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Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response
, Article Journal of Biomolecular Structure and Dynamics ; Volume 40, Issue 6 , 2022 , Pages 2575-2585 ; 07391102 (ISSN) ; Ejtehadi, M. R ; Sharif University of Technology
Taylor and Francis Ltd
2022
Abstract
Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic...
Nanomechanical properties of MscL α helices: A steered molecular dynamics study
, Article Channels ; Volume 11, Issue 3 , 2017 , Pages 209-223 ; 19336950 (ISSN) ; Bavi, O ; Vossoughi, M ; Naghdabadi, R ; Hill, A. P ; Martinac, B ; Jamali, Y ; Sharif University of Technology
Taylor and Francis Inc
2017
Abstract
Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during...
N-doped CNT nanocatalyst prepared from camphor and urea for gas phase desulfurization: experimental and DFT study
, Article Journal of the Taiwan Institute of Chemical Engineers ; Volume 85 , April , 2018 , Pages 121-131 ; 18761070 (ISSN) ; Banna Motejadded, H ; Rashidi, A ; Hamzehlouyan, T ; Yousefian, Z
Taiwan Institute of Chemical Engineers
2018
Abstract
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...
Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil
, Article Functional and Integrative Genomics ; Volume 18, Issue 5 , 2018 , Pages 533-543 ; 1438793X (ISSN) ; Niazi, A ; Deihimi, T ; Taghavi, S. M ; Ayatollahi, S ; Ebrahimie, E ; Sharif University of Technology
Springer Verlag
2018
Abstract
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...
Modeling, simulation, and employing dilution–dialysis microfluidic chip (DDMC) for heightening proteins refolding efficiency
, Article Bioprocess and Biosystems Engineering ; Volume 41, Issue 5 , 2018 , Pages 707-714 ; 16157591 (ISSN) ; Masoudi, M. M ; Shamloo, A ; Habibi Rezaei, M ; Moosavi Movahedi, A. A ; Sharif University of Technology
Springer Verlag
2018
Abstract
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...
Personalised deposition maps for micro- and nanoparticles targeting an atherosclerotic plaque: attributions to the receptor-mediated adsorption on the inflamed endothelial cells
, Article Biomechanics and Modeling in Mechanobiology ; Volume 18, Issue 3 , 2019 , Pages 813-828 ; 16177959 (ISSN) ; Forouzandehmehr, M ; Sharif University of Technology
Springer Verlag
2019
Abstract
Endothelial inflammation as a prominent precursor to atherosclerosis elicits a distinct pathological surface expression of particular vascular proteins. To exhibit a site-specific behaviour, micro- and nanoparticles, as carriers of therapeutics or imaging agents, can distinguish and use these proteins as targeted docking sites. Here, a computational patient-specific model capturing the exclusive luminal qualities has been developed to study the transport and adsorption of particles decorated with proper antibodies over an atherosclerotic plaque located in the LAD artery of the patient. Particles, in nano- and micron sizes, have been decorated with Sialyl Lewisx (sLex), P-selectin aptamer...
Challenges and future prospects for the delivery of biologics: oral mucosal, pulmonary, and transdermal routes
, Article AAPS Journal ; Volume 19, Issue 3 , 2017 , Pages 652-668 ; 15507416 (ISSN) ; Fathe, K. R ; Brunaugh, A ; Ferrati, S ; Li, S ; Montenegro Nicolini, M ; Mousavikhamene, Z ; McConville, J. T ; Prausnitz, M. R ; Smyth, H. D. C ; Sharif University of Technology
Springer New York LLC
2017
Abstract
Biologic products are large molecules such as proteins, peptides, nucleic acids, etc., which have already produced many new drugs for clinical use in the last decades. Due to the inherent challenges faced by biologics after oral administration (e.g., acidic stomach pH, digestive enzymes, and limited permeation through the gastrointestinal tract), several alternative routes of administration have been investigated to enable sufficient drug absorption into systemic circulation. This review describes the buccal, sublingual, pulmonary, and transdermal routes of administration for biologics with relevant details of the respective barriers. While all these routes avoid transit through the...
Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues
, Article Journal of Assisted Reproduction and Genetics ; Volume 36, Issue 8 , 2019 , Pages 1743-1752 ; 10580468 (ISSN) ; Shahhoseini, M ; Afsharian, P ; Sharifi Zarchi, A ; Masoudi Nejad, A ; Sharif University of Technology
Springer New York LLC
2019
Abstract
Purpose: Endometriosis is a gynecological disease that causes the uterine lining to appear in other organs outside the uterus. As DNA methylation has an important role in this disorder, its profiling can reveal new information to improve the diagnosis and treatment of endometriosis patients. Methods: We conducted a genome-wide methylation profiling of ectopic and eutopic endometrial tissues from women with and without endometriosis using Infinium Human Methylation 450K BeadChip arrays. DNA methylation samples were collected from nine ectopic and nine eutopic endometrial tissues of endometriosis and six endometrial tissues of healthy controls. Results: Correlation heatmaps and the principal...
Fabrication of biocompatible titanium scaffolds using space holder technique
, Article Journal of Materials Science: Materials in Medicine ; Volume 23, Issue 10 , 2012 , Pages 2483-2488 ; 09574530 (ISSN) ; Sadrnezhaad, S. K ; Shokrgozar, M. A ; Bonakdar, S ; Sharif University of Technology
Springer
2012
Abstract
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...
Synthesis and characterization of rGO/Fe2O3 nanocomposite as an efficient supercapacitor electrode material
, Article Journal of Materials Science: Materials in Electronics ; Volume 31, Issue 17 , 2020 , Pages 14998-15005 ; Nemati, A ; Malek Khachatourian, A ; Golmohammad, M ; Sharif University of Technology
Springer
2020
Abstract
The reduced graphene oxide-Fe2O3 (rGO-Fe2O3) nanocomposites were synthesized by a facile and low-cost hydrothermal method employing rGO and Iron (III) nitrate precursors. The synthesis parameters including the reduction time and presence of reduction aid are studied. The structural and morphological studies of the nanocomposites were investigated by using Raman spectra, Fourier transform infrared spectroscopy, X-ray diffraction, and field emission scanning electron microscopy. The results indicate that Fe2O3 nanoparticles with average particle size of 25 nm are well anchored on graphene sheets and the weight percent of the nanoparticles in the nanocomposites was influenced by the reduction...
Intravenous laser wavelength radiation effect on LCAT, PON1, catalase, and FRAP in diabetic rats
, Article Lasers in Medical Science ; Volume 35, Issue 1 , 2020 , Pages 131-138 ; Mirmiranpour, H ; Sobhani, S. O ; Moazami Goudarzi, N ; Sharif University of Technology
Springer
2020
Abstract
The main purpose of this study is to evaluate the effect of intravenous irradiation of different low-level laser wavelengths on the activity of lecithin-cholesterol acyltransferase (LCAT), paraoxonase (PON1), catalase, and ferric reducing ability of plasma (FRAP) in diabetic rats. First, diabetes was induced in rats using streptozotocin (STZ). Enzymes’ activity was measured in the blood samples and compared before and after intravenous laser blood irradiation. We used four continuous-wave lasers—IR (λ = 808 nm), Red (λ = 638 nm), Green (λ = 532 nm), and Blue (λ = 450 nm)—to compare the wavelength’s effect on different enzymes’ activity. Laser power was fixed at 0.01 mW and laser energy was...
A hepatocellular carcinoma–bone metastasis-on-a-chip model for studying thymoquinone-loaded anticancer nanoparticles
, Article Bio-Design and Manufacturing ; Volume 3, Issue 3 , 2020 , Pages 189-202 ; Yesil Celiktas, O ; Kazan, A ; Maharjan, S ; Saghazadeh, S ; Firoozbakhsh, K ; Firoozabadi, B ; Zhang, Y. S ; Sharif University of Technology
Springer
2020
Abstract
We report the development of a metastasis-on-a-chip platform to model and track hepatocellular carcinoma (HCC)–bone metastasis and to analyze the inhibitory effect of an herb-based compound, thymoquinone (TQ), in hindering the migration of liver cancer cells into the bone compartment. The bioreactor consisted of two chambers, one accommodating encapsulated HepG2 cells and one bone-mimetic niche containing hydroxyapatite (HAp). Above these chambers, a microporous membrane was placed to resemble the vascular barrier, where medium was circulated over the membrane. It was observed that the liver cancer cells proliferated inside the tumor microtissue and disseminated from the HCC chamber to the...
Downregulation of ITM2A gene expression in macrophages of patients with ankylosing spondylitis
, Article International Archives of Allergy and Immunology ; Volume 182, Issue 11 , 2021 , Pages 1113-1121 ; 10182438 (ISSN) ; Pourbadie, H. G ; Jafari, M ; Sharifi Zarchi, A ; Akhtari, M ; Nejatbakhsh Samimi, L ; Jamshidi, A ; Mahmoudi, M ; Sharif University of Technology
S. Karger AG
2021
Abstract
Objectives: Ankylosing spondylitis (AS) is a rheumatic disorder that is mostly determined by genetic and environmental factors. Given the known importance of macrophage in AS pathogenesis, we investigated the transcriptional profile of macrophage cells in the disease. Methods and Results: Two approaches of differential expression and subsequently, weighted gene co-expression network analysis was utilized to analyze a publicly available microarray dataset of macrophages. Integral membrane protein 2A (ITM2A) was among the most significant genes with a decreased trend in the common results of both methods. In order to confirm the finding, the expression of ITM2A was evaluated in...
Association of glomerular and tubular dysfunction with glycaemic control, lipid, lipoprotein, apolipoprotein and antioxidant status in type 2 diabetes mellitus
, Article Singapore Medical Journal ; Volume 48, Issue 9 , 2007 , Pages 840-846 ; 00375675 (ISSN) ; Djalali, M ; Siassi, F ; Farvid, S. S ; Sharif University of Technology
Singapore Medical Association
2007
Abstract
Introduction: This study was conducted to investigate the relationship of glomerular and tubular dysfunctions with glycaemic control, lipid, lipoprotein, apolipoproteins and antioxidant status in 72 patients with type 2 diabetes mellitus. Methods: Urine albumin concentration was measured by immunoturbidimetric and urine N-acetyl-beta-D-glucosaminidase (NAG) and alanine aminopeptidase (AAP) activities with colorimetric methods. Glycated haemoglobin was measured using affinity chromatography. Erythrocyte glu ta thione reductase and glutathione peroxidase activities and serum levels of malondialdehyde, lipids, lipoproteins and apolipoproteins were determined in patients with type 2 diabetes...
A numerical model for predicting hepatocytes ureagenesis and its related inborn enzyme deficiencies: case studies
, Article Scientia Iranica ; Volume 26, Issue 1B , 2019 , Pages 408-420 ; 10263098 (ISSN) ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
Sharif University of Technology
2019
Abstract
One important functionality of liver cells is ammonia detoxification and urea production. In this study, a numerical model of the urea cycle in hepatocytes was developed. Navier Stokes and convection equations were employed to study the process of ammonia elimination and urea production using a microfluidic channel. The concentration of urea and ammonia throughout the channel was obtained. Furthermore, the urea cycle was modelled with respect to its four main enzymes. This resulted in twelve rate equations that were solved to determine the concentration of each metabolite participating in the urea cycle. Application of results implied common disorders such as hyperammonemia types I and II...
A numerical model for predicting hepatocytes ureagenesis and its related inborn enzyme deficiencies: Case studies
, Article Scientia Iranica ; Volume 26, Issue 1B , 2019 , Pages 408-420 ; 10263098 (ISSN) ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
Sharif University of Technology
2019
Abstract
One important functionality of liver cells is ammonia detoxification and urea production. In this study, a numerical model of the urea cycle in hepatocytes was developed. Navier Stokes and convection equations were employed to study the process of ammonia elimination and urea production using a microfluidic channel. The concentration of urea and ammonia throughout the channel was obtained. Furthermore, the urea cycle was modelled with respect to its four main enzymes. This resulted in twelve rate equations that were solved to determine the concentration of each metabolite participating in the urea cycle. Application of results implied common disorders such as hyperammonemia types I and II...
Cell "vision": Complementary factor of protein corona in nanotoxicology
, Article Nanoscale ; Volume 4, Issue 17 , 2012 , Pages 5461-5468 ; 20403364 (ISSN) ; Saeedi-Eslami, S. N ; Shokrgozar, M. A ; Azadmanesh, K ; Hassanlou, M ; Kalhor, H. R ; Burtea, C ; Rothen Rutishauser, B ; Laurent, S ; Sheibani, S ; Vali, H ; Sharif University of Technology
RSC
2012
Abstract
Engineered nanoparticles are increasingly being considered for use as biosensors, imaging agents and drug delivery vehicles. Their versatility in design and applications make them an attractive proposition for new biological and biomedical approaches. Despite the remarkable speed of development in nanoscience, relatively little is known about the interaction of nanoscale objects with living systems. In a biological fluid, proteins associate with nanoparticles, and the amount and the presentation of the proteins on their surface could lead to a different in vivo response than an uncoated particle. Here, in addition to protein adsorption, we are going to introduce concept of cell "vision",...
Protein corona composition of gold nanoparticles/nanorods affects amyloid beta fibrillation process
, Article Nanoscale ; Volume 7, Issue 11 , Feb , 2015 , Pages 5004-5013 ; 20403364 (ISSN) ; Dinarvand, R ; Ghahremani, M. H ; Hormozi-Nezhad, M. R ; Mahmoudi, Z ; Hajipour, M. J ; Atyabi, F ; Ghavami, M ; Mahmoudi, M ; Sharif University of Technology
Royal Society of Chemistry
2015
Abstract
Protein fibrillation process (e.g., from amyloid beta (Aβ) and α-synuclein) is the main cause of several catastrophic neurodegenerative diseases such as Alzheimer's and Parkinson diseases. During the past few decades, nanoparticles (NPs) were recognized as one of the most promising tools for inhibiting the progress of the disease by controlling the fibrillation kinetic process; for instance, gold NPs have a strong capability to inhibit Aβ fibrillations. It is now well understood that a layer of biomolecules would cover the surface of NPs (so called "protein corona") upon the interaction of NPs with protein sources. Due to the fact that the biological species (e.g., cells and amyloidal...
3D ternary Ni: XCo2- xP/C nanoflower/nanourchin arrays grown on HCNs: A highly efficient bi-functional electrocatalyst for boosting hydrogen production via the urea electro-oxidation reaction
, Article Nanoscale ; Volume 12, Issue 30 , 2020 , Pages 16123-16135 ; Shahrokhian, S ; Sharif University of Technology
Royal Society of Chemistry
2020
Abstract
Over the last few years, substantial efforts have been made to develop earth-abundant bi-functional catalysts for urea oxidation and energy-saving electrolytic hydrogen production due to their low cost and the potential to replace traditional noble-metal-based catalysts. Nevertheless, finding a straightforward and effective route to prepare efficient catalysts with unique structural features and optimal supports still is a big challenge. Among the various candidates, metal-organic framework (MOF)-derived materials show great advantages as new kinds of active non-precious catalysts. On the other hand, the controllable integration of MOFs and carbon-based nanomaterials leads to further...
Biomimetic proteoglycan nanoparticles for growth factor immobilization and delivery
, Article Biomaterials Science ; Volume 8, Issue 4 , 2020 , Pages 1127-1136 ; Mostafavi, E ; Shokrgozar, M. A ; Tamjid, E ; Webster, T. J ; Annabi, N ; Simchi, A ; Sharif University of Technology
Royal Society of Chemistry
2020
Abstract
The delivery of growth factors is often challenging due to their short half-life, low stability, and rapid deactivation. In native tissues, the sulfated residual of glycosaminoglycan (GAG) polymer chains of proteoglycans immobilizes growth factors through the proteoglycans'/proteins' complexation with nanoscale organization. These biological assemblies can influence growth factor-cell surface receptor interactions, cell differentiation, cell-cell signaling, and mechanical properties of the tissues. Here, we introduce a facile procedure to prepare novel biomimetic proteoglycan nanocarriers, based on naturally derived polymers, for the immobilization and controlled release of growth factors....