Search for: molecular-biology
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    Inferring Signaling Pathways from RNAi Data Using Machine Learning

    , M.Sc. Thesis Sharif University of Technology Mazloomian, Alborz (Author) ; Beigy, Hamid (Supervisor)
    One of the standing problems in Molecular Biology and Bioinformatics is uncovering signaling pathways. Discovering the causes of many cancer-like diseases and developing better treatments for them, requires a better understanding of the behavior of cellular processes. Understanding signaling pathways can help to realize cellular processes. Due to the fast increase of possible signaling pathways when the number of components increases, the problem seems to have an inherent complexity. One of the recent methods for generating data relating to such networks is RNA interference technique. In this thesis we use data which are provided by this method. We propose two methods to infer signaling... 

    Toward chemical perfection of graphene-based gene carrier via ugi multicomponent assembly process

    , Article Biomacromolecules ; Volume 17, Issue 9 , 2016 , Pages 2963-2971 ; 15257797 (ISSN) Rezaei, A ; Akhavan, O ; Hashemi, E ; Shamsara, M ; Sharif University of Technology
    American Chemical Society 
    The graphene-based materials with unique, versatile, and tunable properties have brought new opportunities for the leading edge of advanced nanobiotechnology. In this regard, the use of graphene in gene delivery applications is still at early stages. In this study, we successfully designed a new complex of carboxylated-graphene (G-COOH) with ethidium bromide (EtBr) and used it as a nanovector for efficient gene delivery into the AGS cells. G-COOH, with carboxyl functions on its surface, in the presence of EtBr, formaldehyde, and cyclohexylisocyanide were participated in Ugi four component reaction to fabricate a stable amphiphilic graphene-EtBr (AG-EtBr) composite. The coupling reaction was... 

    The performances of the chi-square test and complexity measures for signal recognition in biological sequences

    , Article Journal of Theoretical Biology ; Volume 251, Issue 2 , 2008 , Pages 380-387 ; 00225193 (ISSN) Pirhaji, L ; Kargar, M ; Sheari, A ; Poormohammadi, H ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Sharif University of Technology
    With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the... 

    The effect of nanoparticles on spontaneous imbibition of brine into initially oil-wet sandstones

    , Article Energy Sources, Part A: Recovery, Utilization and Environmental Effects ; Volume 41, Issue 22 , 2019 , Pages 2746-2756 ; 15567036 (ISSN) Sobhani, A ; Ghasemi Dehkordi, M ; Sharif University of Technology
    Taylor and Francis Inc  2019
    In this paper, the effect of silica nanoparticles on oil production due to the spontaneous imbibition of brine into oil-wet sandstones has been studied. The imbibed fluids were NaCl 3 wt. % solutions containing various concentrations of nanoparticles and the recovered oil for each solution was compared. The results revealed that nanoparticles yielded more oil recovery. Nanofluid was used after brine imbibition, and the oil recovery increased from 17.8% to 40% while in the case of using the same nanofluid as the first imbibed fluid the oil recovery was 53%. Also, the results indicated that the oil recovery depends on nanoparticle concentrations. © 2019, © 2019 Taylor & Francis Group, LLC  

    Temperature: the "ignored" factor at the nanobio interface

    , Article ACS Nano ; Volume 7, Issue 8 , 2013 , Pages 6555-6562 ; 19360851 (ISSN) Mahmoudi, M ; Abdelmonem, A. M ; Behzadi, S ; Clement, J. H ; Dutz, S ; Ejtehadi, M. R ; Hartmann, R ; Kantner, K ; Linne, U ; Maffre, P ; Metzler, S ; Moghadam, M. K ; Pfeiffer, C ; Rezaei, M ; Ruiz-Lozano, P ; Serpooshan, V ; Shokrgozar, M. A ; Nienhaus, G. U ; Parak, W. J ; Sharif University of Technology
    Upon incorporation of nanoparticles (NPs) into the body, they are exposed to biological fluids, and their interaction with the dissolved biomolecules leads to the formation of the so-called protein corona on the surface of the NPs. The composition of the corona plays a crucial role in the biological fate of the NPs. While the effects of various physicochemical parameters on the composition of the corona have been explored in depth, the role of temperature upon its formation has received much less attention. In this work, we have probed the effect of temperature on the protein composition on the surface of a set of NPs with various surface chemistries and electric charges. Our results... 

    Substrate oscillations boost recombinant protein release from Escherichia coli

    , Article Bioprocess and Biosystems Engineering ; Volume 37, Issue 5 , May , 2014 , Pages 881-890 ; ISSN: 16157591 Jazini, M ; Herwig, C ; Sharif University of Technology
    Intracellular production of recombinant proteins in prokaryotes necessitates subsequent disruption of cells for protein recovery. Since the cell disruption and subsequent purification steps largely contribute to the total production cost, scalable tools for protein release into the extracellular space is of utmost importance. Although there are several ways for enhancing protein release, changing culture conditions is rather a simple and scalable approach compared to, for example, molecular cell design. This contribution aimed at quantitatively studying process technological means to boost protein release of a periplasmatic recombinant protein (alkaline phosphatase) from E. coli.... 

    Solving MEC model of haplotype reconstruction using information fusion, single greedy and parallel clustering approaches

    , Article 6th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2008, Doha, 31 March 2008 through 4 April 2008 ; 2008 , Pages 15-19 ; 9781424419685 (ISBN) Asgarian, E ; Moeinzadeh, M. H ; Sharifian-R, S ; Najafi-A, A ; Ramezani, A ; Habibi, J ; Mohammadzadeh, J ; Sharif University of Technology
    Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, Due to the mutated form in human genome; SNPs (Single Nucleotide Polymorphism) are responsible for some genetic diseases. As a consequence, obtaining all SNPs from human populations is one of the primary goals of studies in human genomics. In this paper, a data fusion method based on multiple parallel classifiers for reconstruction of haplotypes from a given sample Single Nucleotide Polymorphism (SNP) is proposed. First, we design a single greedy algorithm for solving haplotype reconstructions. [2] is used as an efficient approach to be combined with first classification method. The... 

    Simulation of softening kinetics and microstructural events in aluminum alloy subjected to single and multi-pass rolling operations

    , Article Applied Mathematical Modelling ; Volume 40, Issue 17-18 , 2016 , Pages 7571-7582 ; 0307904X (ISSN) Shabaniverki, S ; Serajzadeh, S ; Sharif University of Technology
    Elsevier Inc 
    In this study, a multi-scale model is proposed to assess softening kinetics and microstructural changes during isothermal annealing within an aluminum alloy. In the first stage, an elastic-plastic finite element analysis is performed for computing the distributions of effective plastic strain and stress while the stored energy after cold rolling is defined based on the predicted data and then utilized for generation of the initial conditions in the microstructural analysis. In the next stage, an algorithm based on cellular automata coupled with a first order rate equation is used to determine the progress of softening behavior at elevated temperatures while both recrystallization and... 

    Protein corona impact on nanoparticle-cell interactions: Toward an energy-based model of endocytosis

    , Article Journal of Physics Condensed Matter ; Volume 32, Issue 11 , 2020 Shadmani, P ; Mehrafrooz, B ; Montazeri, A ; Naghdabadi, R ; Sharif University of Technology
    Institute of Physics Publishing  2020
    Upon incubation of nanoparticles in biological fluids, a new layer called the protein corona is formed on their surface affecting the interactions between nanoparticles and targeted cells during the endocytosis process. In the present study, a mathematical model based on the diffusion of membrane mobile receptors is proposed. Opposing the endocytosis proceeding, membrane bending and tension energies are named as resistant energy. Also, the binding energy and free-energy associated with the configurational entropy are collectively termed promoter energy. Utilizing this model, endocytosis of gold nanoparticle (GNP) is simulated to explore the biological media effect. The results reveal that... 

    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) Mirsadeghi, S ; 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
    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... 

    Producing functional recombinant human keratinocyte growth factor in Pichia pastoris and investigating its protective role against irradiation

    , Article Enzyme and Microbial Technology ; Volume 111 , April , 2018 , Pages 12-20 ; 01410229 (ISSN) Bahadori, Z ; Kalhor, H. R ; Mowla, S. J ; Sharif University of Technology
    Elsevier Inc  2018
    Keratinocyte Growth Factor (KGF) is a paracrine-acting, epithelial mitogen that plays a prominent role in the regeneration of damaged epithelial tissues. In spite of different attempts to produce recombinant human KGF in many organisms, including bacteria, mammalian cells, plant cells and insect cells; production of recombinant form suffers from lower yields and recovery relative to other recombinant proteins of similar size and properties. Due to many advantages of Pichia pastoris expression systems for producing industrial enzymes and pharmaceutical proteins, in this study P. pastoris was chosen as a host for KGF expression. For preparing human KGF coding sequence, MCF-7 cell line was... 

    Produced Water Treatment with Simultaneous Bioenergy Production Using Novel Bioelectrochemical Systems

    , Article Electrochimica Acta ; Volume 180 , 2015 , Pages 535-544 ; 00134686 (ISSN) Ghasemi Naraghi, Z ; Yaghmaei, S ; Mardanpour, M. M ; Hasany, M ; Sharif University of Technology
    Elsevier Ltd  2015
    The present study investigated the biological treatment of produced water in a microbial electrochemical cell (MXC). The main objectives were to develop a novel spiral microbial electrochemical cell (SMXC) and test its performance for produced water treatment under highly saline conditions (salinity > 200000 ppm). The bioelectrochemical performance of the system was also evaluated in terms of power and hydrogen production over time. The comparatively inexpensive material and ease of application increased the feasibility of the SMXC configuration for produced water treatment. Optimal SMXC performance as a microbial fuel cell was achieved at a maximum open circuit potential of 330 mV, maximum... 

    Polymer-Coated NH2-UiO-66 for the codelivery of DOX/pCRISPR

    , Article ACS Applied Materials and Interfaces ; Volume 13, Issue 9 , 2021 , Pages 10796-10811 ; 19448244 (ISSN) Rabiee, N ; Bagherzadeh, M ; Heidarian Haris, M ; Ghadiri, A. M ; Matloubi Moghaddam, F ; Fatahi, Y ; Dinarvand, R ; Jarahiyan, A ; Ahmadi, S ; Shokouhimehr, M ; Sharif University of Technology
    American Chemical Society  2021
    Herein, the NH2-UiO-66 metal organic framework (MOF) has been green synthesized with the assistance of high gravity to provide a suitable and safe platform for drug loading. The NH2-UiO-66 MOF was characterized using a field-emission scanning electron microscope, transmission electron microscope (TEM), X-ray diffraction, and zeta potential analysis. Doxorubicin was then encapsulated physically on the porosity of the green MOF. Two different stimulus polymers, p(HEMA) and p(NIPAM), were used as the coating agents of the MOFs. Doxorubicin was loaded onto the polymer-coated MOFs as well, and a drug payload of more than 51% was obtained, which is a record by itself. In the next step, pCRISPR was... 

    Performance assessment of thermophotovoltaic application in steel industry

    , Article Solar Energy Materials and Solar Cells ; Volume 157 , 2016 , Pages 55-64 ; 09270248 (ISSN) Shoaei, E ; Sharif University of Technology
    Elsevier  2016
    The potential for using Thermophotovoltaic (1TPV) generators as an alternative for recovering energy losses in steel production industry is assessed. A mathematical model for the assessment of the performance of TPV application in the iron and steel industry has been developed. In order to support the mathematical model, a sample TPV apparatus in laboratory scale based on an IR emitter has been designed and assembled. The key modeling parameters of TPV generator include: the open circuit voltage, the short circuit current density and fill factor of the TPV cell. These parameters have been considered in the model as functions of several variables such as: the emitter (hot steel slab)... 

    On the natural aging behavior of Aluminum 6061 alloy after severe plastic deformation

    , Article Materials Science and Engineering A ; Volume 580 , 2013 , Pages 202-208 ; 09215093 (ISSN) Farshidi, M. H ; Kazeminezhad, M ; Miyamoto, H ; Sharif University of Technology
    Natural aging behavior of the aluminum 6061 alloy after a novel Severe Plastic Deformation process called Tube Channel Pressing (TCP) was studied. For this purpose, Vickers microhardness test was used to investigate the changes of mechanical properties while TEM and XRD observations were utilized in order to characterize microstructural evolution during natural aging. Results show that Si-enriched precipitates appear and coarsen rapidly in the first few days of natural aging of TCPed aluminum 6061 alloy which causes consecutive increase and decrease of Vickers microhardness, respectively. Similarly, other alloying elements such as Cu and Fe lead to formation of coarse precipitates during... 

    On spatial filtering of flow variables in high-order finite volume methods

    , Article Computers and Fluids ; Volume 132 , 2016 , Pages 19-31 ; 00457930 (ISSN) Ghadimi, M ; Farshchi, M ; Hejranfar, K ; Sharif University of Technology
    Elsevier Ltd  2016
    A new method of spatial filtering in high-order finite volume methods is presented and assessed. The base of this method is to filter face-averaged variables (fluxes) and then the recovery of cell-averaged ones. Two kinds of filtering method are proposed. The first kind is highly dissipative and appropriate for the numerical regions that need high dissipation, e.g. sponge zones. The second kind, on the other hand, is a precise method and hence is suitable for applying the high-order finite difference filters to the finite volume methods. Applying high-order finite difference filters directly to the high-order finite volume methods without using the proposed method causes stability problems... 

    OmpF, a nucleotide-sensing nanoprobe, computational evaluation of single channel activities

    , Article Physica A: Statistical Mechanics and its Applications ; Volume 457 , 2016 , Pages 215-224 ; 03784371 (ISSN) Haji Abdolvahab, R ; Mobasheri, H ; Nikouee, A ; Ejtehadi, M. R ; Sharif University of Technology
    Elsevier B.V  2016
    The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage... 

    Multifunctional core-shell nanoplatforms (gold@graphene oxide) with mediated NIR thermal therapy to promote miRNA delivery

    , Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 14, Issue 6 , 2018 , Pages 1891-1903 ; 15499634 (ISSN) Assali, A ; Akhavan, O ; Adeli, M ; Razzazan, S ; Dinarvand, R ; Zanganeh, S ; Soleimani, M ; Dinarvand, M ; Atyabi, F ; Sharif University of Technology
    Elsevier Inc  2018
    Recent insights into the nanomedicine have revealed that nanoplatforms enhance the efficacy of carrier in therapeutic applications. Here, multifunctional nanoplatforms were utilized in miRNA-101 delivery and NIR thermal therapy to induce apoptosis in breast cancer cells. Au nanorods (NRs) or nanospheres (NSs) covered with graphene oxide (GO) were prepared and functionalized with polyethylene glycol as a stabilizer and poly-L-arginine (P-L-Arg) as a targeting agent. In nanoplatforms, coupling Au@GO prepared stable structures with higher NIR reactivity. P-L-Arg substantially enhanced the cellular uptake and gene retardation of stuffs coated by them. However, rod-shape nanoplatforms indicated... 

    Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation

    , Article Heliyon ; Volume 6, Issue 12 , December , 2020 Kordzadeh, A ; Ramazani Saadatabadi, A ; Hadi, A ; Sharif University of Technology
    Elsevier Ltd  2020
    A coronavirus identified as COVID-19 is the reason for an infection outbreak which is started in December 2019. NO completely effective drugs and treatments are not recognized for this virus. Recently, saffron and its compounds were used to treat different viral diseases. Saffron extract and its major ingredients have shown antiviral effects. In this study, the steered molecular dynamics simulation was used for investigating the effect of four main components of saffron that include: crocin, crocetin, safranal, and picrocrocin as candidate for drug molecules, on COVID-19. The binding energies between drug molecules and spike protein and the main protease of the virus were evaluated. The... 

    Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering

    , Article Journal of Biotechnology ; Volume 212 , 2015 , Pages 71-89 ; 01681656 (ISSN) Shamloo, A ; Mohammadaliha, N ; Mohseni, M ; Sharif University of Technology
    Elsevier  2015
    This review aims to propose the integrative implementation of microfluidic devices, biomaterials, and computational methods that can lead to a significant progress in tissue engineering and regenerative medicine researches. Simultaneous implementation of multiple techniques can be very helpful in addressing biological processes. Providing controllable biochemical and biomechanical cues within artificial extracellular matrix similar to in vivo conditions is crucial in tissue engineering and regenerative medicine researches. Microfluidic devices provide precise spatial and temporal control over cell microenvironment. Moreover, generation of accurate and controllable spatial and temporal...