In vitro assessments of nanoplexes of polyethylenimine-coated graphene oxide-plasmid through various cancer cell lines and primary mesenchymal stem cells.

Efficient gene therapy relies on an efficient gene delivery system. Viral gene delivery approaches excel in transferring and expressing external genes; however, their immunogenicity and difficulty in large-scale production limit their clinical applications. In contrast, nanoparticle-based gene delivery systems have gained increasing attention due to less immunogenicity and more convenience for large-scale production. Nevertheless, their poor transfection efficiency compared to viral systems remains a significant obstacle. In the present study, we investigated the transfection efficiency of our PEI-coated graphene oxides in HEK293T, Calu-3, Calu-6 cell lines, and primary human bone marrow mesenchymal stem cell (MSC). The high surface ratio and good biocompatibility of graphene oxide make it an appealing tool for gene delivery systems. However, the low dispersity of graphene oxide in aqueous environments is the first barrier that needs to be conquered. For this, we enhanced the dispersity and stability of graphene oxide in water by sonicating it for at least 5 hours at a pH of 7. Then, graphene oxide was conjugated with branched PEI (25 kDa) to have a positive charge, enabling it to condense nucleic acids with a naturally negative potential. The physio-chemical characteristics of our synthesized nano-carriers (GO-PEI) were determined by DLS, FT-IR, and AFM. The utilized plasmid in polyplexes contained a GFP gene, allowing us to verify transfection efficiency through fluorescent microscopy and flow cytometry. While GO-PEI carriers were highly efficient in transfecting HEK293T cells, the transfection efficiency in MSCs and Calu-3 cells was notably low. We suppose that the main reason for the low transfection efficiency of GO-PEI in these cells is due to its higher toxicity. Despite this, considering the various advantages of graphene oxide in drug delivery as well as its optical and electrical applications in biomedicine, we propose to functionalize graphene oxide with more biocompatible materials to enhance its potential as a successful gene carrier in these cell types.

Long non-coding RNA SOX2-OT enhances cancer biological traits via sponging to tumor suppressor miR-122-3p and miR-194-5p in non-small cell lung carcinoma.

The oncogenic role of long non-coding RNA SOX2 overlapping transcript (SOX2-OT) has been demonstrated as a miRNA decay system that sponges tumor suppressor miRNA, including miR-122-3p in glioblastoma and miR-194-5p in glioblastoma, gastric, and colorectal cancers. However, the molecular function of SOX2-OT remains unknown in most cancers, including lung cancer. In the current study, we aimed to evaluate the downstream regulatory function of SOX2-OT in A549 and Calu-3 lung cancer cell lines. We knocked down SOX2-OT expression using an RNA interference system, which significantly decreased expression in A549 and Calu-3 cells. The expression of down-regulating miRNAs (miR-122-3p and miR-194-5p) was evaluated, revealing increased expression of miR-122-3p and miR-194-5p. Additionally, the expression of miRNAs downstream mRNA, including FOXO1 (Forkhead Box O1) and FOXA1 (Forkhead Box O1), changed. Recently, critical roles of FOXO1 and FOXA1 proteins in pathways involved in proliferation, metastasis and apoptosis have been demonstrated. Downstream changes in cellular traits were assessed using MTT, flow cytometry, metastasis and apoptosis assays. These assessments confirmed that the biological behaviors of lung cancer cells were influenced after SOX2-OT knockdown. In summary, the present study highlights the oncogenic role of SOX2-OT through the regulation of miR-122-3p/FOXO1 and miR-194-5p/FOXA1 pathways.

Multi-Objective Optimization of Copper Bioleaching: Comparative Study of Pure and Co-Cultured Cultivation.

Background: Bioleaching is a practical method to recover metals from low-grade mineral sulfides. The most frequent bacteria involved in the bioleaching of metals from ores are Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. Experimental design is a method through which the optimum activity condition will be obtained, avoiding numerous trials and errors. Objectives: This study aimed to optimize the bioleaching condition of two indigenous iron- and sulfur-oxidizing bacteria from the Meydouk mine, Iran, and evaluate their function in a semi-pilot operation in pure and mixed cultures. Material and Methods: After treatment with sulfuric acid, the bacterial DNA was extracted, and further 16S rRNA was sequenced to characterize the bacterial species. The cultivation condition of these bacteria was optimized using Design-expert (6.1.1 version) software. The copper recovery rate and the differentiation in the ORP rate in the percolation columns were also investigated. These strains were isolated from the Meydouk mine for the first time. Results: 16S rRNA analysis revealed that both bacteria belong to the Acidithiobacillus genus. The factors with the most significant impact on Acidithiobacillus ferrooxidans with their optimum level were temperature=35 °C, pH=2.5, and initial FeSO4 concentration=25 g.L-1. Also, initial sulfur concentration had the most significant impact on Acidithiobacillus thiooxidans with the optimum level of 35 g.L-1. Moreover, the mixed culture determined higher bioleaching efficiency compared with the case of employing the pure cultures. Conclusions: Utilizing a mixture of both bacteria, Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans elevated the Cu recovery rate due to the synergetic function of the strains. Also, introducing an initial dosage of sulfur and pre-acidification could elevate metal recovery efficiency.

SOX2 Overlapping Transcript (SOX2-OT) Enhances the Lung Cancer Malignancy Through Interaction with miR-194-5p/SOX5 Axis.

Background: Lung cancer is one of the most common types of cancer and a leading cause of cancer-related deaths worldwide. Therefore, it is useful to know the biomarkers involved in the malignancy of lung cancer. Objectives: This study aimed to show that SOX2-OT as a long non-coding RNA (IncRNA) regulates gene expression via the SOX2-OT/miR-194-5p/SOX5 axis molecular pathway in lung cancer. Materials and Methods: A549 cells transfected with siRNA-SOX2-OT and the expression of SOX2-OT and miR-194-5p genes were analyzed by real-time PCR before and after transfection. In addition, the expression of the B-catenin, MMP9, phosphorylated and activated STAT3 (p-STAT3), SOX5, and VEGF proteins before and after transfection was investigated by Western blotting. Results: After using siRNA-SOX2-OT, an increase in the expression of miR-194-5p and a decrease in the expression of B-catenin, SOX5, p-STAT3 activated STAT3, VEGF, and MMP9 proteins was observed. Conclusions: According to the results of the present study, an increase in SOX2-OT in lung cancer seems to stimulate the expression of beta-catenin, SOX5, MMP9, and VEGF thus support the malignancy of lung cancer cells.

The role of long intergenic non-coding RNA for kinase activation (LINK-A) as an oncogene in non-small cell lung carcinoma.

The oncogenic role of long intergenic non-coding RNA for kinase activation (LINK-A) has been appraised in triple-negative breast cancer. However, the molecular function of LINK-A is still unclear in most cancers including lung cancer. The present study aimed to evaluate the impact of down-regulation of LINK-A in A549 and Calu-3 cell lines as cellular models of non-small cell lung carcinoma (NSCLC). We used the RNA interference system to knock down LINK-A. LINK-A expression was significantly reduced by siRNA transfection in A549 and Calu-3 cell lines. LINK-A down-regulation significantly reduced cell viability, colony-forming ability and cell migration, as measured by MTT, colony formation and invasion assays. Finally, cell cycle analysis and Annexin-V/7AAD staining indicated that apoptosis was influenced by LINK-A silencing. Taken together, LINK-A can be proposed as an oncogene in NSCLC.

Evaluating the effect of siRNA on SOX2OT expression in the human neuron-committed teratocarcinoma NT2 cell line.

Non-coding RNA elongated (lncRNAs) have recently attracted as molecules that regulate gene expression of the pluripotent properties (pluripotency) of stem cells. Recently our colleagues examined the role of one of these RNAs called SOX2OT in esophageal squamous cell carcinoma, and found a concomitant increase in its expression with some regulatory genes of cell proliferation. In the present study, using the design of suitable primers from SOX2OT gene, we investigated the effect of siRNA on expression of SOX2OT.

Study of the application of gold nanoparticles for early detection of prostate cancer.

Studies on the blood of patients with prostate cancer using Dynamic Light Scattering (DLS) and corona protein size changes have shown that this test is highly specific and sensitive, but this method has not been studied in Iran, and therefore this study intends to perform this procedure using gold nanoparticles in prostate cancer detection. Blood samples of 60 male subjects aged 40-90 years were collected from 20 healthy, 20 benign and 20 prostate cancer patients. Optical scattering changes were measured by the level of gold nanoparticles mixed with these sera, and the responses were compared with the PSA index (Prostate Specific Antigen) of the subjects. Results of D2/D1 ratio analysis were performed using SPSS statistical software R. No significant differences were found in the size of the corona protein structure between the three groups of males with cancer, males with benign tumor, and healthy males. No correlation was found between the light scattering concentration and PSA serum level Due to changes in ambient temperature, prolonged test duration or high IgG levels in apparently healthy individuals, this test is not feasible in Iran. Performing this test requires advanced equipment to maintain the same temperature that do not exist in Iran. DLS also has major limitations for prostate cancer detection, so it cannot be a simple and accurate method for the early detection of prostate cancer, and it is suggested that other methods be used to diagnose.

LINK-A long non-coding RNA and VEGF RNA expression in epithelial ovarian cancer patients.

LINK-A (long intergenic non-coding RNA for kinase activation) is a newly identified long non-coding RNA with oncogenic function, which leads to the hyperactivation of AKT and HIF1α. thereby, fosters cell proliferation, mobility and metastasis. VEGF (vascular endothelial growth factor), a well-known cytokine has an important role in angiogenesis. In this study, we quantified RNA expression of LINK-A and VEGF on 45 tumor specimens obtained from Iranian patients diagnosed with Epithelial Ovarian Cancer (EOC). Our goal was to evaluate expression of LINK-A lncRNA and VEGF mRNA in ovarian cancer tissues and find the probable correlation of LINK-A with VEGF as a major transcription target for HIF1α. LINK-A and VEGF were remarkably overexpressed in EOC tissues compared to normal tissues (P value: 0.004, 0.0001, respectively), but we did not find correlation between LINK-A and VEGF RNA expressions in this study. LINK-A was significantly overexpressed in higher stages of cancer and tumor grades. VEGF was only significantly elevated in higher stages. This study confirms importance of novel lncRNA of LINK-A in Iranian EOC patients.

Surface modification of superparamagnetic iron oxide (SPION) and comparison of cytotoxicity effect of mPEG2000-PEI-SPION and mPEG750-PEI-SPION on the human embryonic carcinoma stem cell, NTERA2 cell line.

Non-viral carriers based on nanoparticles are promising vectors for drug and gene delivery into the target cells. The data provided in this article are related to research entitled "Efficiency of surface modified SPION". In this article the surface of superparamagnetic iron oxide (SPION) (core) coated with poly (ethylene glycol)-grafted polyethylenimine (mPEG-co-PEI) shell. PEI was used to increase gene transfection efficiency and poly (ethylene glycol) methyl ether was applied to reduce cytotoxicity of nanoparticles, because our goal is that two sets of mPEG-co-PEI coated SPIONs (mPEG-750 and 2000) were prepared as carrier for the purpose of gene delivery. Structure of the mPEG-co-PEI product was elucidate by using 1H-NMR spectroscopy. Physicochemical features of the modified-SPIONs were evaluated by zeta-potential analysis. Cytotoxic effect of Nano carries were then assayed by MTT in NT2 cell line. Data analyzed by excel and p< 0.05 was considered significant. Finally siRNA absorption Ability of mPEG750-PEI-SPION and mPEG2000-PEI-SPION was tested by N/P ratio test (gel retardation assay). Our data shown that mPEG750-G-Pei-Spion and mPEG2000-G-Pei-Spion were non-toxic up to 100 µg/ml in vitro for NT2 cell line.

MTT assay dataset of polyethylenimine coated graphenoxide nanosheets on breast cancer cell lines (MCF7, MDA-MB-231, MDA-MB-468).

Graphen oxide has emerged as a promising tool in medical biotechnology due to its outstanding properties applicable in several fields as well as cell imaging, drug and gene delivery. Monolayer structure and high surface area of Graphen benefits elevated loading capacity of drugs rather than other nanomaterials. However Graphen oxide in physiological solutions has unfavourable reactions which confine it's application in biomedical field without additional surface functionalization. Coating of graphenoxide by polyethylenimine is an approach to enhance biocompatibility of graphen oxide and also provides desirable physicochemical features for oligonucleotides delivery. The data presented here is related to graphenoxide-PEI characterisation and it's cytotoxicity assay on variouse breast cancer cell lines including MDA-MB-468 and MDA-MB-231 and MCF7 by MTT assay.

Dataset on cytotoxicity effect of polyethylenimine-functionalized graphene oxide nanoparticles on the human embryonic carcinoma stem cell, NTERA2 cell line.

The data provided in this article are related to research entitled "Efficiency of graphene oxide nanoparticles as delivery system of SOX2OT siRNA". In this research, the goal is to use PEI-functionalized graphene oxide (PEI-GO) as a carrier for SOX2OTsiRNA delivery. In this article describes how GO coated with PEI and it was tested whether it can be siRNA carrier in NTERA2? Can it absorb siRNA? Whether Go-PEI affects the viability of NTERA2 (NT2: human embryonic carcinoma stem cell), and HeLa cell lines. In this experiment, graphene oxide nanoparticles functionalized with a polycationic polymer, polyethylenimine (PEI). GO-PEI formation was verified with DLS, FTIR tests and zeta sizer. siRNA absorption ability of GO-PEI was tested by gel retardation assay in various weight ratios of GOPEI/siRNA (GOPEI weight/siRNA weight) (w/w ratio). The cell lines were treated with different concentrations of GO-PEI nanoparticles for 24 and 48 hours. Also, the NT2 cells were treated with different concentrations of GO-PEI nanoparticles and PEI for 36 hours. Cytotoxicity of GO-PEI were investigated by calculating the percent of cell survival by MTT assay. MTT data analyzed in excel. Researchers, who want to research on different drugs, could transfer the drug to NT2, HeLa and other cancer cells on GO-PEI (concentration 0 up to 100 mg/L).

Investigation of Desulfurization Activity, Reusability, and Viability of Magnetite Coated Bacterial Cells.

BACKGROUND: Magnetic separation using magnetic nanoparticles can be used as a simple method to isolate desulfurizing bacteria from a biphasic oil/water system. OBJECTIVES: Magnetite nanoparticles were applied to coat the surface of Rhodococcus erythropolis IGTS8 and Rhodococcus erythropolis FMF desulfurizing bacterial cells, and the viability and reusability of magnetite-coated bacteria evaluated by using various methods. MATERIAL AND METHODS: Magnetite nanoparticles were synthesized through a reverse co-precipitation method. Glycine was added during and after the synthesis of magnetite nanoparticles to modify their surface and to stabilize the dispersion of the nanoparticles. The glycine-modified magnetite nanoparticles were immobilized on the surface of both oil-desulfurizing bacterial strains. Reusability of magnetite-coated bacterial cells was evaluated via assessing the desulfurization activity of bacteria via spectrophotometry using Gibb's assay, after the separation of bacterial cells from 96h-cultures with the application of external magnetic field. In addition, CFU and fluorescence imaging were used to investigate the viability of magnetite-coated and free bacterial cells. RESULTS: TEM micrographs showed that magnetite nanoparticles have the size approximately 5.35±1.13 nm. Reusability results showed that both magnetite-coated bacterial strains maintain their activity even after 5 × 96h-cycles. The viability results revealed glycine-modified magnetite nanoparticles did not negatively affect the viability of two bacterial strains R. erythropolis IGTS8 and R. erythropolis FMF. CONCLUSIONS: In conclusion, the glycine-modified magnetite nanoparticles have great capacity for immobilization and separation of desulfurizing bacteria from suspension.

Genotypic identification of Pseudomonas aeruginosa strains isolated from patients with urinary tract infection.

BACKGROUND: Numerous nosocomial infections including urinary tract infection (UTI) have been reported to be linked to Pseudomonas aeruginosa (P. aeruginosa). This bacterium is one of the most common pathogen colonized in the urinary tract. The main purpose of this study was to evaluated the presence of antibiotic resistance genes and also the most frequent genotype patterns of P. aeruginosa in the patients with UTI hospitalized in different wards of hospitals. MATERIALS AND METHODS: In this study, 70 strains of P. aeruginosa isolated of urine samples from the patients with UTI were assessed. The isolated strains were genotyped using Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) method. We have also analyzed the presence of TEM and SHV resistant genes in the isolates. RESULTS: A total of 70 P. aeruginosa strains was isolated from the UTI patients. Based on MLVA method, 61 various genotypes of P. aeruginosa were identified which grouped into two main clusters and 4 sub-clusters. Moreover, approximately 80% and 70% of isolated strains carried the TEM and SHV resistance genes, respectively. CONCLUSION: Our findings showed that the majority of patients hospitalized in different wards of hospitals have experienced the urinary tract infection caused by P. aeruginosa. According to the genotyping results, a high diversity of the P. aeruginosa population was observed in the patients with UTI. Our results can provide a better understanding of the P. aeruginosa genotype distribution and epidemiology of infection, which can be applied as basic data for future antibiotic therapies.

Assessment of SGO1 and SGO1-AS1 contribution in breast cancer.

Shugoshin-like protein 1 (SGO1) participated in the proper progression of mitosis. This fundamental role has indicated the importance of this gene in the pathogenesis of cancer as a disorder of mitotic cell division. A previous high throughput study of long non-coding RNAs (lncRNAs) expression in lung cancer has identified aberrant expression of SGO1-antisense 1 (SGO1-AS1) in these specimens. In the current study, we quantified expression of SGO1 and SGO1-AS1 in 39 breast cancer tissues and their paired adjacent non-cancerous tissues (ANCTs). Expression of SGO1-AS1 was considerably decreased in tumoral tissues compared with ANCTs (expression ratio = 0.49, P value = 0.03). However, we could not identify significant difference in expression of SGO1 between these two sets of specimens (expression ratio = 2.9, P value = 0.2). Transcript quantities of SGO1-AS1 were associated with age at disease onset (P= 0.01). Expression of either gene was associated with hormone receptors status or clinical features such as grade and stage. There was an inverse correlation between expressions of genes in both sets of samples. Finally, transcript amounts of SGO1-AS1 could distinguish these two sets of samples with accuracy of 63% (P value = 0.03). Our results imply significance of SGO1-AS1 in breast cancer and necessitate conduction of mechanistic studies to find the molecular pathways in this regard.

Mutagenesis of the rpoS gene involved in alteration of outer membrane composition.

BACKGROUND AND OBJECTIVES: rpoS is a bacterial sigma factor of RNA polymerase which is involved in the expression of the genes which control regulons and play a critical role in survival against stresses. Few suitable vectors are available which could be maintained successfully in Flexibacter chinesis cells and could in particular be used as a suicide vector to make mutation in the rpoS gene. The aim of this study was to investigate if rpoS mutagenesis has impact on bacterial morphology in addition to cell division. MATERIALS AND METHODS: A 0.603 kb BamHI-PstI fragment subclone of pICRPOS38Ω was cloned into linearized pLYLO3. The final construct, pLRPOS38 suicide vector, was introduced into Flexibacter chinesis. Then the cytoplasm of mutant strain and wild-type were investigated by transmission electron microscopy. RESULTS: After successful subcloning of suicide vector into F. chinesis, based on TEM study, it was demonstrated that mutation in rpoS gene leads to decomposition of outer membrane of F. chinesis. CONCLUSION: A suitable vector to make suicide mutation in rpoS was constructed for F. chinesi.

Effect of superparamagnetic nanoparticles coated with various electric charges on α-synuclein and ß-amyloid proteins fibrillation process.

BACKGROUND: Most of nanoparticles are nontoxic and have high absorption capability. Therefore, nanoparticles binding can effectively restrain fibrillation of ß-amyloid and α-synuclein proteins and eventually prevent the toxicity of pathogenesis peptide of Alzheimer. Super paramagnetic iron oxide nanoparticles (SPIONs) contain iron oxide core which can be connected to a special part through magnetic coating. MATERIALS AND METHODS: In this study, the effect of SPIONs with different charges was simultaneously examined on the fibrillation of both ß-amyloid and α-synuclein proteins by applying Thioflavin-T assay. RESULTS: According to the results of the investigation on amyloid-fibrillation mechanism in both ß-amyloids and α-synucleins, it was revealed that negatively-charged nanoparticles encoded to -COOH by dextran-coating were able to have a considerable absorption decrease from 17,000-12,000 after 320 minutes delay to lag phase and decrease in binding level of thioflavin-T particles to ß-sheets. CONCLUSION: The different concentrations of these nanoparticles and special coating of each particle had an effect on the kinetics of ß-amyloid and α-synuclein fibrillations.

The non-coding RNA rprA can increase the resistance to ampicillin in Escherichia coli.

OBJECTIVES: The non-coding RNA rprA can increase the resistance to ampicillin in Escherichia coli. METHODS: Bacterial DNA was extracted by boiling method and then amplified using polymerase chain reaction (PCR) with two different primer sets. Recombinant pET28a/rprA-sense and -antisense plasmids were separately transferred into the competent E. coli BL21 (DE3) by chemical methods using heat shock. The expression was analyzed at the RNA level using Semi quantitative RT PCR. The turbidity difference between the bacteria was checked by Broth Dilution method. RESULTS: The statistical analysis showed that the turbidity difference between the up regulated and control bacteria is significant (p value < 0.0001). The ANOVA test also showed the significant difference between the down regulated and control bacteria (p value < 0.0001). CONCLUSION: Considering this mechanism, there are some reports indicating the role of rprA in antibiotic resistance. However, the role of rprA in ampicillin resistance is remained to be unknown. The aim of this study was to analyze the up regulation and down regulation of rprA and check their effects on ampicillin resistance in Escherichia coli. It was found that the up regulation and down regulation of rprA can lead into more antibiotics resistance and susceptibility, respectively. Our results showed the potential role of rprA expression in the response to ampicillin stress in E. coli.

Dataset on the relation of synthetic super para magnetic nanoparticles coated with various electric charges and fibrillation of albumin protein.

The data provided in this article are related to the research article entitled "Effect of Super Magnetic Nanoparticles Coated with Various Electric Charges on α-Synuclein Protein Fibrillation Process" (Javdani et al.). This article describes how electrically different charged and concentrated iron oxide nanoparticles synthesized using reverse co-precipitation method affects the fibrillation of albumin protein.

Expression, characterization and one step purification of heterologous glucose oxidase gene from Aspergillus niger ATCC 9029 in Pichia pastoris.

Glucose Oxidase (GOD), is a common flavoprotein from Aspergillus niger ATCC 9029 with a broad application in biotechnology, food and medical industries. In this study, GOD gene was cloned into the expression vector, pPIC9 and screened by the alcohol oxidase promoter. The enzyme production increased at 28 °C. GOD activity induced by 1.0% methanol and the highest level of GOD production was the result of shaking rate at 225 rpm. The highest enzyme activity obtained at a pH value ranged from 5 to 7 at 50 °C. The enzyme was stable at a broad pH range and temperature.

Cloning and over expression of non-coding RNA rprA in E.coli and its resistance to Kanamycin without osmotic shock.

Recent reports have indicated that small RNAs have key roles in the response of the E.coli to stress and also in the regulating of virulence factors. It seems that some small non-coding RNAs are involved in multidrug resistance. Previous studies have indicated that rprA can increase the tolerance to Kanamycin in RcsB-deficient Escherichia coli K-12 following osmotic shock. The current study aims to clone and over-express the non-coding RNA rprA in E.coli and investigate its effect on the bacterial resistance to Kanamycin without any osmotic shock. For this purpose, rprA gene was amplified by the PCR and then cloned into the PET-28a (+) vector. The recombinant plasmid was transformed into wild type E.coli BL21 (DE3). The over expression was induced by IPTG and confirmed by qRT-PCR. The resistance to the kanamycin was then measured in different times by spectrophotometry. The statistical analysis showed that the rprA can increase the resistance to Kanamycin in Ecoli K12. The interaction between rprA and rpoS was reviewed and analyzed by in silico methods. The results showed that the bacteria with over-expressed rprA were more resistant to Kanamycin. The present study is an important step to prove the role of non-coding RNA rprA in bacterial resistance. The data can be the basis for future works and can also help to develop and deliver next-generation antibiotics.