Sharif Digital Repository

Complex networks serve as generic models for many biological systems that have been shown to share a number of common structural properties such as power-law degree distribution and small-worldness. Real-world networks are composed of building blocks called motifs that are indeed specific subgraphs of (usually) small number of nodes. Network motifs are important in the functionality of complex networks, and the role of some motifs such as feed-forward loop in many biological networks has been heavily studied. On the other hand, many biological networks have shown some degrees of robustness in terms of their efficiency and connectedness against failures in their components. In this paper we... 

The acidity and stability constants of M-Met (M: M2+; Met 1: L-methionine) complexes, determined by potentiometric pH titrations, were used to make a comparative investigation with L-cysteine (Cys). It is shown that regarding to M ion - binding properties vital differences on complex bilding were considered. It is demonstrated, that in M-Met complexes, M ion is coordinated to the carboxyl group, M ion is also able to build macrochelate over amine group. The upmentioned results demonstrate that for M-Met complex the stability constants is also largly determined by the affinity of Cu2+ for amino group but in opposite to Met, some metal ions such as Co2+, Cu2+, and Zn2+ build with Cys 2... 

Gold nanoparticles (AuNPs) of less than 50 nm diameter were electrodeposited from cyanide solution by pulsating electric current on modified copper and indium tin oxide (ITO) films coated on glass. Morphology, size, and composition of the deposited AuNPs were studied by X-ray photoelectron spectroscopy, atomic force microscopy, and field emission scanning electron microscopy. Effects of peak current density, pulse frequency, potassium iodide and cysteine on grain size, and morphology of the AuNPs were determined. Experiments showed that cathode current efficiency increases with the pulse frequency and the iodide ion. Size of the AuNPs increased with the current density. The number of... 

Cell culture feeds optimization is a critical step in process development of pharmaceutical recombinant protein production. Amino acids are the basic supplements of mammalian cell culture feeds with known effect on their growth promotion and productivity. In this study, we reported the implementation of the Plackett-Burman (PB) multifactorial design to screen the effects of amino acids on the growth promotion and productivity of a Chinese hamster ovary DG-44 (CHO-DG44) cell line producing bevacizumab. After this screening, the amino acid combinations were optimized by the response surface methodology (RSM) to determine the most effective concentration in feeds. Through this strategy, the... 

In this paper, we present a simple platform for colorimetric detection of glutathione using gold nanorods (AR ∼ 6.5 ± 0.2) as a plasmonic sensor. The functional mechanism of the sensor is based on shifts of longitudinal plasmon resonance during selective transverse overgrowth induced by preferential binding of glutathione at the nanorod tips. Under the optimum conditions, a calibration curve showed two linear regimes at the range of 50 nM to 20 μM of glutathione with a detection limit as low as 40 nM. The nanosensor maintains relatively high selectivity for determination of glutathione in the presence of several other amino acids. However, cysteine at similar concentration levels strongly... 

The cellular microenvironment can be engineered through the utilization of various nano-patterns and matrix-loaded bioactive molecules. In this study, a multilayer system of electrospun scaffold containing chitosan nanoparticles was introduced to overcome the common problems of instability and burst release of proteins from nanofibrous scaffolds. Bovine serum albumin (BSA)-loaded chitosan nanoparticles was fabricated based on ionic gelation interaction between chitosan and sodium tripolyphosphate. Suspension electrospinning was employed to fabricate poly-e{open}-caprolacton (PCL) containing protein-loaded chitosan nanoparticles with a core-shell structure. To obtain the desired scaffold... 

La0.3Sr0.7FeO3-δ (LSF) perovskite was prepared according to two methods: (1) applying new phenolic derivative of serine amino acid (L) as chelating agent, and (2) in absence of L as ligand-free perovskite (LFP). The newly prepared aminophenolic ligand L was fully characterized by 1H and 13C NMR, IR as well as elemental analysis while the LSF perovskite samples were characterized using the IR spectra, powder x-ray diffraction (PXRD) patterns, and SEM micrographs. The PXRD pattern obtained for the perovskite prepared by L (PPP) indicated on the presence of pure perovskite phase. The hydrogen permeation through PPP and LFP membranes with thickness of 1.0mm were measured as a function of... 

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... 

The partition constants of l-lysine HCl were measured in polymer-salt aqueous two-phase systems. These systems contain poly(ethylene glycol) with a nominal molecular weight of 4000 or 10000 and two different salts (dipotassium hydrogen phosphate or trisodium citrate 5-hydrate). The experimental data were obtained at temperatures of (293.15, 298.15, and 303.15) K. The effects of temperature, pH, polymer and salt concentrations, polymer molecular weight, and salt type on the partitioning of l-lysine HCl were also studied. The results showed that salt concentration has a significant effect on the partition constant while temperature has less effect. The Diamond and Hsu model was used to... 

As the delay time and hence nuclei formation play a crucial role in the pathophysiology of sickle cell disease, MD simulation and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations have been performed on three systems of hemoglobin; namely dimer of hemoglobin with valine (Hb S), tryptophan (Hbβ6W), and phenylalanine (Hbβ6F) at β6 position. The structural changes due to these aromatic substitutions are investigated. It is shown that β subunits have significant impact on the differences between a dimer and other crystal structures. Transition from a dimer to polymer for Hb S system affects the donor molecule more than that of the acceptor. In the case of donor and... 

A carbon paste electrode (CPE) chemically modified with TiO2 nanoparticles and quinizarine (QZ) was used as a selective electrochemical sensor for the simultaneous determination of minor amounts of d-penicillamine (D-PA) and tryptophan (Trp). This modified electrode showed very efficient electrocatalytic activity for anodic oxidation of both d-PA and Trp. Substantial decreases of anodic overpotentials for both compounds made this analysis possible. Results of square wave voltammetry (SWV) using this modified electrode showed two well-resolved anodic waves for the oxidation of d-PA and Trp, which makes the simultaneous determination of both compounds possible. The peak potential for the... 

The chemical synthesis and in vitro drug delivery response of folate-modified, polyethylene glycol-functionalized gold nanoparticles were studied. Lysine-capped gold nanoparticles were first prepared. Subsequently, the widely used anticancer agent doxorubicin (DOX) was successfully attached to the surface of folate-modified, polyethylene glycol-functionalized gold nanoparticles. Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM) were used to confirm the functionalization and conjugation steps in the chemical synthesis. The DOX-loading efficiency determined by UV-vis spectrometer was 80%. Drug release experiments displayed a controlled-release behavior... 

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... 

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... 

Sulfur Mustard (SM) is a potent alkylating agent and its effects on cells and tissues are varied and complex. Due to limitations in the diagnostics of sulfur mustard exposed individuals (SMEIs) by noninvasive approaches, there is a great necessity to develop novel techniques and biomarkers for this condition. We present here the first nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC/MS) metabolic profiling of serum from and healthy controls to identify novel biomarkers in blood serum for better diagnostics. Of note, SMEIs were exposed to SM 30 years ago and that differences between two groups could still be found. Pathways in which differences between SMEIs and... 

The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of 13Cα chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of 13Cβ, and 1Hα chemical shifts nor on the variation of absolute deviation of 13Cα chemical shifts relative to ψ dihedral angle. The 13Cα absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of... 

The present study is aimed at the synthesis of MnFe2O4@SiO2@PMIDA in terms of highly efficient sensing platform for anti-prostate specific membrane antigen (PSMA) immobilization. Superparamagnetic manganese ferrite nanoparticles were synthesized following co-precipitation method and then SiO2 shell was coated on the magnetic core with tetraethyl orthosilicate (TEOS) through a silanization reaction to prevent oxidation, agglomeration and, increase the density of OH groups on the surface of MnFe2O4. Subsequently, MnFe2O4@SiO2@PMIDA obtained as a result of the reaction between N-(phosphonomethyl)iminodiacetic acid (PMIDA) and MnFe2O4@SiO2. The reactive carboxyl groups on the surface of magnetic... 

Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD... 

Sulfur mustard (SM) is a vesication chemical warfare agent for which there is currently no antidote. Despite years of research, there is no common consensus about the pathophysiological basis of chronic pulmonary disease caused by this chemical warfare agent. In this study, we combined chemometric techniques with nuclear magnetic resonance (NMR) spectroscopy to explore the metabolic profile of sera from SM-exposed patients. A total of 29 serum samples obtained from 17 SM-injured patients, and 12 healthy controls were analyzed by Random Forest. Increased concentrations of seven amino acids, glycerol, dimethylamine, ketone bodies, lactate, acetate, citrulline and creatine together with the... 

Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD...