Sharif Digital Repository

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... 

We consider chaperone-assisted translocation of biopolymers with two distinct monomers or bases A and B, with the size of the chaperones being λα, where α is a monomer's size. The probability that A and B are neighbors in the biopolymer is PAB. A master equation is used, together with the detailed-balanced condition, in order to derive analytical results for the statistics of the first-passage times of the biopolymer as a function of PAB, λ, and the biopolymer's configuration. Monte Carlo simulations have also been carried out in order to compute the same quantities for biopolymers with 100-900 monomers and several λ. The results indicate nontrivial dependence of the variance of the... 

Developments of sensitive, rapid, and cheap systems for identification of a wide range of biomolecules have been recognized as a critical need in the biology field. Here, we introduce a simple colorimetric sensor array for detection of biological thiols, based on aggregation of three types of surface engineered gold nanoparticles (AuNPs). The low-molecular-weight biological thiols show high affinity to the surface of AuNPs; this causes replacement of AuNPs' shells with thiol containing target molecules leading to the aggregation of the AuNPs through intermolecular electrostatic interaction or hydrogen-bonding. As a result of the predetermined aggregation, color and UV-vis spectra of AuNPs... 

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... 

Crohn's disease and celiac disease belong to a group of autoimmune conditions that affect the digestive system, specifically the small intestine. They both attack the digestive tract and share many symptoms. Thus, the discovery of proper methods would be a major step toward differentiating celiac disease from Crohn's disease. The aim of this study was to search for the metabolic biomarkers to differentiate between these two diseases. Proton nuclear magnetic resonance spectroscopy (1H NMR) was employed as the metabolic profiling method to look for serum metabolites that differentiate between celiac disease and Crohn's disease. Classification of celiac disease and Crohn's disease was done... 

Parkinson's disease (PD) is a neurodegenerative disease, which is not easily diagnosed using clinical tests and the discovery of proper methods would be a major step towards a successful diagnosis. In the present study, we employed metabolic profiling using proton nuclear magnetic resonance spectroscopy to find metabolites in serum, which are helpful for the diagnosis of PD. Classification of PD and healthy subject was done using random forest. Serum levels of selenium measured by atomic absorption spectrometry in PD group were lower than the serum selenium levels in the control group. The metabolites causing selenium changes in PD patients were identified using random forest, and a model... 

A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30°C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals... 

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... 

To obtain potentially applicable microorganisms to an effective in situ microbial enhanced oil recovery operation, bacteria that were compatible with the harsh conditions of a petroleum reservoir were isolated from a crude oil sample. The application of an oil spreading technique showed that all of the isolates were capable of producing biosurfactants from both the glucose and crude oil as carbon sources. The secreted biosurfactants could at least reduce the surface tension 20 mN/m and for one of the isolates; the surface tension value dropped below 40 mN/m. In addition, the contact angle measurements revealed that the produced biosurfactants could effectively alter the wettability of the... 

The physical properties and chemical structure of a new biosurfactant (licheniformin) produced by Bacillus licheniformis MS3 were investigated. The purified biosurfactant was identified as a lipopeptide with amino acid sequence of Gly, Ala, Val, Asp, Ser, Gly, Tyr and a lactone linkage between the carboxyl group of Aspargine and hydroxyl group of Tyrosine residue. The fatty acid moiety was attached to N-terminal amino acid residue through an amide bond. The purified licheniformin could lower the surface tension of water from 72 to 38 mN/m at concentrations higher than 15 μg/mL and its relative emulsion volume (EV%) was equal to 36%. It also showed stable surface activity over a wide range of... 

A novel kind of a biopolymer-based superabsorbent composite, salep-g-poly(sodium acrylate)/alumina, was prepared from salep, sodium acrylate, and alumina by aqueous polymerization, using N,N'-methylenebisacrylamide (MBA) as a cross-linker and ammonium persulfate (APS) as an initiator. The reaction parameters [i.e., acrylic acid (AA), MBA, APS amounts, and neutralization percentage of AA as well as alumina/salep weight ratio] affecting the water absorbency of the hydrogel composite were optimized using systematic method to achieve a composite with high swelling capacity as possible. The swelling behavior of optimum superabsorbent composite was measured in various pH solutions. In addition,... 

This study deals with the large-scale production of biosurfactant from soybean oil soapstock by Pseudomonas aeruginosa MR01. The production of biosurfactant was carried out in a newly designed bioreactor equipped with recycling flow under three operational conditions. Kinetic studies were conducted at both shake flask and 5-L bioreactor scales during fermentation in a soapstock medium. Mathematical equations were developed to model the kinetic patterns at both scales. RESULT: Statistical analyses demonstrated the goodness of fit, with regression r-squared, R2, between 0.97and 0.99 for different models. Furthermore, biosurfactant concentration in the bioreactor including the recycling flow,... 

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,... 

A bacterial strain was isolated and cultured from the oil excavation areas in tropical zone in southern Iran. It was affiliated with Pseudomonas. The biochemical characteristics and partial sequenced 16S rRNA gene of isolate, MR01, was identical to those of cultured representatives of the species Pseudomonas aeruginosa. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties. Compositional analysis revealed that the extracted biosurfactant was composed of high percentages lipid (∼65%, w/w) and carbohydrate (∼30%, w/w) in addition to a minor fraction of protein (∼4%, w/w). The best production of 2.1 g/l was obtained when the cells were grown on... 

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)... 

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... 

Gas-phase acidities of nucleosides, combined with the knowledge of deprotonation sites, could improve our understanding of chemical reactions to biological systems. In this paper, we mainly focus our attention on the influence of cation coordination on acidities of multiple sites in cytosine nucleosides. The acidities of multiple sites in M +-L (where L represents cytosine nucleosides and M + is an alkali metal ion, including Li +, Na + and K +) complexes have been investigated theoretically, employing B3LY P6-311++G(d,p) basis sets. The geometrical characters, gas-phase acidities, sugar puckering and electronic properties of non-deprotonated and/or deprotonated complexes have been... 

The binding of Mg 2+, Ca 2+, Zn 2+ and Cu + metal cations to 2′-deoxyguanosine has been analyzed, using the hybrid B3LYP, Density Functional Theory (DFT) method and 6311++G(d,p) orbital basis sets. Coordination geometries, absolute metal ion affinities, and free energies for the most stable complexes formed by Mg 2+, Ca 2+, Zn 2+ and Cu + with the nucleoside, 2′-deoxyguanosine, have been determined. Furthermore, the influences of metal cationization on the strength of the N-glycosidic bond, torsion angles and angle of Pseudorotation (P) have been studied. With respect to the results, it has been found that metal binding significantly changes the values of the phase angle of Pseudorotation... 

Optical tweezers (OT) are widely used for pico (and femto)-Newton range force measurements. The appropriate choice of the bead size is not well understood for biopolymer stretching applications of OT. We have shown, both by theory and experiment, that wrong choice of the bead size could cause errors as large as 295% in the measured force. We provide a simple map for correct choice of the bead size and the direction of pulling for such applications. There is a good agreement between our theoretical and experimental results  

The effect of an efficient biosurfactant produced from Pseudomonas aeroginosa MR01, a bacterial strain isolated from oil excavation areas in southern Iran, on the recovery of residual oil trapped within carbonate rocks, was investigated. In a core holder set-up, bearing a number of limestone-and dolomite-containing core samples, biosurfactant flooding resulted in oil recoveries as large as 20% to 28% Residual Oil (R.O). Biosurfactant injection in less permeable rocks in a range of 0.5 to 32 md was more successful, in terms of oil production. In the case of the least oil recovery via biosurfactant flooding, incubation of the core with a biosurfactant solution at reservoir conditions,...