Sharif Digital Repository

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison... 

Being the second cause of mortality across the globe, there is now a persistent effort to establish new cancer medication and therapies. Any accomplishment in treating cancers entails the existence of accurate identification systems empowering the early diagnosis. Recent studies indicate CTCs’ potential in cancer prognosis as well as therapy monitoring. The chief shortcoming with CTCs is that they are exceedingly rare cells in their clinically relevant concentration. Here, we simulated a microfluidic construct devised for immunomagnetic separation of the particles of interest from the background cells. This separation unit is integrated with a mixer subunit. The mixer is envisioned for... 

In the present work, the effect of graphene oxide (GO) nanosheets on the antibacterial activity of CuO nanowire arrays under visible light irradiation is shown. A combined thermal oxidation/electrophoretic deposition technique was employed to prepare three-dimensional networks of graphene oxide nanosheets hybridized with vertically aligned CuO nanowires. With the help of standard antibacterial assays and X-ray photoelectron spectroscopy, it is shown that the light-activated antibacterial response of the hybrid material against gram-negative Escherichia coli is significantly improved as the oxide functional groups of the GO nanosheets are reduced. In order to explore the physicochemical... 

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... 

Highly porous nanocomposites of graphitic-carbon nitride and tin oxide (g-C3N4/SnO2) were prepared through simple pyrolysis of urea molecules under microwave irradiation. The initial amount of tin was varied in order to investigate the effect of SnO2 content on preparation and properties of the composites. The synthesized nanocomposites were well-characterized by XRD, FE-SEM, HR-TEM, BET, FTIR, XPS, DRS, and PL. A homogeneous distribution of SnO2 nanoparticles with the size of less than 10 nm on the porous C3N4 sheets could be obtained, suggesting that in-situ synthesis of SnO2 nanoparticles was responsible for the formation of g-C3N4. The process likely occurred by the aid of the large... 

Miniaturized systems based on the principles of microfluidics are widely used in various fields, such as biochemical and biomedical applications. Systematic design processes are demanded the proper use of these microfluidic devices based on mathematical simulations. Aggregated proteins (e.g., inclusion bodies) in solution with chaotropic agents (such as urea) at high concentration in combination with reducing agents are denatured. Refolding methods to achieve the native proteins from inclusion bodies of recombinant protein relying on denaturant dilution or dialysis approaches for suppressing protein aggregation is very important in the industrial field. In this paper, a modeling approach is... 

High rates of mortality and morbidity stemming from cardiovascular diseases unveil extreme limitations in current therapies despite enormous advances in medical and pharmaceutical sciences. Following myocardial infarction (MI), parts of myocardium undergo irreversible remodeling and is substituted by a scar tissue which eventually leads to heart failure (HF). To address this issue, cardiac patches have been utilized to initiate myocardial regeneration. In this study, a porous cardiac patch is fabricated using a mixture of decellularized myocardium extracellular matrix (ECM) and chitosan (CS). Results of rheological measurements, SEM, biodegradation test, and MTT assay showed that the... 

Calcium release-activated calcium (CRAC) channels open upon depletion of Ca2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison... 

In this work, the synthesized graphene oxide/TiO2/doxorubicin (GO/TiO2/DOX) composites were loaded into the chitosan/poly(lactic acid) (PLA) solutions to fabricate the electrospun chitosan/PLA/GO/TiO2/DOX nanofibrous scaffolds via electrospinning process. The synthesized composites and nanofibers were characterized using X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis. Three-factor three-level central composite design was used to determine the influence of PLA to chitosan ratio, TiO2/DOX content and GO/TiO2/DOX content on the release of DOX from nanofibrous scaffolds. Drug loading efficiency and drug release behavior from... 

The pharmaceutical industry is facing enormous challenges due to high drug attribution rates. For the past decades, novel methods have been developed for safety and efficacy testing, as well as for improving early development stages. In vitro screening methods for drug-receptor binding are considered to be good alternatives for decreasing costs in the identification of drug candidates. However, these methods require lengthy and troublesome labeling steps. Biosensors hold great promise due to the fact that label-free detection schemes can be designed in an easy and low-cost manner. In this paper, for the first time in the literature, we aimed to compare the potential of label-free optical and... 

Bioremediation of soil and groundwater sites contaminated by petroleum hydrocarbons is known as a technically viable, cost-effective, and environmentally sustainable technology. The purpose of this study is to investigate laboratory-scale bioremediation of petroleum-hydrocarbon contaminated soil through development of eight bioreactors, two bioreactors for each bioremediation mode. The modes were: (1) natural attenuation (NA); (2) biostimulation (BS) with oxygen and nutrients; (3) bioaugmentation (BA) with hydrocarbon degrading isolates; (4) a combination of biostimulation and bioaugmentation (BS-BA). Total petroleum hydrocarbons (TPH) mass balance over the bioreactors showed about 2% of... 

In the present work, mesoporous nitrogen-doped carbon nanotubes (N-CNTs) were synthesized by using a low-cost and unique set of precursors (camphor and urea). The CVD method at 1000 °C was used with different camphor/urea ratios, and Co-Mo/MgO nanocatalyst was utilized as growth catalyst. Application of mesoporous N-CNTs in selective oxidation of H2S was studied experimentally and N-CNTs interactions with H2S was also investigated using DFT calculations. The as-synthesized N-CNTs were characterized using FTIR, FE-SEM, elemental analysis, X-ray diffraction (XRD), XPS and nitrogen adsorption/desorption. The N-CNT2 sample with urea to camphor ratio (U/C) of 1 showed the highest sulfur yield at... 

A magnetic nanocomposite was prepared by entrapment of Fe3O4 nanoparticles into the cross-linked ionic liquid/epoxy type polymer. The resulting support was used for covalent immobilization of cellulase through the reaction with epoxy groups. The ionic surface of the support improved the adsorption of enzyme, and a large amount of enzyme (106.1 mg/g) was loaded onto the support surface. The effect of the presence of ionic monomer and covalent binding of enzyme was also investigated. The structure of support was characterized by various instruments such as FT-IR, TGA, VSM, XRD, TEM, SEM, and DLS. The activity and stability of immobilized cellulase were investigated in the prepared support. The... 

The effect of Solid State Fermentation (SSF) on Chitosan production by A. niger was investigated. A. niger BBRC 20004 from Biochemical and Bioenvironmental Research Centre of Sharif University of Technology (Tehran, Iran), was grown on corn residue. Chitosan was extracted from the fungal mycelia using hot alkaline and acid treatment. A. niger was incubated for 12 days on corn residue with moisture content of 35 % and 1.12 % of nitrogen. The Chitosan was obtained and 10.9 g/kg of Urea dry residue was added in various amounts to the medium in order to evaluate the effect of the nitrogen concentration in the production of Chitosan. The highest amount of Chitosan obtained by 6.5 g of urea after... 

Keratinocyte Growth Factor (KGF) is a paracrine-acting, epithelial mitogen that plays a prominent role in the regeneration of damaged epithelial tissues. In spite of different attempts to produce recombinant human KGF in many organisms, including bacteria, mammalian cells, plant cells and insect cells; production of recombinant form suffers from lower yields and recovery relative to other recombinant proteins of similar size and properties. Due to many advantages of Pichia pastoris expression systems for producing industrial enzymes and pharmaceutical proteins, in this study P. pastoris was chosen as a host for KGF expression. For preparing human KGF coding sequence, MCF-7 cell line was... 

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the α-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the... 

The catalytic activity of highvalent iron-oxo active species of heme enzymes is known to be dependent on the nature of the axial ligand trans to the iron-oxo group. In a similar fashion, experimental studies on iron-oxo porphyrin biomimetic systems have shown a significant axial ligand effect on ethylbenzene hydroxylation, with an axial acetonitrile ligand leading to phenyl hydroxylation products and an axial chloride anion giving predominantly benzyl hydroxylation products. To elucidate the fundamental factors that distinguish this regioselectivity reversal in iron-oxo porphyrin catalysis, we have performed a series of density functional theory calculations on the hydroxylation of... 

Chondroitinase ABCI (cABCI) is a drug enzyme that can be used to treat spinal cord injuries. Due to low thermal stability of cABCI, this enzyme was immobilized on Fe3O4 nanoparticle to increase its thermal stability. The size and morphology, structure and magnetic property of the Fe3O4 nanoparticles were characterized by the analyses of SEM, XRD and VSM, respectively, and FTIR spectroscopy was employed to confirm the immobilization of cABCI on the surface of Fe3O4 nanoparticles. The results indicated that the optimum conditions for pH, temperature, cABCI-to-Fe3O4 mass ratio and incubation time in immobilization process were 6.5, 15 °C, 0.75 and 4.5 h, respectively, and about 0.037 mg cABCI... 

The phase-pure multiple ternary or quaternary metal selenides in energy boosting, have not been reported yet. Here, self-supported porous crystalline Zn–Ni–Co/Cu selenides microballs arrays were constructed by selenation of the designed tubular Cu(OH)2 arrays decorated with ultrathin Zn–Co–Ni tri-metallic hydroxide on carbon cloth substrate. For this rational engineering, a novel precursor sample was firstly prepared by conversion of deposited Cu layer to hollow tubular Cu(OH)2 arrays on carbon cloth, then, Zn-Co–Ni layered ternary hydroxides with a thin layer structure was deposited around this tubular arrays. The selenation with an exciting morphology change from amorphous tube to highly... 

IL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix. Here a combination of molecular dockings and molecular dynamics simulations of the unglycosylated, partially N-glycosylated and fully N-glycosylated IL-1RI EC domain in the apo, GAG-bound and IL-1β-bound states were carried out to explain the co-occurring...