotoxin A., as enterotoxin A expression was 4.5 and 8.23 fold lower than control at days 5 and 20, and enterotoxin C expression, at days 5 and 20, decreased 5.11 and 8.94 fold compared to control. The results of this study showed that EO from C. copticum is an effective component in reducing bacterial growth rate and staphylococcal enterotoxins production in kilka surimi.  

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Backgrounds: Aspergillus fumigatus is a pathogen responsible for invasive aspergillosis and the main leading cause of death in immunosuppressed individuals. The present study aimed to evaluate the impact of eugenol-loaded chitosan nanoparticles on the expression of CYP51a and CYP51b, two well-known genes responsible for triazole drug resistance in A. fumigatus.
Materials & Methods: The minimum inhibitory concentration (MIC) of eugenol-loaded chitosan nanoparticles, chitosan, eugenol, and itraconazole was determined based on the Clinical and Laboratory Standards Institute M38-E3 method at concentrations of 4.6-2400, 11.7-12000, 2-2048, and 1-256 μg/mL, respectively. The expression of CYP51A and CYP51B was evaluated in A. fumigatus exposed to 0.5, 1, and 2× of MIC concentration of NPs and itraconazole using the real-time polymerase chain reaction.
Findings: The obtained results showed that eugenol-loaded chitosan nanoparticles sucessfully reduced A. fumigatus fungal growth at 300 μg/mL concentration. MIC of chitosan, eugenol, and itraconazole was measured to be 6000, 256, and 4 μg/mL, respectively. The results of real-time PCR also revealed that eugenol-loaded chitosan nanoparticles increased the expression of both CYP51A and CYP51B in a dose-dependent manner. The expression of fungal CYP51A and CYP51B at mRNA level was significantly increased 1.26, 1.93, and 3.1-fold as well as 1.2, 2.1, and 2.4-fold at concentrations of 150, 300, and 600 μg/mL, respectively (p<.05). However, it seems that the prepared nanoparticles had a lower impact on the expression of these genes compared to itraconazole.
Conclusion: Overall, these findings suggest that the treatment of A. fumigatus with eugenol-chitosan nanoparticles could increase the expression of the CYP51 gene, suggesting the anti-fungal property of these nanoparticles.

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Aims: Considered as one of the marine resources and due to their effective compounds, cyanobacteria activate the cell death process in cancer cells and, thus, may be used as a new source. The aim of the current research was to evaluate the effect of oscillatoria cyanobacterium extract on breast cancer cell line and NM23 gene expression.
Materials and Methods: In the present experimental study, oscillatoria cyanobacterium was cultured in a negative zayander medium at 26°C to 28°C with a light intensity of 350 to 3500lux, under 12-hour lighting and 12-hour darkness, and the MCF-7 cell line was prepared. Breast cancer cells were treated by hydroalcoholic extracts of oscillatoria with different concentrations. The effect of extract on cell survival was evaluated by MTT assay and the effect of the extract on the changes of NM23 gene expression was investigated by Real-Time PCR.
Findings: The morphology of MCF-7 cell line showed that the oscillatoria cyanobacterium extract significantly altered the treated cells compared with control cells. The survival of cells decreased with increasing concentration, and there was a significant difference compared to the control sample. After 24 hours, the extract inhibited 50% cell survival at a concentration of 0.6mg/ml (p<0.001). The NM23 gene expression significantly increased over a 24-hour period compared with the control sample.

Conclusion: Oscillatoria Cyanobacterium extract decreases the breast cancer cell line and increases the NM23 gene expression.

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In most cancers, the expression level of heat shock proteins is increased, which makes cancer cells resistant to drug therapy and has a poor prognosis. They have also been linked to cell proliferation, invasion and metastasis. Lycopene, as a carotenoid, is an effective antioxidant used to prevent the growth of cancerous glands. Prostate cancer is one of the most common cancers seen in men. To treat this disease, surgery and chemotherapy are mostly used, which have many complications after treatment and are costly. In this study, prostate cancer was treated with lycopene and raw microarray big data were received from GEO section of NCBI database. Then, the expression changes of heat shock proteins (hsp27) were determined using bioinformatics tools and methods, and comparing the expression levels of lycopene-treated genes with non-treated ones showed that the expression level of HSPB8 gene was drastically reduced and also, no significant changes were observed in the expression level of other gene families in this group. Results show that lycopene can cause stress in cancer cells and this stress predisposes the cell to apoptosis.
 

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Background and Objectives: Alzheimer’s disease is the most common neurodegenerative disease and the memory impairment is the main prominent symptom of this disease. The hippocampus of the brain, is the first region that undergoes changes in Alzheimer’s. Systems biology tools such as high-throughput techniques, enable us to explore signature genes involved in disease initiation and advancement which can be considered as new therapeutic and diagnostic candidates in complex diseases like Alzheimer’s.
Methods: A total of 85 samples obtained from the hippocampus of the brain of healthy individuals and individuals with Alzheimer’s were selected from two datasets. Differential expression analysis was performed independently for both datasets and the results were integrated. Genes with the same expression pattern in the two datasets were used to construct a gene-gene network using the STRING database. The obtained network analysis was performed to detect key genes associated with the disease.
Results: In this study, 73 genes with the same expression pattern were found in the two datasets. The obtained network analysis led to the identification of SNAP25, UNC13A, SYN2 and AMPH as key genes connected with Alzheimer’s disease.
Conclusion: The role of the reported key genes in endocytosis, neurotransmitters release and synaptic vesicle cycle facilitate proper functioning of memory. Expressional changes and mutations in each of these genes effect other pathways and lead to Alzheimer’s. Thus, the key genes reported in this study, can be considered as potential markers in developing diagnostic and therapeutic methods for Alzheimer’s.

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Listeria monocytogenes is one of the most dangerous bacteria in food products which caused about 20 to 30% fatalities. One of the major foods which caused listeriosis is ready to eat (RTE). So, appropriate heating processing methods are need for elimination of L. monocytogenes. These bacteria has ability entering into viable but nonculturable (VBNC) form in unfavorable conditions. So this investigation was aimed to considering behavior of this pathogen at higher temperatures from recommended for elimination of these bacteria. For this purpose, bacteria in 5×10⁶ counts in mid log phase were inoculated into two medium BHI Broth and fish Broth (FB) and they exposed to 85 ºC for 10 minutes. Direct plate count on listeria choromogenic agar, BacLight^® Live/Dead and gene expression of 16S rRNA, the housekeeping gene, were done before and after heat shock. The results show that these bacteria lose their culturability during high heat shock. The results of fluorescent dyes showed the viability of these bacteria after heat shock (p< 0.01). The results of gene expression considering confirmed the results of fluorescence dyes and showed that 16S rRNA gene was expressed in nonculturable bacteria. According to these results, there is a big question on the D value on quality control for these bacteria in food processing processes, especially for RTE foods.

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Objective: In this study quantitative expression of MDR1 and hOCT1 genes in CML patients and normal people were measured using Real-Time PCR. Materials and Methods: To study quantitative expression of these genes by real-time PCR, master-mix with syber green was used. Peripheral blood samples from 30 CML patients and 27 normal persons were harvested. Real-time PCR results were analyzed with relative quantification method. Result: This study showed that in the patients group who were under treatment with Imatib, MDR1 gene expression was increased which was statistically significant. This increase has a direct relation with disease progress. Gene expression in AP and BP patients was also higher than CP patients. In contrast, hOCT1 expression in patients group in comparison with normal group was not statistically significant. Conclusion: MDR1 increase in leukemic cell membrane results in the reduction of intra-cellular drug concentration. Thus, optimal concentration of drug for inhibition of BCR-ABL tyrosine kinase is not achieved which culminated in disease progression to AP and BP phases. Moreover changes in hOCT1 gene expression as an influx transporter of Imatib could affect intracellular concentration of drug and finally determine therapy outcome. However, in this study hOCT1 gene expression was variable and was not statistically significant.

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Objective: Aflatoxin is important in the food industry, in animal husbandry and the medical area; there are enormous negative economic impacts due to this toxin. Numerous studies have researched extracts and plant compounds with the intent to reduce the growth of aflatoxin-producing organisms, inhibit toxin production and suppress the major toxin encoded genes (i.e., aflR) in these organisms. Licorice is an important plant in traditional medicine that possesses numerous antimicrobial activities. There is no report regarding the effects of licorice or its mechanism of action on the aflatoxin-producing Aspergillus species. The present study focuses on the inhibitory effects of licorice extract on aflR gene expression and the growth and survival of Aspergillus parasiticus (A. parasiticus). Methods: After the culture of A. parasiticus in toxin-inducer medium, we measured the minimal inhibitory concentration (MIC) for licorice extract. The aflatoxin concentration in the control and treated media was determined by HPLC. After harvesting the fungi from the toxin-inducing medium, its mRNA was extracted and cDNA synthesized by universal primers. The quantitative change in the aflR expression was analyzed via real-time PCR. Statistical analysis was performed by SPSS (v16). Results: The production of fungal mycelium decreased with increasing concentrations of licorice extract. The highest inhibitory concentration observed was 500 mg/ml of the extract. HPLC analyses revealed that the 10 mg/ml concentration of licorice extract inhibited toxin production by 99.9%. At this concentration, aflR gene expression was suppressed up to 40% as documented by quantitative RT-PCR analysis. Conclusion: Overall we concluded that the Licorice extract could inhibit the aflR gene expression and consequently the aflatoxin production efficiently in the A. parasiticus.

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The response of plants to drought stress depends on several factors including the plant developmental stage and the length and severity of the stress applied. Common bean (Phaseolus vulgaris L.) is the most important pulse crop that is cultivated worldwide for human consumption. Understanding of the mechanisms responsible for its response to drought is, therefore, essential. An increasing number of reports show that withdrawal of water from plants growing in the controlled conditions is accompanied by changes in the expression of a number of genes. To our knowledge, regulation of gene expression in flower buds of P. vulgaris under stress conditions has not been reported. Our aim was to identify transcription sensitivity of CA7 and NCED genes under water deficit stress at vegetative and reproductive stages of different bean genotypes. Two experiments were carried out. Within each experiment, the groups of drought-stressed plants were subjected to water withholding, while the control plants were watered every other day. Stressed plants were re-irrigated when RWC reached 66±2 percent. Our study showed that CA7 and NCDE were genes differentially expressed in the studied genotypes under drought stress. The expression of these genes was strongly induced in response to drought stress in flower buds of the cultivar Jules and the line KS-21191. It seems that under stress conditions, these genes express more in the tolerant than the susceptible genotypes. Therefore, these two genes could probably be used to obtain plants relatively tolerant to water deficit stress, especially in the reproductive stage of plant growth.

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Objective: The incidence of breast cancer is approximately one million which makes this cancer one of the most common among women worldwide. Breast cancer comprises 7% of the total death rate caused by cancers. Several strategies that use tumor-associated antigen (TAA) vaccination and early detection of breast cancer are clinically being developed. Breast cancer is caused by increased over expression of certain genes. HER-2 is a tyrosine kinase receptor in the epidermal growth factor family. The role of HER-2 in breast cancer has been extensively studied. HER-2 is found in 25%-30% of breast cancer patients. Herceptin, a human antibody, is used as a therapeutic target for HER-2. The purpose of this study is to produce recombinant protein HER-2 for early detection of breast cancer cells. Methods: We used specific primers to amplify the HER-2 gene. The amplified gene was cloned into pET28a as an expression vector. Cloning was confirmed by restriction analysis and sequencing. Expression was induced using IPTG and the recombinant protein was analyzed by SDS-PAGE. Results: Cloning of the HER-2 gene was confirmed by enzyme digestion and sequencing. The gene was expressed in E.coli BL21 DE3. The pET-28a vector which contained the HER-2 gene showed a high level of expression. The recombinant protein was confirmed by Western blot analysis. Conclusions: A portion of the HER-2 gene was expressed as a recombinant in E.coli. This could be a good diagnostic test for breast cancer.

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Vicia sativa L., an annual winter growing leguminous plant, is a valuable source of protein and minerals for cattle. Drought is one of the key stress factors that influence plant growth and development. In order to investigate common vetch physiological and molecular responses under Normal irrigation (N) and two levels of drought stress [S₁= 30% and S₂= 10% Field Capacity (FC)], a greenhouse experiment was carried out on two genotypes, namely, Mahalimaraghe and 41,and some physiological traits [e.g. Relative Water Content (RWC), Electro Leakage (EL), total protein, chlorophyll (a, b), and carotenoid content] were measured and expression patterns of three genes (sod, aq1 and bzip) were evaluated by real-time quantitative RT-PCR analysis. Results showed that expression pattern of all three genes and physiological responses had significantly changed in response to the stress. The highest increase in the expression of each of the three genes was observed in Mahalimaraghegenotype in S₁ condition compared to N. In contrast, under S₂ condition compared to N, the highest increase in expression of the three genes was observed in genotype 41. In comparison of S₂ with S₁, the highest changes in expression of all the three genes was observed in Mahalimaraghe genotype. All together, the obtained results may facilitate the understanding of molecular mechanism of V. sativa in response to drought stress, and also provide the basis of effective genetic engineering strategies for improving stress tolerance of V. sativa.

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Drought sensitivity is considered as a major concern for chickpea (C. arietinum) seed production. Determination of drought adaptation mechanisms is an essential constituent of this crop breeding programs. With this purpose, the present research was conducted to distinguish the molecular basis of chickpea drought tolerance using cDNA-AFLP approach. The expression profile was compared between drought tolerant (ICCV2 and FLIP9855C) and susceptible lines (ILC3279) of chickpea under three drought treatments including well-watered, intermediate, and severe stress; where soil water content was kept at 85–90%, 55–60%, and 25–30% of Field capacity, respectively. Totally, 295 transcript-derived fragments (TDFs) were visualized. Among the differentially expressed TDFs, 72 TDFs were sequenced. Sequenced cDNAs were categorized in different functional groups involved in macromolecules metabolism, cellular transport, signal transduction, transcriptional regulation, cell division and energy production. Based on the results, ribosomal protein S8, mitochondrial chaperone, proteases, hydrolases, UDP -glucuronic acid decarboylase, 2-hydroxyisoflavanone dehydratase, NADPH dehydrogenase, chloride channels, calmodulin, ABC transporter, histone deacetylase and factors involved in chloroplast division were among genes that were affected by drought stress. Similarity search in data base showed that cell wall elasticity, isoflavonoids, maintenance of structure and function of proteins through increase in expression of mitochondrial chaperones, programed cell death, and remobilization of storage material from leaves to seeds were among mechanisms that distinguished differences between drought tolerant and drought susceptible lines.

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Accurate prediction of the sediment load is one of the important issues to water engineering. Due to complexity of sedimentation phenomenon and influence of various parameters on estimation of sediment transport rate, determining the governing equations are difficult, and classical mathematical models are not sufficiently accurate in this regard. In the present study the applicability of Gene-Expression Programming (GEP) for modeling bed load discharge in sewer pipes with different boundary conditions was assessed (i.e. fixed and movable beds). Therefore different input models based on theoretical concepts were defined for each boundary condition. In order to develop the models, under two scenarios, different input combinations were considered, first scenario (Scenario1) which uses only hydraulic characteristics and second scenario (Scenario2) which uses both hydraulic and sediment characteristics as inputs for modeling bedload discharge. The sewer pipes experimental data available in the literature were applied for training and testing the employed GEP. For evaluating the efficiency of the models three statistical indexes which called: Determination Coefficient (DC), Correlation Coefficient (R) and Root Mean Square Errors (RSME) were used. Then the accuracy and capability of several available bed load formulas such as Ackers, Neilsen, May, Mayerle and Laursen were investigated and compared with GEP- best modes in each boundary. Also with considering this point that may there is no information about bed boundary condition and for evaluating the applicability of applied technique for a wide range of data; all data series of sediment transport were combined. Then, for predicting Cv, as the dependent variable, several models of Scenarioa 2 analyzed for the combined data. The obtained results confirmed the efficiency of Gene-Expression Programming method for estimation sediment discharge in sewage pipes, and proved this method superior to the semi- theoretical relationships. According to the results it was found that in scenario 1, for all of the cases, model (IV) with input parameters of Fr and y0/D presented better performance than the others models, however it was observed that Scenario 2, which took advantage of both hydraulic and sediment parameters as inputs for modeling sediment discharge in sewer pipes performed more successful than Scenario1 which used only combinations of hydraulic parameters as input variables for models. Comparison between the results of separate data sets and combined data set revealed that analyzing data sets separately led to more accurate outcome. According to the results from fixed beds, it was found that adding Frm and d50/y as an input parameter increased the accuracy of the models. For both smooth and rough beds, the model with input parameters λs, Frm, Dgr, d50/y presented better results from the RMSE, R, and DC viewpoints (i.e. highest R and DC and lowest RMSE). For movable beds condition in the two cases of separate dunes and continuous loos bedform, the model with input parameters of ys/D, Frm, Wb/y0 showed more accuracy. This model showed the influence of flow depth and width and depth of movable bed in estimating of bedload transport in sewer pipes. For loose beds Frm has dominant role than other parameters.