Sharif Digital Repository

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... 

Metabolomics is the science of studying small molecules (metabolites) in biological systems with the aim of getting insight into cells, biofluids and organisms. Chemometric methods are powerful tools to address data problems generated in metabolomic studies and to extract valuable information. This review focuses mainly on a range of chemometric methods used for processing of metabolomics data generated from gas chromatography-mass spectrometry (GC-MS) and comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC-MS). Herein, essential skills used for preprocessing of raw data, multivariate resolution, pattern recognition, variable selection and identification of... 

The ultimate goal of new food packaging technologies, in addition to maintaining the quality and safety of food for the consumer, is to consider environmental concerns and reduce its impacts. In this regard, one of the solutions is to use eco-friendly biopolymers instead of conventional petroleum-based polymers. However, the challenges of using biopolymers in the food packaging industry should be carefully evaluated, and techniques to eliminate or minimize their disadvantages should be investigated. Many studies have been conducted to improve the properties of biopolymer-based packaging materials to produce a favorable product for the food industry. This article reviews the structure of... 

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... 

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 primary challenge of spectroscopic techniques in selective detection and characterization of tautomeric structures of DNA and RNA bases, and moreover, the accurate interpretation and explanation of the experimental results are the main motives of theoretical studies. Surface-enhanced Raman spectroscopy (SERS) can be a powerful approach to distinguish cytosine in the presence of its tautomers. For this respect, herein, the theoretical simulation of the SERS spectra of cytosine and its three most stable tautomers adsorbed on silver clusters is carried out. The calculations of SERS spectra is based on the excited-state energy gradient approximation as a well-established approach that gives... 

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... 

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... 

Once in biological fluids, the surface of nanoparticles (NPs) is rapidly covered with a layer of biomolecules (i.e., the "protein corona") whose composition strongly determines their biological identity, regulates interactions with biological entities including cells and the immune system, and consequently directs the biological fate and pharmacokinetics of nanoparticles. We recently introduced the concept of a "personalized protein corona" which refers to the formation of different biological identities of the exact same type of NP after being exposed to extract plasmas from individuals who have various types of diseases. As different diseases have distinct metabolomic profiles and... 

In the current study, a novel approach which takes into account the effectiveness of both convectional surfactants and biosurfactants was investigated. The biosurfactant produced by Enterobacter cloacae strain was utilized concomitant with conventional surfactant (sodium dodecyl benzene sulfonate (SDBS)) to evaluate its capability to reduce the SDBS adsorption on rock surface (biosurfactant acts as sacrificial agent) or synergistically enhance the effectiveness of the SDBS. In this regard, the wettability alteration and interfacial tension (IFT) measurements and calculation of spreading coefficient were performed considering two different scenarios. In the first scenario, SDBS was added to... 

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... 

Rhamnolipids are the most common biosurfactants and P. aeruginosa strains are the most frequently studied microorganisms for the production of rhamnolipids. Eco-friendly advantages and promising applications of rhamnolipids in various industries are the major reasons for pursuing the economic production of these biosurfactants. This study shows that cultivation of P. aeruginosa MR01 in medium contained inexpensive soybean oil refinery wastes which exhibited similar levels and homologues of rhamnolipids. Mass spectrometry indicated that the Rha-C10-C10 and Rha-Rha-C10-C10 constitute the main rhamnolipids in different cultures of MR01 including one of oil carbon source analogues. Moreover,... 

Owning to interesting properties of biosurfactants such as biodegradability and lower toxicity, they have broad application in the food industry, healthy products, and bioremediation as well as for oil recovery. The present study was aimed to develop a GA-ANFIS model for predicting the breakthrough curves for rhamnolipid adsorption over activated carbon. To that end, a set of 296 adsorption data points were utilized to train the proposed FIS structure. Different graphical and statistical methods were also used to evaluate the model's accuracy and reliability. Results were then compared to those of the previously reported Artificial Neural Network (ANN) and Group Method Data Handling (GMDH)... 

The present study is aimed at the development of a novel approach based on the magnetic improvement of DNA-directed antibody immobilization to prepare a highly efficient sensing platform. Magnetic nanoparticle substrates with high surface area capture the dual DNA-conjugated antibodies in a solution. This allows overcoming the typical mass transport limitation of the surface-based antibody immobilization. Antibody-magnetic nanoparticle conjugation is based on a robust hybridization between a DNA tether (attached to the antibody) and its complementary sequence (immobilized on the nanoparticle). Conventional antibody immobilization for the detection of proteins is often insignificant for the... 

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... 

Chromatographic fingerprinting is an effective methodology for authentication and quality control of herbal products. In the presented study, a chemometric strategy based on multivariate curve resolution-alternating least squares (MCR-ALS) and multivariate pattern recognition methods was used to establish a gas chromatography-mass spectrometry (GC-MS) fingerprint of saffron. For this purpose, the volatile metabolites of 17 Iranian saffron samples, collected from different geographical regions, were determined using the combined method of ultrasound-assisted solvent extraction (UASE) and dispersive liquid-liquid microextraction (DLLME), coupled with GC-MS. The resolved elution profiles and... 

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)... 

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... 

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...