Sharif Digital Repository

The performances of gas chromatography with mass spectrometry and of comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry are examined through the comparison of Daphnia magna metabolic profiles. Gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with mass spectrometry were used to compare the concentration changes of metabolites under saline conditions. In this regard, a chemometric strategy based on wavelet compression and multivariate curve resolution–alternating least squares is used to compare the performances of gas chromatography with mass spectrometry and comprehensive two-dimensional gas chromatography with... 

The potential of hydrogen (pH) is a basic and critical parameter representing the function of numerous chemicals/biomolecules. Due to the widespread applications of pH in diverse fields, the development of rapid and simple yet reliable probes for the determination of pH has attracted significant interest. In this paper, by using AuNRs, silver ions, and ascorbic acid as colorimetric pH sensor, a multicolorimetric nanosensor is described for pH measurement. The reduction of silver ions by ascorbic acid which is strongly influenced by pH, results in silver nanoshell deposition on the surface of AuNRs. Consequently, the formation of Au@Ag core-shell NRs causes a series of blue shifts in the... 

The application of silicon nanowire (SiNW) biosensor as a subtle, label-free, and electrical tool has been extensively demonstrated by several researchers over the past few decades. Human ability to delicately fabricate and control its chemical configuration, morphology, and arrangement either separately or in combination with other materials as lead to the development of a nanomaterial with specific and efficient electronic and catalytic properties useful in the fields of biological sciences and renewable energy. This review illuminates on the various synthetic methods of SiNW, with its optical and electrical properties that make them one of the most applicable nanomaterials in the field of... 

The potential of an indigenous bacterial strain isolated from an Iranian oil field for the production of biosurfactant was investigated in this study. After isolation, the bacterium was characterized to be Paenibacillus alvei by biochemical tests and 16S ribotyping. The biosurfactant, which was produced by this bacterium, was able to lower the surface tension of media to 35. mN/m. Accordingly, thin layer chromatography (TLC) and FT-IR has been carried out to determine compositional analysis of the produced biosurfactant. After all the tests related to characterization of the biosurfactant produced by the isolated bacterium, it was characterized as lipopeptide derivative. The combination of... 

Biosurfactant production from two indigenous consortia has already been investigated in two previous studies. In this study, comparison and modification of those models for having as much biosurfactant as possible was conducted. After characterization of bacteria by biochemical tests and 16S ribotyping, a fully modification on the final models was presented. Response surface methodology has the ability to investigate the liability of the parameters and models by the help of Desirability mode and R2 coefficient in Design Expert software. Our models in the previous works follow the style of (y=f(A,B,. . .)) and two Desirability of 0.968 and 0.996 for Paenibacillus alvei ARN63 and Bacillus... 

In this study, we have investigated the potential of a native bacterial strain isolated from an Iranian oil field for the production of biosurfactant. The bacterium was identified to be Bacillus mycoides by biochemical tests and 16S ribotyping. The biosurfactant, which was produced by this bacterium, was able to reduce the surface tension of media to 34 mN/m. Biosurfactant production was optimized by the combination of central composite design (CCD) and response surface methodology (RSM). The factor selected for optimization of growth conditions were pH, temperature, glucose and salinity concentrations. The empirical model developed through RSM in terms of effective operational factors... 

In this study, we have investigated the potential of a native bacterial strain isolated from an Iranian oil field for the production of biosurfactant. The bacterium was identified to be Bacillus mycoides by biochemical tests and 16S ribotyping. The biosurfactant, which was produced by this bacterium, was able to reduce the surface tension of media to 34. mN/m. Compositional analysis of the produced biosurfactant has been carried out by thin layer chromatography (TLC) and FT-IR. The biosurfactant produced by the isolate was characterized as lipopeptide derivative. Biosurfactant production was optimized by the combination of central composite design (CCD) and response surface methodology... 

The aim of this review is to cover advances in noble metal nanoparticle (MNP)-based biosensors and to outline the principles and main functions of MNPs in different classes of biosensors according to the transduction methods employed. The important biorecognition elements are enzymes, antibodies, aptamers, DNA sequences, and whole cells. The main readouts are electrochemical (amperometric and voltametric), optical (surface plasmon resonance, colorimetric, chemiluminescence, photoelectrochemical, etc.) and piezoelectric. MNPs have received attention for applications in biosensing due to their fascinating properties. These properties include a large surface area that enhances biorecognizers... 

Abstract: In recent years, temporary skin grafts (TSG) based on natural biopolymers modified with carbon nanostructures have received considerable attention for wound healing. Developments are required to improve physico-mechanical properties of these materials to match to natural skins. Additionally, in-deep pre-clinical examinations are necessary to ensure biological performance and toxicity effect in vivo. In the present work, we show superior acute-wound healing effect of graphene oxide nanosheets embedded in ultrafine biopolymer fibers (60 nm) on adult male rats. Nano-fibrous chitosan-based skin grafts crosslinked by Genepin with physico-mechanical properties close to natural skins were... 

The significant role of protein nanoparticle interactions in nanomedicine and nanotoxicity is emerging recently through the identification of the nanoparticles (NP) protein (biomolecule) corona. The dynamic layer of proteins and/or other biomolecules adsorbed to the nanoparticle surface determines how a NP interacts with living systems and thereby modifies the cellular responses to the NP. Ehrenberg and co-workers used cultured endothelium cells as a model for vascular transport of polystyrene NP with various functional groups, which showed that the capacity of the various NP surfaces to adsorb proteins was indicative of their tendency to associate with cells. The quantification of the... 

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were... 

We previously reported that MR01, an indigenous strain of Pseudomonas aeruginosa, was able to produce a rhamnolipid-type biosurfactant. Here, we attempted to define the structural properties of this natural product. The analysis of the extracted biosurfactant by thin-layer chromatography (TLC) revealed the presence of two compounds corresponding to those of authentic mono- and di-rhamnolipid. The identity of two structurally distinguished rhamnolipids was confirmed by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. Liquid chromatography/mass spectrometry (LC/MS) of extracted biosurfactant revealed up to seventeen different rhamnolipid congeners. Further quantification showed... 

The process of imaging a biomolecule by atomic force microscope (AFM) is modeled using molecular dynamics (MD) simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the noncontact mode of AFM (NC-AFM) is employed as the operating mode. The biosample is scanned using a carbon nanotube (CNT) as the AFM probe. CNTs because of their small diameter, high aspect ratio and high mechanical resistance attract many attentions for imaging purposes. The tip-sample interaction is simulated by the MD method. The protein, which has been considered as the biomolecule, is ubiquitin and a... 

Microbial Enhanced Oil Recovery (MEOR) as a tertiary process employs microorganisms and their metabolites to reduce the residual oil saturation of the reservoir mainly through interfacial tension (IFT) reduction and wettability alteration. In spite of its great potential and the mentioned advantages, application of MEOR has been limited because of the lack of practical convincing experimental results. In this study, the effects of MEOR process on wettability changes and the reduction of residual oil saturation have been examined by providing microscopic visualization of two phase flow in transparent glass micromodels. Biosurfactant producing bacterial strain (Enterobacter cloacae) was... 

Introduction: Carbon nanotubes (CNT) have recently been studied as novel and versatile drug and gene delivery vehicles. When CNT are suitably functionalized, they can interact with various cell types and are taken up by endocytosis.Areas covered: Anti-cancer drugs cisplatin and doxorubicin have been delivered by CNT, as well as methotrexate, taxol and gemcitabine. The delivery of the antifungal compound amphotericin B and the oral administration of erythropoietin have both been assisted using CNT. Frequently, targeting moieties such as folic acid, epidermal growth factor or various antibodies are attached to the CNT-drug nanovehicle. Different kinds of functionalization (e.g., polycations)... 

In recent years miscellaneous smart micro/nanosystems that respond to various exogenous/endogenous stimuli including temperature, magnetic/electric field, mechanical force, ultrasound/light irradiation, redox potentials, and biomolecule concentration have been developed for targeted delivery and release of encapsulated therapeutic agents such as drugs, genes, proteins, and metal ions specifically at their required site of action. Owing to physiological differences between malignant and normal cells, or between tumors and normal tissues, pH-sensitive nanosystems represent promising smart delivery vehicles for transport and delivery of anticancer agents. Furthermore, pH-sensitive systems... 

The ever-increasing growth of nano-technology has elevated the necessity for development of new computational methods that are capable of evaluating large systems at nano-scale. The existing techniques, such as the molecular dynamics, lack the ability to simulate large systems of practical size and time scales. In order to provide a realistic simulation of large models, the multi-scale methods such as coarse-graining, have therefore become very popular. The coarse-grained models have mostly been used to simulate large biomolecules, such as proteins, lipids, DNA and polymers. In this paper, the Iterative Boltzmann Inversion (IBI) coarse-graining technique is applied to FCC nano-crystals; the... 

The bacterial strain MJ01 was isolated from stock tank water of one of the Iranian south oil field production facilities. The 16S rRNA gene of isolate, MJ01, showed 99% similarity to Bacillus subtilis. The results revealed that biosurfactant produced by this strain was lipopeptide-like surfactin based on FTIR analysis. Critical micelle concentration of produced surfactin in distilled water was 0.06 g/l. Wettability study showed that at zero salinity surfactin can change original oil-wet state to water-wet state, but in seawater salinity it cannot modify the wettability significantly. To utilize this biosurfactant in ex situ MEOR process, economical and reservoir engineering technical... 

In upstream oil industry, microorganisms arise some opportunities and challenges. They can increase oil recovery through microbial enhanced oil recovery (MEOR) mechanisms, or they can increase production costs and risks through reservoir souring process due to H2S gas production. MEOR is mostly known by bioproducts such as biosurfactant or processes such as bioclogging or biodegradation. On the other hand, when it comes to treatment of reservoir souring, the only objective is to inhibit reservoir souring. These perceptions are mainly because decision makers are not aware of the effect microorganisms’ cell can individually have on the wettability. In this work, we study the individual effect... 

Changing the wettability of reservoir rock towards strongly water-wet state is effective way to enhance oil recovery from fractured carbonate reservoirs which are typically oil-wet. Regarding this fact, the injection of surfactant and the bacterial solution as EOR agents is proposed in the current work as a potential method to alter the wettability of rock surface reservoir. Nevertheless, there is a definite lack of experimental data regarding this method and the synergistic effect of both chemical and bacterial solutions on this process. In this study, the sole and combined effects of the bacterial solution using an Enterobacter cloacae strain as a biosurfactant-producer are compared with...