Modares Journal of Biotechnology

Abstract Background and Objective: Polyhydroxyalkanoates (PHAs) are polymers with biodegradable and biocompatible properties that are produced by some bacteria. In the present study, petroleum sediments were applied to screen PHA-producing bacteria. Method: The industrial culture medium of petroleum effluent was used as a low-cost and economical medium for isolating and identifying the superior PHA-producing strain. Finally, the chemical and physical properties of the extracted biopolymer were investigated by Fourier-transform infrared spectroscopy, differential scanning calorimetry, and proton nuclear magnetic resonance. Results: In general, 11 out of 76 isolated bacterial strains could produce biopolymers among which, the Sb8 strain was selected as the best PHA-producing strain in the industrial medium with the cell dry weight of 44.13% and 1.2 g/l in 27 h. This strain was identified as Citreicella thiooxidans by sequencing determination. Eventually, the results of physicochemical analyses revealed that polyhydroxybutyrate (PHB) was the extracted biopolymer. Conclusion: The present study is the first report on PHB production by Iranian native Citreicella thiooxidans strain by focusing on identifying and separating producing bacteria, as well as determining the type of the produced biopolymer and the production capability in a low-cost culture medium of the petroleum effluent. Considering the production of the biopolymer with a relatively high yield percentage without adding any supplement to the petroleum effluent medium, the isolated wild strain has the potential to produce PHB.

Abstract NIR Laser application in bacteria is often focused on mortality and antibiotic efficacy. The literature records on this point are absolutely diverse from mortality in different degrees to immortality and even viability enhancement. The aim of this study is to investigate 808 nm laser effects on E.coli-DH5α viability and Growth with CFU, MTT and FCM assays. To obtain the purpose, bacteria in LB media put on with 808nm laser on 100 and 200 J/cm² dosages and were investigated and compared by CFU, MTT and FCM assay. CFU assay results after 24 hours incubation were not significantly different between laser treatments and control. (P=0.06). In contrast, MTT assay results after 1 hours from laser treatment indicated significant deleterious effects in 200 J/cm² laser treatment compared with control(P=0.006). On the other hand, FCM assay results of laser treatments with using of PI and Triton X100 not only approved MTT assay results but also revealed some dose dependent changes on bacteria ranging from increase membrane permeability to lethal damages. As a conclusion of the results in these method assays, we can state that these different laser doses produce diverse effects on viability and growth in E.coli-DH5α. Consequently the laser treatments could be planned for antibiotic purposes or enhancing gene transformation process.

Abstract DNA methylation detection by a novel fluorimetric nanobiosensor for early cancer diagnosis Quantum­ dots as a fluorescent probe are applied for cell biology, DNA transformation, biomedical imaging and cancer therapy. Biological based synthesis of nanoparticles would be more efficient and environment friendly rather than chemical approaches. In the present study, quantum dots have been synthesized through leaf methanolic extracts. The obtained results by UV-vis spectroscopy, TEM, FT-IR and fluorescence spectroscopy showed the presence of synthesized CdS quantum dots. Yellow and orange colors of obtained solution was also indicated the successful synthesis of CdS quantum dots. The maximum UV-Vis spectrum absorption of quantum dots was observed at 410 nm. Results of fluorescence analysis also showed that emission bands were at 475, 490 and 675 respectively which indicated the synthesis of different CdS quantum dots in different pH values. Obtained nanoparticle were spherical and at the range between 2-10 nm according to TEM analysis. FT-IR analysis also showed that the proteins, leucine and lysine amino acids, phenols and other functional groups present in physalis extracts would be determining factors for reducing CdS ions and converting them to quantum dots.

Abstract Abstract
Urinary tract infection is one of the most common and common bacterial infections, accounting for a significant proportion of hospital admissions (about 30-40%). Silver nanoparticles work by releasing silver ions against various bacteria. The fact that bacteria are not resistant to nanoparticles is very important and therefore will affect a wide range of bacteria.
Materials and Methods
In this study, 50 specimens of positive cultures with urinary tract infection referred to Imam Reza Hospital Laboratory in Bojnourd were studied. Resistance and susceptibility of the isolates were determined by disk diffusion method. In this study, antibacterial effects of silver nanoparticles were investigated by microdilution method using aqueous extract of Ganoderma leucidum. Vegetative electron microscopy was used to measure the size and shape of silver nanoparticles. In addition, infrared spectroscopy analysis was performed to investigate possible organic compounds involved in the synthesis of nanoparticles.
Results: The highest antibiotic resistance was related to ampicillin (84%). The resulting nanoparticles were 20 to 45 nm in size.
Conclusion:
The produced nanoparticles have antimicrobial activity and can be a good alternative in the treatment of antibiotic resistant infectious diseases.

Abstract Biosurfactants are produced by microorganisms. Surfactin is one of the main lipopeptide biosurfactants produced by different species of Bacillus subtilis. This study aims to analyze the effect of starch-coated Fe⁰and Fe³⁺nanoparticles on the biosurfactant production of Bacillus subtilis. Out of 70 soil samples, 20 Bacillus were isolated and genome sequenced by biochemical methods and 16S rRNA gene. Quantitative and qualitative screening methods were used to isolate and detect biosurfactant production. For the aim of this study, 61 and 63 (Bacillus subtilis subsp. Inaquosorum) were selected. Then, hemolytic activity, surfactant production and reduction of surface tension in Minimal Salt Medium containing Fe⁰ and Fe³⁺ nanoparticles were examined after 48h, 72h and 96h of culture. The binding of the nanoparticles to the surfactant was confirmed by SEM. Strain 61 was the best bacterium and Fe³⁺ was the best nanoparticle and it was cultured. The results were compared with the results of non-nanoparticle bioreactor. Surfactin from strain 61 culture in the Fe³⁺ nanoparticle bioreactor after 72 hours of growth showed higher production than the same strain culture after 72 hours without Fe³⁺, if continuing the research, this strain can be commercialized in the future.

Abstract In this study, cellulase enzyme production by Trichoderma reesei on three lignocellulosic substrates (corn bran, sawdust and wheat bran) and percentage of different combinations of sawdust and wheat bran by solid-state fermentation method for 6 days in scale checked out. Then, under optimal substrate component proportions obtained from Erlenmeyer-scale, the effect of aeration at three levels of 0.5, 1 and 1.5 liters per hour of initial dry substrate (l/(h.gds)) on the production of this enzyme in 0.5-Liter packed-bed bioreactor was studied. The initial substrate moisture and pH were 70 %(w/w) and 5 respectively, and the heating temperature was set at Erlenmeyer-scale and bioreactor at 30 and 28 °C, respectively. Cellulase enzyme production was evaluated based on the activity of endoglucanase and exoglucanase enzymes. The highest amount of endoglucanase and exoglucanase activity at substrate combination of 75% wheat bran and 25% sawdust in Erlenmeyer-scale at day 6 and 3 were obtained 13 and 6.4 U/gds, respectively, and in bioreactor at aeration of 1.5 (l/(h.gds)) at day 3 were attained 36 and 10 U/gds, respectively.

Abstract ABSTRACT
Aims: Epithelial to mesenchymal transition (EMT) is an essential step in the developmental process, wound healing and cancer progression. In many cancers, EMT can increase aggressive properties including invasion, metastasis and Tumor resistance to apoptosis. Recently, miRNAs as a new class of non-coding RNAs that post-transcriptionally regulate gene expression have been demonstrated to have a crucial role in the regulation of EMT. However, the detailed mechanisms of miRNAs involvement in EMT in human cancer cells are still unclear. This study aimed to clarify this issue by using bioinformatics tools for predicting competent miRNAs target the main gens in EMT.
Materials and Methods: To ascertain an effective miRNA for the EMT, we assessed five genes from EMT/MET as key genes. Then, to predict the most suitable miRNA: target interactions, different online databases including DIANA, TargetScan, and miRSystem were applied.
Results: Possible targeting effects of different miRNAs on candidate genes were analyzed. Merging data from databases has shown that 11 miRNAs with strong possibility communally can be involved in EMT/MET.
Conclusion: To conclude, it can be predicted that according to high interaction scores of these elected miRNAs with candidate genes in the above-mentioned databases, these miRNAs probably can have critical roles in EMT/MET. Hence, these miRNAs can be introduced as appropriate candidates for future investigations.

Abstract The eukaryotic genome contains several replication Origins. Studies showed that the phenomenon and order of the origin activation is in a a particular discipline, called the “Replication Timing". Recent studies show that many factors are involved in regulating the timing of the replication process. One of the most important factors amongst them is the Rap1 interacting Factor 1 (Rif1) protein, which plays a key role in regulating the replication schedule in yeast and more advanced eukaryotes. Structure of this protein is mostly irregular and these properties prevent Rif1 from being expressed in a stable manner and makes it difficult to study.
The aim of the present study was to investigate the expression of recombinant C-terminal domain of mouse-Rif1(muRif1-CTD) protein in solution. For this purpose, the muRif1-CTD gene was extracted from eukaryotic constructs containing the complete Rif1 gene by PCR and was inserted into the pPAL7 expression vector comprising the Profinity eXact tag. Protein solubilization was carried out using different detergents and then detergent removal was performed by dialysis. In order to ensure that the soluble protein is active, the interaction analysis of the Rif1 protein with the G4 structures (previously reported to bind Rif1) was investigated using the gel shift assay. The results of this study showed the use of detergent for Rif1 solubilization without affecting its purification steps. But in the case of this protein, if the detergent is removed completely, it will not remain soluble.

Abstract Protein deposition due to the process of accumulation inside or outside cells causes many neurological diseases such as Alzheimerchr('39')s, Huntingtonchr('39')s or Parkinsonchr('39')s seizures. Parkinsonchr('39')s disease is the second most common neurological disease after Alzheimerchr('39')s, in which patients develop disorders due to the accumulation of leprosy and the destruction of dopamine neurons. Alpha-synuclein protein contains 140 amino acids, the main protein known in lewy body accumulations. During the aggregation process, alpha-synuclein protein monomers bind together as oligomers and eventually become amyloid filaments. So far, there is no drug to stop or delay the progression of Parkinsonchr('39')s, but studies on the molecular mechanism of amyloid formation and the identification of inhibitors are increasing. For this purpose, in this study, the effect of BRICHOS domain resulting from BRI2, which can have various functions, including antimicrobial properties, on the process of alpha-synuclein accumulation as a model protein was investigated.The gene was first optimized and synthesized and then multiplied by PCR. The product was digested by enzymes Xho I and Nde1 and entered the expression vector pET28 a, which was transformed into E. coli bacteria.Finally, the peptide was purified by nickel chromatography. The alpha-synuclein gene was also expressed separately and purified.The anti-cumulative effect of BRICHOS domain on alpha-synuclein fibrillation was investigated using Toflavin T fluorescence method and TEM technique.