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    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)
    Abstract
    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... 

    Numerical Simulation of Glucose Metabolism and Hepatocyte Viability within a Microfluidic

    , M.Sc. Thesis Sharif University of Technology Nejadnasrollah, Farzam (Author) ; Firoozabadi, Bahar (Supervisor)
    Abstract
    The advent of microfluidics as suitable environments for culturing cells is associated with some challenges such as shear stresses applied on the cells. In fact, hepatocytes lose their function as exposed to high shear stresses similar to other cell types. Moreover, among all factors needed for cell viability, feeding hepatocytes with adequate oxygen is of great importance due to their high demand for oxygen compared the other cells. In this thesis, different types of cultures including 2D and 3D has been used in order that shear stresses would be in allowed range and provision of hepatocytes with sufficient oxygen concentrations has been ensured as well. In addition to supplying hepatocytes... 

    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)
    Abstract
    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  

    Modeling the Endothelial Function in the Brachial Artery Using Photoplethysmography

    , M.Sc. Thesis Sharif University of Technology Mashayekhi, Ghoncheh (Author) ; Zahedi, Edmond (Supervisor) ; Jahed, Mehran (Supervisor)
    Abstract
    Flow Mediated Dilation (FMD) is a non-invasive method for endothelial function assessment providing an index extracted from ultrasonic B-mode images. Although utilized in the research community, the difficulty of its application and high cost of ultrasonic device prevent it from being widely used in clinical settings. In this study we show that substituting the ultrasonic device with more easily handled and low cost photoplethysmography and electrocardiography is possible. We introduce new indices based on the photoplethysmogram (PPG) and electrocardiogram (ECG) and show that they are correlated with the ultrasound-based FMD index. To this end, conventional ultrasound FMD test was carried... 

    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)
    Abstract
    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... 

    A Library For Developing Optimization Algorithms In Metabolic Network Analysis

    , M.Sc. Thesis Sharif University of Technology Ghadimi Deylami, Iman (Author) ; Tefagh, Mojtaba (Supervisor)
    Abstract
    In systems biology, one of the most important biological systems that is analyzed and investigated is the metabolic network. A metabolic network is a complete set of metabolic and physical processes that determine the physiological and biochemical characteristics of a cell. These networks encompass metabolic chemical reactions, metabolic pathways, and regulatory interactions that govern these reactions. Therefore, metabolic networks at the genome scale are immensely large, making even efficient algorithms time-consuming for their analysis. To address this issue, reducing metabolic networks is crucial, as it significantly decreases the execution time of algorithms and enhances computational... 

    Context-Specific Reconstruction and Gap-Filling of Metabolic Networks by Sparse Reconciliation of Data Inconsistencies

    , M.Sc. Thesis Sharif University of Technology Fathi, Ali (Author) ; Tefagh, Mojtaba (Supervisor)
    Abstract
    With the increasingly collected biological data, appropriate usage of this data is of great importance for understanding and predicting biological systems and has been the aim of experiments and data collections. A famous category of biological data is known as “omics” which refers to transcriptomics, proteomics, metabolomics, and fluxomics, from different cells or tissues in various media and conditions. This set of data is regularly used for tasks such as studying cells and organisms, understanding cell states, cancer prediction, etc. and is of great importance in Systems Biology.In this thesis, we concentrate on studying cells or organisms using such data, where during that process, we... 

    Simulation of Optimum Nutrition in Bioreactors

    , M.Sc. Thesis Sharif University of Technology Radfar, Marjan (Author) ; Abdekhodaie, Mohammad Jafar (Supervisor) ; Mehrvar, Mehrab (Supervisor)
    Abstract
    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... 

    Investigation of Anticancer Drug Metabolism in Saccharomyces Cerevisiae as a Drug Resistance Model

    , M.Sc. Thesis Sharif University of Technology Hamed Rahimi, Reza (Author) ; Yaghmaei, Soheila (Supervisor) ; Sardari, Soroush (Supervisor)
    Abstract
    Cancer is a life-threatening group of diseases that arises from the uncontrolled growth and division of cells in the body. Treatment options for cancer include surgery, chemotherapy, radiation therapy, immunotherapy, targeted therapy, and hormone therapy. However, resistance to anticancer drugs can develop through a variety of mechanisms, such as the upregulation of drug efflux pumps and alterations in DNA repair mechanisms. One common mechanism of drug resistance is through changes in metabolism, where cancer cells switch to alternative metabolic pathways to survive and evade the effects of anticancer drugs. The development of new drugs targeting specific molecules and pathways involved in... 

    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)
    Abstract
    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... 

    Degradation of phenanthrene and anthracene by Nocardia otitidiscaviarum strain TSH1, a moderately thermophilic bacterium

    , Article Journal of Applied Microbiology ; Volume 105, Issue 2 , 11 July , 2008 , Pages 398-406 ; 13645072 (ISSN) Zeinali, M ; Vossoughi, M ; Ardestani, S. K ; Sharif University of Technology
    2008
    Abstract
    Aims: The metabolism of phenanthrene and anthracene by a moderate thermophilic Nocardia otitidiscaviarum strain TSH1 was examined. Methods and Results: When strain TSH1 was grown in the presence of anthracene, four metabolites were identified as 1,2-dihydroxy-1,2-dihydroanthracene, 3-(2-carboxyvinyl)naphthalene-2-carboxylic acid, 2,3-dihydroxynaphthalene and benzoic acid using gas chromatography-mass spectrometry (GC-MS), reverse phase-high performance liquid chromatography (RP-HPLC) and thin-layer chromatography (TLC). Degradation studies with phenanthrene revealed 2,2′-diphenic acid, phthalic acid, 4-hydroxyphenylacetic acid, o-hydroxyphenylacetic acid, benzoic acid, a phenanthrene... 

    Naphthalene metabolism in Nocardia otitidiscaviarum strain TSH1, a moderately thermophilic microorganism

    , Article Chemosphere ; Volume 72, Issue 6 , 2008 , Pages 905-909 ; 00456535 (ISSN) Zeinali, M ; Vossoughi, M ; Ardestani, S. K ; Sharif University of Technology
    2008
    Abstract
    The thermophilic bacterium Nocardia otitidiscaviarum strain TSH1, originally isolated in our laboratory from a petroindustrial wastewater contaminated soil in Iran, grows at 50 °C on a broad range of hydrocarbons. Transformation of naphthalene by strain TSH1 which is able to use this two ring-polycyclic aromatic hydrocarbon (PAH) as a sole source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that strain TSH1 initiates its attack on naphthalene by dioxygenation at its C-1 and C-2 positions to give... 

    Hydrocarbon degradation by thermophilic Nocardia otitidiscaviarum strain TSH1: Physiological aspects

    , Article Journal of Basic Microbiology ; Volume 47, Issue 6 , December , 2007 , Pages 534-539 ; 0233111X (ISSN) Zeinali, M ; Vossoughi, M ; Ardestani, S. K ; Babanezhad, E ; Masoumian, M ; Sharif University of Technology
    2007
    Abstract
    Indigenous thermophilic hydrocarbon degraders are of special significance for the bioremediation of oil-contaminated desert soils with ambient temperature of 45-50°C. The first objective of this study was to demonstrate the hydrocarbon-degrading capability of Nocardia otitidiscaviarum TSH1 (DSM 45036) which grows optimally at 50°C. Analysis of the metabolic profile of the strain TSH1 showed that it could metabolize phenol, intermediate-chain-length n-alkanes and some polycyclic aromatic hydrocarbons (PAHs) ranging in size from two to four fused rings efficiently, but not toluene and xylene. N. otitidiscaviarum TSH1 was able to survive and grow at phenol concentrations up to 875 mg l-1. For... 

    Hybrid multiscale modeling and prediction of cancer cell behavior

    , Article PLoS ONE ; Volume 12, Issue 8 , 2017 ; 19326203 (ISSN) Zangooei, M. H ; Habibi, J ; Sharif University of Technology
    Public Library of Science  2017
    Abstract
    Background: Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. Methods: In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for... 

    Biomimetic proteoglycan nanoparticles for growth factor immobilization and delivery

    , Article Biomaterials Science ; Volume 8, Issue 4 , 2020 , Pages 1127-1136 Zandi, N ; 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.... 

    Early detection of immunization: A study based on an animal model using 1H nuclear magnetic resonance spectroscopy

    , Article Pakistan Journal of Biological Sciences ; Volume 14, Issue 3 , 2011 , Pages 195-203 ; 10288880 (ISSN) Zamani, Z ; Arjmand, M ; Tafazzoli, M ; Ghohzadeh, A ; Pourfallah, F ; Sadeghi, S ; Mirzazadeh, R ; Mirkham, F ; Tahen, S ; Iravam, A ; Bayat, P ; Vahabi, F ; Sharif University of Technology
    2011
    Abstract
    Vaccines require a period of at least three months for clinical trials, hence a method that can identify elicitation of immune response a few days after the first dose is a necessity. Evolutionary variable selections are modeling approaches for proper manipulation of available data which were used to set up an animal model for classification of time dependent 'HNMR metabolomic profiles and pattern recognition of fluctuations of metabolites in two groups of male rabbits. One group of rabbits was immunized with human red blood cells and the other used as control. Blood was obtained every 48 h from each rabbit for a period of six weeks and the serum monitored for antibodies and metabolites by... 

    The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency

    , Article Cell and Bioscience ; Volume 9, Issue 1 , 2019 ; 20453701 (ISSN) Yousefi, M ; Marashi, S. A ; Sharifi Zarchi, A ; Taleahmad, S ; Sharif University of Technology
    BioMed Central Ltd  2019
    Abstract
    Background: Pluripotency is proposed to exist in two different stages: Naive and Primed. Conventional human pluripotent cells are essentially in the primed stage. In recent years, several protocols have claimed to generate naive human embryonic stem cells (hESCs). To the best of our knowledge, none of these protocols is currently recognized as the gold standard method. Furthermore, the consistency of the resulting cells from these diverse protocols at the molecular level is yet to be shown. Additionally, little is known about the principles that govern the metabolic differences between naive and primed pluripotency. In this work, using a computational approach, we tried to shed light on... 

    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
    2013
    Abstract
    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)  

    A study of Acidithiobacillus Ferrooxidans DSMZ 583 Adaptation to Heavy Metals

    , Article Iranian Journal of Biotechnology ; Volume 9, Issue 2 , 2011 , Pages 133-144 ; 17283043 (ISSN) Yaghmaei, S ; Ghobadi, Z ; Sharif University of Technology
    2011
    Abstract
    In this study the ability of Acidithiobacillus ferrooxi-dans, with regard to the biorecovery of heavy metals in shake flask has been investigated. Adaptation experiments with the single metal ions Ni, Co, V, Mo, W and a mixture of the first four metal ions in the medium was developed through serial sub-culturing. Adaptation showed that A. ferrooxidans could tolerate up to 2.3 g/l Ni, 1.4 g/l Co, 1.4 g/l V, 0.045 g/l Mo and 0.005 g/l W, singly. In the presence of multi-metals considering a mixture of Ni-Co-V-Mo, the bacteria was able to tolerate up to 1.5 g/l Ni, 0.8 g/l Co, 0.8 g/l V and 0.05 g/l Mo in steps of 50-100 mg/l for Ni, Co and V, while for Mo and W with increments in concentration... 

    Structural stability and sustained release of protein from a multilayer nanofiber/nanoparticle composite

    , Article International Journal of Biological Macromolecules ; Volume 75 , April , 2015 , Pages 248-257 ; 01418130 (ISSN) Vakilian, S ; Mashayekhan, S ; Shabani, I ; Khorashadizadeh, M ; Fallah, A ; Soleimani, M ; Sharif University of Technology
    Elsevier  2015
    Abstract
    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...