Sharif Digital Repository

An effect-directed analysis (EDA) of fresh and artificially weathered (evaporated, photooxidized) samples of North Sea crude oil and residual heavy fuel oil is presented. Aliphatic, aromatic, and polar oil fractions were tested for the presence of aryl hydrocarbon receptor (AhR) agonist and androgen receptor (AR) antagonist, demonstrating for the first time the AR antagonist effects in the aromatic and, to a lesser extent, polar fractions. An extension of the typical EDA strategy to include an N-way partial least-squares (N-PLS) model capable of relating the comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) data set to the bioassay data... 

It is estimated that 20% of couples are infertile, and half of these infertility cases are linked to men. One of conditions that can affect male fertility is asthenozoospermia. We applied Raman spectroscopy to the analysis of the metabolome of the human seminal plasma, and used chemometrics on the patterns of Raman spectra obtained. Significant changes were observed in the metabolome of the human seminal plasma of asthenozoospermic patients  

Graphene oxide nanoribbons (GONRs) were synthesized using an oxidative unzipping of multi-walled carbon nanotubes. The interactions of the GONRs with various concentrations of fetal bovine serum or human plasma serum indicated that the GONRs were functionalized substantially by the albumin originated from the two different protein sources. Then, concentration-dependent cytotoxicity of the protein-functionalized GONRs on human epithelial cells was studied. Although the GONRs with concentrations ≤50 μg/mL did not exhibit significant cytotoxicity on the cells (with the cell viability >85%), the concentration of 100 μg/mL exhibited significant cytotoxicity including prevention of cell... 

Reduced graphene oxide nanoplatelets (rGONPs) were synthesized by sonication of covalently PEGylated GO sheets followed by a chemical reduction using hydrazine and bovine serum albumin. Human mesenchymal stem cells (hMSCs), as a fundamental factor in tissue engineering, were isolated from umbilical cord blood (as a recently proposed source for extracting fresh hMSCs) to investigate, for the first time, the size-dependent cyto- and geno-toxic effects of the rGONPs on the cells. The cell viability test showed significant cell destructions by 1.0 μg/mL rGONPs with average lateral dimensions (ALDs) of 11±4 nm, while the rGO sheets with ALDs of 3.8±0.4 μm could exhibit a significant cytotoxic... 

Phytochemical investigation of the aerial parts of Salvia eremophila led to the isolation of a lupane triterpenoid, 3β, 20-dihydroxylupane-28-oic acid (1), together with eight other compounds, comprising three diterpene, two triterpene, two flavonoids and a steroidal glucoside. Their structures were elucidated by interpretation of their one-dimensional and two-dimensional NMR spectra and completed by the analysis of the HRESIMS data. Compounds 1, 2-4 and 8 were evaluated for their cytotoxicities against five human tumour cell lines. Compounds 1 and 3 hold a good potential for use in future studies due to their anti-cancer properties  

Open-pore titanium scaffolds were fabricated by sintering of compressed mixtures of TiH1.924 and urea. Spherical and irregular shaped space holders were used to investigate the effect of pore shape on cellular behavior. After removal of the space holder, the shape of the spacers was replicated to the pores. Average diameter of the pores was in the range of 300-600 lm. SEM images showed that titanium hydride resulted in higher surface roughness and larger micro porosities than pure titanium. In vitro evaluationswere carried out by using MTT assay, measuring alkaline phosphatase activity and alizarin red staining in flow perfusion bioreactor for cell culture. Observations revealed excellent... 

Arms bearing ureido-pyrimidinone functional groups with self-association capability (through quadruple hydrogen bonds) were successfully grafted onto hydroxyapatite nanoparticles. The supramolecularly modified nanoparticles (nHApUPy) exhibited enhanced colloidal stability compared to the original hydroxyapatite nanoparticles and were uniformly dispersed in supramolecular polycaprolactone in PCL(UPy)2/HApUPy nanocomposites at different filler loadings. The combined atomic force microscopy, mechanical, and rheological analyses confirmed a high degree of compatibility of HApUPy nanoparticles with the polymer matrix. The temperature dependence of the supramolecular structure in PCL(UPy)2/HApUPy... 

Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational... 

Abstract: In this study, chitosan–Laponite nanocomposite coatings with bone regenerative potential and controlled drug-release capacity are prepared by electrophoretic deposition technique. The controlled release of a glycopeptide drug, i.e. vancomycin, is attained by the intercalation of the polymer and drug macromolecules into silicate galleries. Fourier-transform infrared spectrometry reveals electrostatic interactions between the charged structure of clay and the amine and hydroxyl groups of chitosan and vancomycin, leading to a complex positively-charged system with high electrophoretic mobility. By applying electric field the charged particles are deposited on the surface of titanium... 

Hydrogels made of natural polymers [chitosan (CS) and gelatin (G)] have been prepared having mechanical properties similar to those of muscle tissues. In this study, the effect of polymer concentration and scaffold stiffness on the behavior of seeded muscle-derived cells (MDCs) on the CS-G hydrogel sheets has been evaluated. Both variables were found to be important in cell viability. Viability was assessed by observation of the cell morphology after 1 day as well as a 14-day MTT assay. The CS-G hydrogels were characterized using Fourier transform infrared (FTIR) analysis, which revealed evidences of strong intermolecular interactions between CS and G. Hydrogel samples with intermediate... 

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... 

This paper reports on the development of conductive porous scaffolds by incorporating conductive polyaniline/graphene (PAG) nanoparticles into a chitosan/gelatin matrix for its potential application in peripheral nerve regeneration. The effect of PAG content on the various properties of the scaffold is investigated and the results showed that the electrical conductivity and mechanical properties increased proportional to the increase in the PAG loading, while the porosity, swelling ratio and in vitro biodegradability decreased. In addition, the biocompatibility was evaluated by assessing the adhesion and proliferation of Schwann cells on the prepared scaffolds using SEM and MTT assay,... 

Reduced graphene oxide nanomeshes (rGONMs), as p-type semiconductors with band-gap energy of ~1. eV, were developed and applied in near infrared (NIR) laser stimulation of human neural stem cells (hNSCs) into neurons. The biocompatibility of the rGONMs in growth of hNSCs was found similar to that of the graphene oxide (GO) sheets. Proliferation of the hNSCs on the GONMs was assigned to the excess oxygen functional groups formed on edge defects of the GONMs, resulting in superhydrophilicity of the surface. Under NIR laser stimulation, the graphene layers (especially the rGONMs) exhibited significant cell differentiations, including more elongations of the cells and higher differentiation 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... 

Core-shell iron-gold (Fe@Au) nanoparticles were synthesized by a facile reverse micelle procedure and the effect of water to surfactant molar ratio (w) on the size, size distribution and magnetic properties of the nanoparticles was studied. MTT assay was utilized to evaluate the cell toxicity of the nanoparticles. To functionalize the particles for MRI imaging and targeted drug delivery, the particles were coated by polyglycerol through capping with thiol followed by polymerization of glycidol. The characteristics of the particles were examined by X-ray diffraction (XRD), transmission electron microscopy (TEM), vibrating sample magnetometere (VSM), UV-visible spectroscopy, and Fourier... 

Porous gelatin-chitosan microcarriers (MCs) with the size of 350 ± 50 μm were fabricated with blends of different gelatin/chitosan (G/C) weight ratio using an electrospraying technique. Response surface methodology (RSM) was used to study the quantitative influence of process parameters, including blend ratio, voltage, and syringe pump flow rate, on MCs diameter and density. In the following, MCs of the same diameter and different G/C weight ratio (1, 2, and 3) were fabricated and their porosity and biocompatibility were investigated via SEM images and MTT assay, respectively. The results showed that mesenchymal stem cells (MSCs) could attach, proliferate, and spread on fabricated porous MCs... 

Superparamagnetic iron oxide nanoparticles (SPIONs) functionalized with antimicrobial agents are promising infection-targeted therapeutic platforms when coupled with external magnetic stimuli. These antimicrobial nanoparticles (NPs) may offer advantages in fighting intracellular pathogens as well as biomaterial-associated infections. This requires the development of NPs with high antimicrobial activity without interfering with the biology of mammalian cells. Here, we report the preparation of biocompatible antimicrobial SPION@gold core-shell NPs based on covalent immobilization of the antimicrobial peptide (AMP) cecropin melittin (CM) (the conjugate is named AMP-NP). The minimal inhibitory... 

It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was... 

Ground-state pluripotency is a cell state in which pluripotency is established and maintained through efficient repression of endogenous differentiation pathways. Self-renewal and pluripotency of embryonic stem cells (ESCs) are influenced by ESC-associated microRNAs (miRNAs). Here, we provide a comprehensive assessment of the “miRNome” of ESCs cultured under conditions favoring ground-state pluripotency. We found that ground-state ESCs express a distinct set of miRNAs compared with ESCs grown in serum. Interestingly, most “ground-state miRNAs” are encoded by an imprinted region on chromosome 12 within the Dlk1-Dio3 locus. Functional analysis revealed that ground-state miRNAs embedded in the...