نشریه زیست فناوری دانشگاه تربیت مدرس
سال دهم شماره 3 (پیاپی 22، تابستان 1398)

Burns are one of the most important accidents related to human health. Receiving proper treatment is very important due to the intense complications associated with them. The improvement and elimination of ulcer effect can be achieved by controlling the wound infection. According to this, wound dressing containing antibiotics is one of the effective methods in wound's infection treatment. The use of silver in burns caring has been considered a long time ago, but silver deposits on the liver that causes some problems which can be overcome with the help of nanotechnology. In this study, Silver-Oak nanoparticles were green synthesized by using the ethanol extraction of Iranian Oak with the help of reducing agent. Nanoparticles formation were followed by UV-Visible spectrum and they characterize with SEM images and XRD spectrum. Then Gelatin-Alginate Hydrogel was prepared as a wound dressing and their properties were investigated by the presence of nanoparticles, oak extraction and without any additives. Nanoparticles' diameter is about 30-65nm which are dispersed in the hydrogel with regular pore size about 30-100μm. Oak extraction increase the hydrogel water uptake that improve the wound hilling. Antibacterial properties of wound dressing against Staphylococcus aurous and pseudomonas are investigated by inhibiting zone.

Ibuprofen, 4-isobutyl-propionic acid, is an important well-known member of NSAIDs which is widely utilized in inflammatory therapy like treatment of rheumatoid arthritis and various degrees of analgesic. Despite the high medical activity and low toxicity of ibuprofen, it is supplied as a racemic mixture. In this research enantioselective resolution of (R, S)-ibuprofen by immobilized preparations of Rhizomucor miehei lipase (RML) on silica and silica nanoparticles was investigated. For this, chemical modification of silica and silica mesoporous nanoparticles was performed by the simultaneous use of two coupling linkers; Octyltriethoxysilane (OTES) for hydrophobic interaction and glycidoxypropyltrimethoxylsilane (GPTMS) for covalent linkage of RML. The results showed that immobilization of RML on octyl-functionalized supports produces specific activity almost 1.5-2 folds greater than the specific activity of the free enzyme. The observed hyper-activation decreased with increasing epoxy groups on the supports confirming the enhancement of covalent nature of the attachment. Regarding the specific activity of the immobilized preparations and desorption percentages of RML from each support, the most suitable carrier obtained from the functionalization of the supports in the presence of GPTMS and OTES in the ratio of 1:1. The selected biocatalysts were then used for enantioselective resolution of (R, S)-ibuprofen by esterification reaction at different conditions. The results revealed that the most suitable biocatalysts are those prepared by immobilization of RML on SBA-15 and silica modified with GPTMS and OTES in the ratio of 1:1 which produced high E values at ambient temperature.

The large biological networks increase computational complexity during the execution of the algorithm and create constraints for working with such networks. By preserving the behavior and output of the main network, complexity is reduced, and the process of obtaining results and analyzing the network is quickly accomplished. Using mathematical and computational tools to simplify the biology networks provides better results in various sciences, especially in applications of biological sciences. Boolean modelling and finding adsorbents in biological networks will make it easy to display and analyze. This study was carried out through Boolean modelling on the Abscise Acid signal transduction network. Abscise Acid is one of the most important and effective regulators in plant growth. Our method started from an initial state and according to the rules of updating, found network adsorbents. Our proposed method, in contrast to other methods, will be able to simultaneously detect the absorbing points while plotting the state transition graph. In this way, finding all the system adsorbents is guaranteed.

Recently, polymer-based nanofibrous scaffolds have attracted great attention due to their significant antibacterial properties in the field of dermatological applications. In this study, a polycaprolactone-based nanofibrous scaffold has been fabricated using the electrospinning method. The aim of this study was to evaluate the antibacterial effect of electrospun nanofibrous structures.

In this experimental study, the structure and bacterial attachment on polymeric nanofibrous scaffolds were studied by Scanning Electron Microscopy (SEM). In addition, antibacterial properties of nanofibrous scaffolds were studied on two gram-negative bacteria of Escherichia coli and Pseudomonas aeruginosa and two gram-positive bacteria of Staphylococcus aureus and Streptococcus mutans, using microdilution method and biofilm assay. Moreover, MTT assay was performed on HeLa and human fibrosarcoma cell line (HT1080) cancerous cell lines to evaluate the cell viability.

The results of this study showed that nanofibrous scaffold revealed a significant antimicrobial and anti-biofilm formation effect on all of the studied bacterial strains, but in microscopic observations and microdilution assay was observed on Pseudomonas aeruginosa in 1mg/ml of nanofibrous scaffold extract concentration, while the major effect in biofilm assay was observed in 8µg/ml of extract concentration. Moreover, the cell viability studies showed that the most significant effect was shown on HT1080 cell line which has drastically decreased by 40% after 48 hours in comparison with the control.

These results show that electrospun nanofibrous PCL-based scaffolds are potentially promising for dermal tissue engineering applications, due to anti-biofilm effects and capability of reducing the number of cancerous cells in the wound site.

With urbanization expansion, application of concrete and construction materials is widely increasing throughout the world. Therefore, the use of a mechanism that can effectively extend the life of concrete structures is essential. Durable reinforced concrete structures are generally affected by the crack. Cracks in concrete are caused due to various reasons such as an environmental attack, overloading or accidental damage. Surface cracks in concrete facilitate the penetration of chemicals and corrosive chlorine, so as a result of these factors steel rebars corroded and caused the destruction of concrete structures. Calcium carbonate precipitates have proved their ability as a microbial sealant to fill the cracks and the gaps in Granites and sand. In this method, urea is hydrolyzed by the urease secreting bacteria and calcium carbonate is formed in the presence of calcium ion, which improves the stability and properties of concrete in the long term. Therefore, the use of microbial precipitation in concrete restoration can be considered as a natural and environmentally friendly strategy. This paper reviews current progress and potential of this technology.

Datura (Datura stramonium) is known as a rich source of tropane alkaloids, including scopolamine and hyoscyamine as parasympatholytics that competitively antagonize acetylcholine. Production of secondary metabolites often occurs in plants against the various elicitors or signal molecules. In this study, the effect of yeast extract as a biotic elicitor on tropane alkaloid production was evaluated. Surface-sterilized Datura seeds were cultured on 1/2 MS medium supplemented with different concentrations of yeast extract (0, 1.5, and 3g/L). One month after germination, alkaloid yield of Datura plantlets was measured by the use of High-Performance Liquid Chromatography (HPLC). Also, total protein content and antioxidative enzymes activity were determined by spectrophotometry method. According to the results, the fresh weight of root and shoot parts of Datura plantlets at 1.5g/L yeast extract was increased about 2 and 4 times, respectively. Yeast extract (1.5g/L) caused to 1.7 times increase of hyoscyamine amount of root and shoot parts and 2.5 folds scopolamine of Datura plantlets. Moreover, on yeast extract (1.5g/L)-treated plantlets, total protein content, and activity of catalase and guaiacol peroxidase were almost the same as the control group. Altogether, yeast extract (1.5g/L) can be used as a good candidate for enhancement production of tropane alkaloids especially hyoscyamine and scopolamine with high medicinal value.

Transtympanic Promontory Stimulation Test (TPST) has been suggested to be a useful tool in predicting the effectiveness of cochlear implant surgery. This test is helpful for patients with poor auditory neuron functioning and individuals with a long auditory deprivation. It can provide a way to find a correlation between the dynamic range of the auditory nerve with the electrical dynamic range of the cochlear implant and estimate sound perception. In this study, an electrical stimulation device is designed and constructed that can produce stimulation with specific features. The device has two parts, hardware, and software. Software is designed as a user interface which installed on PC and helps the user to do a lot of operations for creating a desired electrical stimulation easily utilizing software menus. The data are transferred via serial port and network to hardware and finally, the stimulation is done through an active electrode that located in auditory canal and a passive electrode that can be placed on the mastoid or forehead. To ensure the proper functioning of the device, electrical tests have been done in different conditions. The results are shown that currently generated in a constant load resistance is linear and independent of load resistance.

Quantum dots have received great attention for the past years as fluorescent markers for physical, chemical, and biological applications due to their unique size-dependent electrical and optical properties such as high extinction coefficient, broad absorption with narrow symmetric size-tunable fluorescent spectra, and strong resistance to photobleaching with significant luminescence quantum yield. In this study, at first the CdSe/ZnS quantum dots coated with oleylamine surface ligand were synthesized by high temperature injection method under vacuum conditions and stable nitrogen at 320°C. Then, in order to investigate the quenching effect of azo dyes, which is one of the most carcinogenic chemical colors used in various industries, on the emission of these nanoparticles, we used mercaptopropionic acid as a suitable hydrophilic ligand at the surface modification of quantum dots in the ligand exchange process as a proper aqueous phase transfer strategy. After confirming the proper synthesis of CdSe/ZnS nanoparticles by the transmission electron microscopy (TEM) test and the synthesized nanoparticle core and shell standard powder diffraction files (pdfs) in X-ray diffraction (XRD), the results of the studies showed that the methyl red due to its absorption spectrum overlapping with the emission spectrum of these quantum dots has a very powerful quenching effect on the emission of synthesized nanoparticles.

Nanotechnology is currently one of the promising approaches for cancer diagnosis and treatment. Among different materials that so far have been used for drug delivery, the systems based on the polymers are more attractive, due to their simple manufacturing processes and diversity in polymer functionalization and modification methods. Polyethyleneglycol (PEG) and polycaprolactone (PCL) are two FDA approved and biocompatible synthetic polymers which frequently have been used in the pharmaceutical industry. Apart from the delivery carriers, the active ingredient’s safety is also very challenging in case of cancer therapeutics. The chemotherapy agent’s side effects are one of the main patients’ death in many cancers. The naturally extracted curcumin is one of the most interesting anti-cancer agents with a proven selective effect on the cancerous cells which results in minimum side effects during the treatment. Curcumin has been tested as the main agent or in combination therapy of various cancers. Numerous studies have shown the safety and efficacy of curcumin at different administered doses. However, the main obstacle in the application of curcumin is its low aqueous solubility and low and variable bioavailability after administration. For that, in this study, we tried to enhance the solubility of curcumin using a novel diblock copolymer of PEG-PCL nanoparticulate system. At first, the PEG-PCL copolymer was synthesized and then characterized by GPC, FTIR, and H NMR methods. After that, curcumin was loaded in the micellar structure of PEG-PCL at an optimized encapsulation approach and then the toxicity of the prepared nanoparticles was assessed in MCF-7 cell culture. The results showed that the prepared nanoparticles could efficiently entrap the hydrophobic molecules of curcumin, improve its solubility and increase in vitro activity against cancer cell line.

The retinal pigment epithelium cells (RPE) have crucial roles in the health and functionality of retina. Any damage or dysfunction of these cells can lead to severe retinopathies. Identification of signaling pathways and biological processes involved in RPE differentiation can be useful in devising more robust therapeutic approaches.

In the present study, we used the intersection of three online prediction databases and their ::union:: with one experimental database to select microRNAs gene targets. Next, by the intersect of the targeted genes with an increase in their expression in epithelial to mesenchymal transition (EMT) of RPE cells, we tried to build a microRNA-mRNA integrative network. Further, several pathway analyses tools were used to perform a more accurate and comprehensive analysis of the signaling pathways and biological processes being regulated by selected miRs in the EMT of the RPE cells.

Our study revealed that among the 3406 genes being upregulated over the course of EMT in RPE cells, adj p-value≤0.05, fold change≥1.5, 93 genes were miR-204-5p and miR 211-5p target genes. Further analysis of the obtained target gene list demonstrated that these two microRNAs are mostly involved in maintaining RPE cells from going through EMT via regulation of cell adhesion and secretion subnetworks and also MAPK and TGF-β1 signaling pathways while preserving cells from apoptosis and neuronal fates.

This study indicated that miR-204-5p and miR 211-5p are involved in protecting RPE cells from EMT and reinforce their epithelial cell identity.

Prediction of three-dimensional structure from a sequence of amino acids is one of the important problems in structural bioinformatics. Proteins select a special structure among many possible conformations in order of seconds. Levinthal paradox expresses that random searches could not be an effective way to form a native structure and a principal mechanism should be available. Reduced alphabet fewer than 20 have been interested in protein structure because it could sufficiently simplify the protein folding problem. It is generally assumed that the native structure form in the lowest free energy among all conformational states. Therefore, it is needed to design a trustworthy potential function that could discriminate protein fold from incorrect ones.

Knowledge-based potential functions are one type of energy functions derived from a database of known protein structures. In this study, we introduce a knowledge-based potential and assess the power of five amino acids ALA, LEU, ILE, VAL, and PHE in discrimination of native structure using the reduced model. In the reduced model only the energy between the aforementioned amino acids are calculated.

The reduced model was evaluated using four criteria. The results indicate that there is no significant difference between the 20- amino acid model and the reduced model.

The presented model indicates that the power of discrimination of native structure is originally from the interaction between the aforementioned amino acids. Therefore, it needed a new strategy to capture the remaining interactions to improve the power of knowledge-based potential function.

Physalis alkekengi L. is planted in gardens and green spaces because of the beautiful and colorful sepals surrounding the fruit. The species is widely used in traditional medicine and treating a range of diseases. Micropropagation of P. alkekengi was evaluated using the node and internode explants. After sterilization and seed germination, sterile seedlings were transformed to basal MS medium to create sterilized seedlings as a source of explants. Regeneration of nodes and internodes explants was studied at various concentrations of growth regulators of 2, 4-D and BAP as well as in medium lacking growth regulators or control (11 various media). The experiment was conducted in a completely randomized design with three replicates. The internodal explants produced shoot on media 2 (0.2mgl-12, 4-D), 3 (0.2mgl-12, 4-D+0/2mgl-1 BAP ), and 4 (0.5mgl-12, 4-D+0.2mgl-1 BAP ) and then were rooted on these media. The nodal explants in control and different hormonal treatments generated shoots; interestingly, shoots generated in control medium successfully established roots on the same medium after 7 days (70%). The other regenerated shoots in different media (10) were rooted on ½ MS medium containing 1mgl-1IBA. The rooted plants were transplanted into pots containing sand as well as perlite to be well acclimated before transfer to the greenhouse. They grew well later in the greenhouse at a 100% success This study shows high in vitro regeneration capability of this species as an important medicinal and ornamental plant. Therefore, it is suggested to use this species in molecular and genetic studies, somaclonal variation, and the production of herbal medicine.

Due to their unique properties, functionalized GNPs provide a high potential for solving many problems, such as diagnosis and treatment of genetic diseases using nanotechnology. Depending on the purpose of each experiment, a particular interaction of DNA and nanoparticle is desirable that can be achieved by changing various parameters. The purpose of this study was to investigate the effect of gold nanoparticles surface charge on the conjugation process and the type of DNA interactions, as well as increasing the loading of DNA on the surface of gold nanoparticles.

Two types of 30nm gold nanoparticles with positive and negative charge were synthesized. Gold nanoparticles were functionalized with three different concentrations of DNA. Bioconjugation was investigated using UV-Vis and fluorescence spectroscopy. Quantification of the DNA loading on each nanoparticle surface was done using two methods by fluorescence assay.

The SPR spectrum of nanoparticles confirmed the binding of DNA to the surface of nanoparticles and also illustrates the level of DNA loading to the surface of the nanoparticle, as well as the effect of the surface charge of nanoparticles on the bioconjugation process. The fluorescence assay showed a higher loading of DNA in CTAB-stabilized nanoparticles and more non-specific than citrate-stabilized nanoparticles.

Depending on the surface charge of GNPs, DNA loading on the surface of GNPs occurs with different affinities. Based on the purpose of the study, citrate stabilized GNPs and high concentration of DNA was appropriate to achieve this goal.

Bone morphogenetic proteins (BMPs) belong to the superfamily transforming growth factor-beta. These molecules play a role in fetal development and differentiation of different cells. In this regard, two homodimer molecules BMP-2 and BMP-7 play an important role in the formation of ectopic bone So that two types of recombinant form are available for ectopic use. After binding of the homodimer BMP-2 to its receptor at the cell surface, the accumulation of homodimers of type I and II receptors results in a biological response within the cell. Despite the existence of recombinant types of BMP-2 and BMP-7 due to the dangers of their use, the strategy of using monoclonal antibodies to trap endogenous types is still a priority in research programs. Instead of using monoclonal antibodies, the alternative method is to use the natural receptors of the ligand in the body. In this regard, due to the proper Kd binding of the ectodomain component of the receptor II of the BMP molecule in this project, the expression and purification of this part were attempted to trap BMP-2 endogenous. The protein component of the type II receptor ectodomain was expressed and purified by the bacterial host, which, by evaluating CD, of this recombinant protein showed a similar structure to that of the natural type. Also, its binding to the BMP-2 ligand with ELISA was evaluated and then calculated as Kd. Based on the results, the type II receptor ectodomain can be connected to the BMP-2 with a suitable binding property at the nM concentration, and in subsequent studies, it can be used as an alternative to a monoclonal antibody to Trap endogenous BMP molecules.

The unique physicochemical properties of nanoscale plasmonic materials have attracted considerable attention in the fabrication of hybrid nano-bio structures because of their promising applications in biosensing, imaging, and controlled-release drug delivery. The purpose of this study was the synthesis of functionalized gold nanorods (GNRs) to both reduce the toxicity and increase the biocompatibility for further applications such as the design of a therapeutic nanocarrier for nucleic acid delivery to cancerous cells. In this study, GNRs were prepared by seed-mediated method and their surface was modified by polystyrene sulfonate (PSS) polymer. Then, peptide-functionalized GNRs was fabricated via ligand exchange method through the Au-S bond. The CTAB-GNRs and functionalized nanostructures were characterized using ultraviolet-visible spectrophotometry, transmission electron microscopy (TEM), and zeta potential measurement. Finally, the cytotoxicity effects of functionalized GNRs on Hela cells were studied by MTT assay. The optimal concentration of PSS and peptide, which did not cause any aggregation and morphological perturbations of the nanostructure were obtained 50μM and 1mM respectively. The survival percentage of treated Hela cells significantly increased by surface modification of GNRs with PSS and functionalization with peptide compared to CTAB-GNRs. While LC50 of functionalized GNRs was calculated 50nM, treated cells with the same concentrations of CTABGNRs survived less than 20%. Functionalization of GNRs increases its biocompatibility and improves applications of this nanostructure as a therapeutic carrier in cancerous cells.

CEL I endonuclease pertaining to the S1 endonuclease family. The enzyme, with its high specificity, has the ability to identify different types of mutations and base replacement in the DNA molecule, which makes it important in commercial products to use in research and clinical laboratories. Although the enzyme exists in the celery plant, the extraction of the enzyme is a time-consuming process and not economical and the yield of the final product is low. In addition, due to its post-translational modifications to achieve the final active structure, no report has published to indicate the expression of the active form of this enzyme in the bacterial hosts yet. Therefore, one of the production sources of the active form of this enzyme is its cloning and expression in eukaryotic hosts, including yeast and mammalian cell lines. In this study, in order to express CEL I endonuclease, its gene sequence was optimized and synthesized in host eukaryotic HEK293T. CEL I was subcloned by double digest with KpnI and XhoI enzymes in the pBudCE4.1expression vector. The expression construct was transfected into the HEK293T cell line by lipofectamine transfection. Expression of the recombinant protein after transfection into HEK293T cells was confirmed by multiple methods including polyacrylamide gel electrophoresis, ELISA, RT-PCR, and western blot reaction. The analysis of SDS-PAGE and western blot data confirmed the molecular weight of approximately 30kDa. Purification was carried out with the Ni-NTA column and the amount of purified protein was determined to be about 0.2mg/ml. Finally, the activity of endonuclease enzyme was investigated on both normal and mutated heteroduplex DNA amplified by PCR. The results showed that the expression of this protein in HEK293T host had shown sufficient activity.

Uricase (EC 1.7.3.3) was first utilized in the 1970s, to prevent the uric acid increase in the blood stream and the formation of urate crystals. Later, this enzyme was produced using recombinant DNA technology. However, immunogenic responses towards the alien protein in some patients has led to searching for new uricases with more desirable properties. Considering the interesting characteristics of enzymes of halophilic and halotolerant bacteria, the potential of 85 native Iranian halophilic bacteria isolated from Urmia salt lake for uricase production was evaluated, and the best producer was identified by means of 16S rRNA gene sequencing with more than 99% similarity to Halomonas sulfidaeris. In the following, significant physicochemical and environmental factors for optimal production of uricase by the selected strain were determined. The best combination of effective factors for the enzyme production was identified by Response Surface Methodology (RSM). The optimum enzyme production was found to be at pH=8, 34.5°C, 3% NaCl, and 7.5g/L of uric acid which resulted in the significant production of 32.5U/ml. This strain can be used in subsequent studies regarding the therapeutic application of this halotolerant enzyme.

Antioxidant, anticancer, anti-inflammatory, and anti-microbial activities are evidences for the invaluable benefit of this herbal extract in human health and therapy. The anticancer effect of curcumin is due to the targeting of a wide range of cellular and molecular pathways involved in cancer progression. However, the limited solubility, low bioavailability and rapid metabolism of curcumin have a serious negative impact on its therapeutic application. In this research, a nano-carrier with appropriate delivery features, prepared through the conjugation of curcumin to the surface of a polyamidoamine dendrimer at generation 4 (PAMAM). The structure of the synthesized dendrimeric curcumin was confirmed by FT-IR and 1H-NMR methods. The particles size and zeta potential were measured by Zetasizer. The loading rate of curcumin molecules on nano-carrier investigated and the cell viability, intracellular reactive oxygen species and induction of apoptosis were evaluated using MTT assay and flow cytometry technique in the follows. The results of this study showed that the prepared dendrimeric curcumin had a hydrodynamic diameter of about 100 nm. The results show that the rate of curcumin loading on this nanostructure system was about four curcumin molecules per each dendrimer. Cell experiments indicated that the toxicity, cellular reactive oxygen species (ROS), and apoptosis caused by dendrimeric nano-carrier were higher than free curcumin. Better performance of dendrimer-Nano-carrier was been through the improvement of physicochemical properties and increased curcumin solubility. Overall, it seems that the prepared dendrimeric curcumin is able to significantly improve the delivery of hydrophobic drugs on cancerous cells.

Three-dimensional (3D) cell culture systems are important because simulating the physiological microenvironment and representing more similarity to in vivo</em> conditions for anticancer drug screening. Taking the advantages of 3D cell culture in cancer therapy field, we have developed the 3D in vitro</em> anaplastic thyroid cancer (ATC) model for determination the cytotoxic dose of "BI-847325" chemotherapy agent in ATC cell lines with different genetic background.
Materials &

C643 and SW1736 ATC cell lines were grown in alginate scaffold. Beads were incubated in medium for one week. Cells were treated with different doses (1–64 μM) of BI-847325 for 24h. The cytotoxic effect of BI-847325 on 3D cultured cell lines was studied by MTT [3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide] assay. Survival rate of alginate-encapsulated cells was analyzed by CFSE (5,6-Carboxyfluorescein N-hydroxysuccinimidyl ester) staining in effective doses for each of the cell lines.

Cytotoxic effect of BI-847325 anticancer drug was different for two ATC cell lines. Effective doses of BI-847325 for C643 and SW1736 cell lines were at 25μM and 43μM, respectively. CFSE staining analysis confirmed these data.

Altogether, the results of the present study showed that the cytotoxic effect of BI-847325 chemotherapy agent was different for two ATC cell lines. The importance of this subject in regard to the 3D cell culture methods can be useful for researchers in the complementary experiences design in order to achieve the most appropriate chemotherapy drug with the most effective dose.

All bacteria have many different secretion systems to transfer of their macromolecules to out. Currently, seven secretion systems have been identified. Transfer, tracing, and horizontal transmission of these gene groups, are many important in our understanding about these gene's application in bacteria and other substances.  In this study, we examined Type III secretion system (T3SS) genes in Pseudomonas with using the bioinformatics software such as SeqWord Genome Browser in some databases for instants, ACLAME, Mobil Elements Genetic (MGEs), and PAthogenicity Islands Data Base (PAIDB).   The results indicate that the T3SS genes transfers are observed with the percentage between 30% and 100%. Our findings also show the P. fluorescens bacterium has the most species with 15 transmitted genes. Bioinformatics predictors showed P. fluorescens F113 subtype with 11 genes had the highest transferability of T3SS cluster genes. The bacteria species such P. Fluorescens Pf-5، P. syringae pv. Glycinea, P. syringae pv. Aptata ، P. syringae pv. Japonica ، P. syringae pv. Pisi ، P. aeruginosa UCBPP-PA14 show up about 100% of horizontal transfer from T3SS.  Our results also indicate that T3SS, which are important in the bacteria disease, have the highest transmission rates. This study indicates can be showing the systematic transmission of disease from host and pathogen during the evolution.