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saccharomyces-cerevisiae
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Optimization of a fed-batch fermenter producing baker's yeast using simulated annealing method
, Article Iranian Journal of Biotechnology ; Volume 7, Issue 3 , 2009 , Pages 157-165+191 ; 17283043 (ISSN) ; Pishvaie, M. R ; Vossoughi, M ; Seyfkordi, A. A ; Sharif University of Technology
2009
Abstract
Modeling of fermentation processes is so complicated and uncertain; therefore it is necessary to provide a robust and appropriate dynamic optimization method. In order to obtain the maximum amount of yeast (Saccharomyces cerevisiae), the bioreactor must be operated under optimal conditions. To determine substrate feeding in a fed-batch bioreactor, a simulated annealing (SA) approach was examined. The optimal glucose feed rate profiles were computed by a stochastic and deterministic problems for various initial conditions to investigate their effects on optimal operation of the fed-batch bioreactor. Results declared a proper capability of SA method for determination of optimal feeding...
NETAL: A new graph-based method for global alignment of protein-protein interaction networks
, Article Bioinformatics ; Volume 29, Issue 13 , 2013 , Pages 1654-1662 ; 13674803 (ISSN) ; Khadem, A ; Hashemifar, S ; Arab, S. S ; Sharif University of Technology
2013
Abstract
Motivation: The interactions among proteins and the resulting networks of such interactions have a central role in cell biology. Aligning these networks gives us important information, such as conserved complexes and evolutionary relationships. Although there have been several publications on the global alignment of protein networks; however, none of proposed methods are able to produce a highly conserved and meaningful alignment. Moreover, time complexity of current algorithms makes them impossible to use for multiple alignment of several large networks together.Results: We present a novel algorithm for the global alignment of protein-protein interaction networks. It uses a greedy method,...
Optimization of Xylitol Production
, M.Sc. Thesis Sharif University of Technology ; Alemzade, Iran (Supervisor)
Abstract
Xylitol is a sugar alcohol or polyol that has been used as a food additive and sweetening agent due to Its high sweetening power, anti-cariogenic properties and possibilities for use in diabetic food products, makes xylitol an attractive sucrose substitute in a wide variety of foods and beverages. Xylitol is a five carbon polyol or pentitol obtained by the hydrogenation of xylose. xylitol could be produced from xylose in rice seed coats medium by Saccharomyces cerevisiae. For xylitol production, S.cerevisiae was grown in preculture medium at 30°C and agitated at 120 rpm on a rotary platform shaker. The cells were harvested after 20hr, were centrifuged and transferred to the production...
Simulation of Saccharomyces Cerevisiae Batch Culture Behavior Using Dynamic Flux Analysis and Nonlinear Objective Functions
, M.Sc. Thesis Sharif University of Technology ; Farhadi, Fathollah (Supervisor) ; Pishvaei, Mahmoud Reza (Supervisor)
Abstract
There are many limitations to determine relationships within biological systems. Among the limitations of these systems, one can consider the lack of sufficient information about them, such as the complete knowledge of many networks, the lack of reaction information, the complexity of the analysis of these reactions, etc. One of the methods to analyze these systems is called flux balance analysis. This method consists of three parts: objective function, equal constraints and unequal constraints. Among the features available in this method, we can mention less need for experimental information and no need for high processing systems. In order to determine the objective functions in this...
Investigation of Anticancer Drug Metabolism in Saccharomyces Cerevisiae as a Drug Resistance Model
, M.Sc. Thesis Sharif University of Technology ; 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...
Use of Membrane Bioreactor to Bioethanol Production from Lignocellulosic Material
, M.Sc. Thesis Sharif University of Technology ; Soltanieh, Mohammad (Supervisor) ; Goodarznia, Iraj ($item.subfieldsMap.e)
Abstract
In this study production of bioethanol from corn fiber that is a lignocellulosic material is investigated. Experiments were performed in a membrane bioreactor. Bioethanol is a second generation biofuel that is considered recently because of the decrease in oil production and pollutions caused by fossil fuels.The feed was corn fiber which is considered suitable due to its low cost and availability in my country. Corn fiber is composed of cellulose, hemicellulose and lignin. We should increase cellulose fraction by pretreatment methods to get a higher conversion rate into bioethanol. We did this by acid pretreatment and the fraction was reached to 41%. In most of previous work experiments were...
Dynamic Simulation and Control of Reactive Systems Involving Metabolic Pathways
, M.Sc. Thesis Sharif University of Technology ; 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...
Integrated system of multiple batches to evaluate the continuous performance of microbial cells in decolourization processes
, Article Journal of Environmental Chemical Engineering ; Volume 6, Issue 1 , February , 2018 , Pages 728-735 ; 22133437 (ISSN) ; Bagheri Lotfabad, T ; Heidarinasab, A ; Ebadipour, N ; Yaghmaei, S ; Sharif University of Technology
Elsevier Ltd
2018
Abstract
Azo dye degradation in wastewater treatment is a subject which has garnered the attention of many research studies. In this study, an innovative approach, namely, an integrated system of five batches (ISFB), was developed to investigate the capability of Saccharomyces cerevisiae ATCC 9763 for continuous degradation of methyl red as a representative azo dye. Toward this end, an expanded immobilized microbial bed (EIMB) reactor was established with a bed of encapsulated yeast cells in sodium alginate. EIMB reactor was run in two modes, single batch and ISFB. Moreover, durability of the microbial cells was evaluated by repeating the continuous decolourization eight sequential times in EIMB at...
A novel pattern matching algorithm for genomic patterns related to protein motifs
, Article Journal of Bioinformatics and Computational Biology ; Volume 18, Issue 1 , 2020 ; Goliaei, S ; Goliaei, B ; Sharif University of Technology
World Scientific Publishing Co. Pte Ltd
2020
Abstract
Patterns on proteins and genomic sequences are vastly analyzed, extracted and collected in databases. Although protein patterns originate from genomic coding regions, very few works have directly or indirectly dealt with coding region patterns induced from protein patterns. Results: In this paper, we have defined a new genomic pattern structure suitable for representing induced patterns from proteins. The provided pattern structure, which is called "Consecutive Positions Scoring Matrix (CPSSM)", is a replacement for protein patterns and profiles in the genomic context. CPSSMs can be identified, discovered, and searched in genomes. Then, we have presented a novel pattern matching algorithm...
Simple, Cost-effective, and continuous 3D dielectrophoretic microchip for concentration and separation of bioparticles
, Article Industrial and Engineering Chemistry Research ; Volume 59, Issue 9 , 2020 , Pages 3772-3783 ; Saidi, M. S ; Kashaninejad, N ; Nguyen, N. T ; Sharif University of Technology
American Chemical Society
2020
Abstract
Dielectrophoresis is a robust approach for manipulating bioparticles in microfluidic devices. In recent years, many groups have developed dielectrophoresis-based microfluidic systems for separation and concentration of various types of bioparticles, where the gradient of the electric field causes dielectrophoresis force acting on the suspended particles. Enhancing the gradient of the electric field with three-dimensional (3D) electrodes can significantly improve the efficiency of the system. Implementing planar electrodes in a 3D arrangement is a simple option to form a 3D-electrode configuration. This paper reports the development of a novel dielectrophoretic microfluidic system for...
Metabolic Engineering of Yeast Saccharomyces Cerevisiae for Production of Fatty Acids and Its Derivatives
, M.Sc. Thesis Sharif University of Technology ; 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...
Degradation of azo dye methyl red by saccharomyces cerevisiae ATCC 9763
, Article International Biodeterioration and Biodegradation ; Volume 125 , 2017 , Pages 62-72 ; 09648305 (ISSN) ; Bagheri Lotfabad, T ; Heidarinasab, A ; Yaghmaei, S
Abstract
Azo dyes are common dye groups widely used in different industries. Industrial effluents which contain these dyes pervade water resources and have various known and unknown physiological effects on living organisms. In this study, methyl red (MR) was proposed as a model azo dye to examine the capability of Saccharomyces cerevisiae ATCC 9763 for cleavage of the azo bond leading to decolourization. The spectrophotometry method showed that complete decolourization occurred statically during ≃12 h and this time reduced to several minutes less than 10 min where cell mass increased. Thin layer chromatography (TLC), mass spectroscopy and Fourier transform infrared (FTIR) confirmed degradation of...
Bio alcohol production from agricultural residues
, Article 3rd International Symposium on Biotechniques for Air Pollution Control, Delft, 28 September 2009 through 30 September 2009 ; 2010 , Pages 167-174 ; 9780415582704 (ISBN) ; Vossoughi, M ; Sharif University of Technology
Abstract
The bioconversion of abundant and renewable cellulosic biomass into ethanol as an alternative to petroleum is gaining importance due to the realization of diminishing natural oil and gas resources. Agricultural and foresty plant residues are an abundant and renewable source of sugar substrates that could be fermented to ethanol. A thermochemical treatment of biomass in which both cellulose and hemicellulose are hydrolyzed to soluble sugar is necessary before yeast fermentation. After thermochemical treatment, cellulase enzymes must be introduced in the system to hydrolyze any remaining cellulose. The simultaneous saccharification and fermentation (SSF), is a method which converts...