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    Evolution of 'ligand-deffusion chreodes' on protein-surface models: A genetic-algorithm study

    , Article Chemistry and Biodiversity ; Volume 4, Issue 12 , 2007 , Pages 2766-2771 ; 16121872 (ISSN) Marashi, A ; Kargar, M ; Katanforoush, A ; Abolhassani, H ; Sadeghi, M ; Sharif University of Technology
    Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed. © 2007 Verlag Helvetica Chimica Acta AG, Zürich  

    PFP-WGAN: Protein function prediction by discovering gene ontology term correlations with generative adversarial networks

    , Article PLoS ONE ; Volume 16, Issue 2 , 2021 ; 19326203 (ISSN) Seyyedsalehi, S. F ; Soleymani, M ; Rabiee, H. R ; Kaazempur Mofrad, M. R ; Sharif University of Technology
    Public Library of Science  2021
    Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as efficient as methods developed and processed for protein sequencing. While more than 70 million protein sequences are available today, only the functionality of around one percent of them are known. These facts have encouraged researchers to develop computational methods to infer protein functionalities from their sequences. Gene Ontology is the most well-known database for protein functions which has a hierarchical structure, where deeper terms are... 

    Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein

    , Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) Asadzadeh, H ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
    Hindawi Limited  2021
    Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

    Metabolic Engineering of Yeast Saccharomyces Cerevisiae for Production of Fatty Acids and Its Derivatives

    , M.Sc. Thesis Sharif University of Technology Homayoonfar, Mohammad (Author) ; Roosta Azad, Reza (Supervisor) ; Sardari, Soroush (Supervisor)
    With the increasing emphasis on production of various chemicals by biotechnology industry, the establishment of optimal cell factories for the maximum production of a specific chemical product will be a serious challenge in large-scale production in this industry. Metabolic engineering is a branch of biochemical engineering that has been developed to achieve this and the approaches in it seek to address this challenge. In this study, focusing on increasing production of fatty acids by yeast cells of Saccharomyces cerevisiae, and using a combination of computational and laboratory methods to present a methodology for the optimal design of culture media. Thus, using the constraint-based... 

    Functional analyses of recombinant mouse hepcidin-1 in cell culture and animal model

    , Article Biotechnology Letters ; Volume 35, Issue 8 , August , 2013 , Pages 1191-1197 ; 01415492 (ISSN) Yazdani, Y ; Keyhanvar, N ; Kalhor, H. R ; Rezaei, A ; Sharif University of Technology
    Hepcidin is a peptide hormone that plays an important role in iron metabolism. We have produced a recombinant mouse hepcidin-1 by using baculovirus expression system. Its expression yield was 25 μg/ml when cell culture media were supplemented with a protease inhibitor cocktail. The recombinant mouse hepcidin-1 and synthetic human hepcidin-25 had similar effects on reducing ferroportin expression in J774A cell line and in peritoneal macrophages. However, synthetic human hepcidin-25 was more efficient than recombinant mouse hepcidin-1 in reducing iron concentration in blood circulation (p < 0.01)  

    Optimization of carbohydrate productivity of Spirulina microalgae as a potential feedstock for bioethanol production

    , Article International Journal of Environmental Science and Technology ; Volume 16, Issue 3 , 2019 , Pages 1303-1318 ; 17351472 (ISSN) Tourang, M ; Baghdadi, M ; Torang, A ; Sarkhosh, S ; Sharif University of Technology
    Center for Environmental and Energy Research and Studies  2019
    The main goal of this research is to use the biomass productivity, carbohydrate content, and carbohydrate productivity as useful responses for optimization of macronutrients concentrations (K2HPO4, NaHCO3, and NaNO3) in cultivation of Spirulina microalgae as a feedstock for bioethanol production. In this study, individual and synergistic effects of medium components on the mentioned responses were investigated. The culture medium was optimized using central composite design for achieving the maximize biomass productivity (165 mg L−1 day−1 at K2HPO4: 438 mg L−1, NaHCO3: 15.92 g L−1, and NaNO3: 0.5 g L−1), carbohydrate content (42.0% of dry mass at K2HPO4: 192 mg L−1, NaHCO3: 5.71 g L−1, and... 

    Gas chromatographic fingerprint analysis of secondary metabolites of Stachys lanata (Stachys byzantine C. Koch) combined with antioxidant activity modelling using multivariate chemometric methods

    , Article Journal of Chromatography A ; Volume 1602 , 2019 , Pages 432-440 ; 00219673 (ISSN) Aminfar, P ; Abtahi, M ; Parastar, H ; Sharif University of Technology
    Elsevier B.V  2019
    S. lanata has been traditionally used as a medicinal plant due to its various biological activities such as antioxidant activity. Therefore, identification and quality control studies of this plant are of great importance. To this end, gas chromatography (GC) combined with chemometrics was proposed for fingerprint analysis of S. lanata samples. This study sought to classify GC fingerprints of twenty-eight S. lanata samples from eight different regions of Iran and more importantly, to correlate fingerprints to the antioxidant activity to select S. lanata volatile antioxidant markers. S. lanata samples were classified into five and three classes using partial least squares-discriminant... 

    3D Bioprinting of oxygenated cell-laden gelatin methacryloyl constructs

    , Article Advanced Healthcare Materials ; Volume 9, Issue 15 , 2020 Erdem, A ; Darabi, M. A ; Nasiri, R ; Sangabathuni, S ; Ertas, Y. N ; Alem, H ; Hosseini, V ; Shamloo, A ; Nasr, A. S ; Ahadian, S ; Dokmeci, M. R ; Khademhosseini, A ; Ashammakhi, N ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Cell survival during the early stages of transplantation and before new blood vessels formation is a major challenge in translational applications of 3D bioprinted tissues. Supplementing oxygen (O2) to transplanted cells via an O2 generating source such as calcium peroxide (CPO) is an attractive approach to ensure cell viability. Calcium peroxide also produces calcium hydroxide that reduces the viscosity of bioinks, which is a limiting factor for bioprinting. Therefore, adapting this solution into 3D bioprinting is of significant importance. In this study, a gelatin methacryloyl (GelMA) bioink that is optimized in terms of pH and viscosity is developed. The improved rheological properties... 

    Hyperbolic and Metabolic Forms and Involutions

    , Ph.D. Dissertation Sharif University of Technology Nokhodkar Hassan Abadi, Amir Hossein (Author) ; Gholamzadeh Mahmoudi, Mohammad (Supervisor) ; Mahdavi-Hezavehi, Mohammad (Supervisor)
    In this thesis, we investigate the involutions of a Clifford algebra induced by involutions of orthogonal group in characteristic two. Several properties of these involutions, such as the relations between their invariants and their decompositions are studied. Also it is shown that a tensor product of quaternion algebras with involution can be expressed as the Clifford algebra of a suitable quadratic form with an involution induced by an involution of orthogonal group. Finally, in connection with the Pfister factor conjecture formulated by D. B. Shapiro, split tensor products of quaternion algebras with involution over a field of characteristic two are investigated  

    Simulation of Optimum Nutrition in Bioreactors

    , M.Sc. Thesis Sharif University of Technology Radfar, Marjan (Author) ; Abdekhodaie, Mohammad Jafar (Supervisor) ; Mehrvar, Mehrab (Supervisor)
    In this study, a semi-structured model for the growth and production of lactase in an aerated bioreactor by Kluyveromyces marxianus, growing on cheese whey, was developed. Three modes of culture, consisting of batch, fed-batch and a controlled-release system were investigated. Modeling was based on three metabolic pathways, representing the growth of Kluyveromyces marxianus. Lactose and oxygen consumption, cell growth, and also lactase and ethanol production rates were determined in the model. Induction was considered as the governing mechanism for enzyme production. The model showed good agreement with the experimental data in batch and fed-batch cultures. Controlled-release system is a... 

    Ontological Study of Metabolic Networks to Develop an Identification Software for Metabolic Networks

    , M.Sc. Thesis Sharif University of Technology Mohammadi Peyhani, Homa (Author) ; Bozorgmehry Boozarjomehry, Ramin (Supervisor)
    Simulation of biological behaviors as the pre requirement for control and optimization, especially for recognition and treating diseases, requires studying involved reactions which may or may not be accessible. In the other side, finding the correct network structures and related mathematical expressions to simulate biological behaviors is a complicated problem due to multi aspect interactions among biological reactions, which imply an approach that integrate the knowledge coming from multiple discipline including biological concepts, mathematical modelling, bioinformatics and advanced programming. In this study we aim to analyze this problem using ontological inference to develop a... 

    Dynamic Simulation and Control of Reactive Systems Involving Metabolic Pathways

    , M.Sc. Thesis Sharif University of Technology Aghaee Foroushani, Mohammad (Author) ; Bozorgmehry Bozarjomehry, Ramin (Supervisor) ; Setoodeh, Payam (Co-Supervisor)
    In this project, modeling, simulation, and control of the Saccharomyces Cerevisiae were studied. In the first section, simulation and control of a structural model of saccharomyces Cerevisiae were performed. Fuzzy Logic Controller (FLC) as a model-independent controller and Global Linearization Controller (GLC) as a model-based controller were designed. Additionally, two types of Kalman filters were designed to predict all states of the structural model: 1-Extended Kalman Filter (EKF), 2- Unscented Kalman Filter (UKF). As a concise explanation, the control action of the GLC is a function of all states of the model, and since that measuring all metabolites is not practical, the EKF and UKF... 

    Relationship between serum level of selenium and metabolites using 1hnmr-based metabonomics in parkinson's disease

    , Article Applied Magnetic Resonance ; Volume 44, Issue 6 , January , 2013 , Pages 721-734 ; 09379347 (ISSN) Fathi, F ; Kyani, A ; Darvizeh, F ; Mehrpour, M ; Tafazzoli, M ; Shahidi, G ; Sharif University of Technology
    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... 

    FBAR Syndapin 1 recognizes and stabilizes highly curved tubular membranes in a concentration dependent manner

    , Article Scientific Reports ; Volume 3 , 2013 ; 20452322 (ISSN) Ramesh, P ; Baroji, Y. F ; S. Reihani, S. Nader ; Stamou, D ; Oddershede, L. B ; Bendix, P. M ; Sharif University of Technology
    Syndapin 1 FBAR, a member of the Bin-amphiphysin-Rvs (BAR) domain protein family, is known to induce membrane curvature and is an essential component in biological processes like endocytosis and formation and growth of neurites. We quantify the curvature sensing of FBAR on reconstituted porcine brain lipid vesicles and show that it senses membrane curvature at low density whereas it induces and reinforces tube stiffness at higher density. FBAR strongly up-concentrates on the high curvature tubes pulled out of Giant Unilamellar lipid Vesicles (GUVs), this sorting behavior is strongly amplified at low protein densities. Interestingly, FBAR from syndapin 1 has a large affinity for tubular... 

    Retina-choroid-sclera permeability for ophthalmic drugs in the vitreous to blood direction: quantitative assessment

    , Article Pharmaceutical research ; Volume 30, Issue 1 , January , 2013 , Pages 41-59 ; 1573904X (ISSN) Haghjou, N ; Abdekhodaie, M. J ; Cheng, Y. L ; Sharif University of Technology
    To determine the outward permeability of retina-choroid-sclera (RCS) layer for different ophthalmic drugs and to develop correlations between drug physicochemical properties and RCS permeability. A finite volume model was developed to simulate pharmacokinetics in the eye following drug administration by intravitreal injection. The RCS permeability was determined for 32 compounds by best fitting the drug concentration-time profile obtained by simulation with previously reported experimental data. Multiple linear regression was then used to develop correlations between best fit RCS permeability and drugs physicochemical properties. The RCS drug permeabilities had values that ranged over 3 ×... 

    Graphene oxide strongly inhibits amyloid beta fibrillation

    , Article Nanoscale ; Volume 4, Issue 23 , 2012 , Pages 7322-7325 ; 20403364 (ISSN) Mahmoudi, M ; Akhavan, O ; Ghavami, M ; Rezaee, F ; Ghiasi, S. M. A ; Sharif University of Technology
    Since amyloid beta fibrillation (AβF) plays an important role in the development of neurodegenerative diseases, we investigated the effect of graphene oxide (GO) and their protein-coated surfaces on the kinetics of Aβ fibrillation in the aqueous solution. We showed that GO and their protein-covered surfaces delay the AβF process via adsorption of amyloid monomers. Also, the large available surface of GO sheets can delay the AβF process by adsorption of amyloid monomers. The inhibitory effect of the GO sheet was increased when we increase the concentration from 10% (in vitro; stimulated media) to 100% (in vivo; stimulated media). Conclusion: our results revealed that GO and their surface... 

    Escherichia coli bacteria reduce graphene oxide to bactericidal graphene in a self-limiting manner

    , Article Carbon ; Volume 50, Issue 5 , 2012 , Pages 1853-1860 ; 00086223 (ISSN) Akhavan, O ; Ghaderi, E ; Sharif University of Technology
    Interactions of chemically exfoliated graphene oxide (GO) nanosheets and Escherichia coli bacteria living in mixed-acid fermentation with an anaerobic condition were investigated for different exposure times. X-ray photoelectron spectroscopy showed that as the exposure time increased (from 0 to 48 h), the oxygen-containing functional groups of the GO decreased by ∼60%, indicating a relative chemical reduction of the sheets by interaction with the bacteria. Raman spectroscopy and current-voltage measurement confirmed the reduction of the GO exposed to the bacteria. The reduction was believed to be due to the metabolic activity of the surviving bacteria through their glycolysis process. It was... 

    Solid state fermentation for production of chitosan by aspergillus niger

    , Article International Journal of Engineering, Transactions B: Applications ; Volume 22, Issue 1 , 2009 , Pages 1-6 ; 1728-144X (ISSN) Maghsoodi, V ; Razavi, J ; Yaghmaei, S ; Sharif University of Technology
    Materials and Energy Research Center  2009
    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... 

    Design and analysis of an original powered foot clearance creator mechanism for walking in patients with spinal cord injury

    , Article Disability and Rehabilitation: Assistive Technology ; Volume 14, Issue 4 , 2019 , Pages 333-337 ; 17483107 (ISSN) Maleki, M ; Badri, S ; Shayestehepour, H ; Arazpour, M ; Farahmand, F ; Mousavi, M. E ; Abdolahi, E ; Farkhondeh, H ; Head, J. S ; Golchin, N ; Mardani, M. A ; Sharif University of Technology
    Taylor and Francis Ltd  2019
    Background: The aim of this study was to assess the performance of an original powered foot clearance creator (PFCC) mechanism worn in conjunction with an isocentric reciprocal gait orthosis (IRGO) and evaluate its effect on trunk compensatory movements and spatiotemporal parameters in nine healthy subjects. Method: A PFCC motorized mechanism was designed that incorporated twin sole plates, the movements of which enabled increased toe to floor clearance during swing phase. A prototype was constructed in combination with an IRGO, and hence was re-named as an IRGO-PFCC orthosis. The effects of IRGO-PFCC usage on the spatiotemporal parameters and trunk compensatory movements during walking were... 

    Dynamics of a magnetically rotated micro swimmer inspired by paramecium metachronal wave

    , Article Progress in Biophysics and Molecular Biology ; Volume 142 , 2019 , Pages 32-42 ; 00796107 (ISSN) Nematollahisarvestani, A ; Shamloo, A ; Sharif University of Technology
    Elsevier Ltd  2019
    In the past few years, a significant body of research has been devoted to designing magnetic micron scale robotic systems for minimally invasive medicine. The motion of different microorganisms is the nature's solution for efficient propulsion of these swimmers. So far, there has been a considerable effort in designing micro swimmers based on the propulsion of bacteria while the motion of numerous other microorganisms has not been a source of inspiration for designing micro swimmers yet. Inspired by propulsion of Paramecium which is a ciliate microorganism, a novel micro swimmer is proposed in this article which is capable of cargo transport. This novel swimmer is composed of multiple...