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    Development of simple and efficient Lab-on-a-Disc platforms for automated chemical cell lysis

    , Article Scientific Reports ; Volume 10, Issue 1 , 6 July , 2020 Khorrami Jahromi, A ; Saadatmand, M ; Eghbal, M ; Parsa Yeganeh, L ; Sharif University of Technology
    Nature Research  2020
    Abstract
    Cell lysis is the most important first step for molecular biology and diagnostic testing. Recently, microfluidic systems have attracted considerable attention due to advantages associated with automation, integration and miniaturization, especially in resource-limited settings. In this work, novel centrifugal microfluidic platforms with new configurations for chemical cell lysis are presented. The developed systems employ passive form of pneumatic and inertial forces for effective mixing of lysis reagents and cell samples as well as precise fluidic control. Characterizations of the developed Lab-on-a-Discs (LoaDs) have been conducted with dyed deionized (DI) waters and white blood cells... 

    Multi-Target tracking of human spermatozoa in phase-contrast microscopy image sequences using a hybrid dynamic bayesian network

    , Article Scientific Reports ; Volume 8, Issue 1 , 2018 ; 20452322 (ISSN) Arasteh, A ; Vosoughi Vahdat, B ; Salman Yazdi, R ; Sharif University of Technology
    Nature Publishing Group  2018
    Abstract
    Male infertility is mostly related to semen and spermatozoa, and any diagnosis or treatment requires the investigation of the motility patterns of spermatozoa. The movements of spermatozoa are fast and involve collision and occlusion with each other. In order to extract the motility patterns of spermatozoa, multi-target tracking (MTT) of spermatozoa is necessary. One of the most important steps of MTT is data association, in which the newly arrived observations are used to update the previous tracks. Dynamic Bayesian network (DBN) is a powerful tool for modeling and solving various types of problems such as tracking and classification. There can also be a hybrid-DBN (HDBN), in which both... 

    High antimicrobial activity and low human cell cytotoxicity of core-shell magnetic nanoparticles functionalized with an Antimicrobial Peptide

    , Article ACS Applied Materials and Interfaces ; Volume 8, Issue 18 , 2016 , Pages 11366-11378 ; 19448244 (ISSN) Maleki, H ; Rai, A ; Pinto, S ; Evangelista, M ; Cardoso, R. M. S ; Paulo, C ; Carvalheiro, T ; Paiva, A ; Imani, M ; Simchi, A ; Durães, L ; Portugal, A ; Ferreira, L ; Sharif University of Technology
    American Chemical Society  2016
    Abstract
    Superparamagnetic iron oxide nanoparticles (SPIONs) functionalized with antimicrobial agents are promising infection-targeted therapeutic platforms when coupled with external magnetic stimuli. These antimicrobial nanoparticles (NPs) may offer advantages in fighting intracellular pathogens as well as biomaterial-associated infections. This requires the development of NPs with high antimicrobial activity without interfering with the biology of mammalian cells. Here, we report the preparation of biocompatible antimicrobial SPION@gold core-shell NPs based on covalent immobilization of the antimicrobial peptide (AMP) cecropin melittin (CM) (the conjugate is named AMP-NP). The minimal inhibitory... 

    Human Cells Separation Via Imprinted Polymer

    , M.Sc. Thesis Sharif University of Technology Sabaghi, Davood (Author) ; Abdekhodaie, Mohammad Jafar (Supervisor)
    Abstract
    The goal of this research is to elucidate the mechanism of Cell recognition in molecularly imprinted polymers (MIPs) using already utilized techniques. Our approach employs a more flexible non-covalent imprinting method which starts from a readily available polymer and utilizes an aqueous environment for both MIP synthesis and testing. Cell MIPs against MG-63 cell were synthesized. The synthesis procedure was optimized to obtain better binding characteristics to the targeted cell. Adsorption of target cell onto imprinted Alginate Spheres was facilitated by these macromolecular fingerprints as revealed by various microscopical examinations The imprinted Spheres showed high selectivity toward... 

    Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization

    , Article Bioinformatics ; Volume 35, Issue 20 , 2019 , Pages 4081-4088 ; 13674803 (ISSN) Fooladi, H ; Moradi, P ; Sharifi Zarchi, A ; Hosein Khalaj, B ; Berger, B ; Sharif University of Technology
    Oxford University Press  2019
    Abstract
    The molecular mechanisms of self-organization that orchestrate embryonic cells to create astonishing patterns have been among major questions of developmental biology. It is recently shown that embryonic stem cells (ESCs), when cultured in particular micropatterns, can self-organize and mimic the early steps of pre-implantation embryogenesis. A systems-biology model to address this observation from a dynamical systems perspective is essential and can enhance understanding of the phenomenon. Results: Here, we propose a multicellular mathematical model for pattern formation during in vitro gastrulation of human ESCs. This model enhances the basic principles of Waddington epigenetic landscape... 

    Fabrication and characterization of a starch-based nanocomposite scaffold with highly porous and gradient structure for bone tissue engineering

    , Article Biomedical Physics and Engineering Express ; Volume 4, Issue 5 , 2018 ; 20571976 (ISSN) Mirab, F ; Eslamian, M ; Bagheri, R ; Sharif University of Technology
    Institute of Physics Publishing  2018
    Abstract
    Starch based scaffolds are considered as promising biomaterials for bone tissue engineering. In this study, a highly porous starch/polyvinyl alcohol (PVA) based nanocomposite scaffold with a gradient pore structure was made by incorporating different bio-additives, including citric acid, cellulose nanofibers, and hydroxyapatite (HA) nanoparticles. The scaffold was prepared by employing unidirectional and cryogenic freeze-casting and subsequently freeze-drying methods. Fourier transform infrared (FTIR) spectroscopy confirmed the cross-linking of starch and PVA molecules through multiple esterification phenomenon in the presence of citric acid as a cross-linking agent. Field emission scanning... 

    Magnetoelectric nanocomposite scaffold for high yield differentiation of mesenchymal stem cells to neural-like cells

    , Article Journal of Cellular Physiology ; Volume 234, Issue 8 , 2019 , Pages 13617-13628 ; 00219541 (ISSN) Esmaeili, E ; Soleimani, M ; Ghiass, M. A ; Hatamie, S ; Vakilian, S ; Zomorrod, M. S ; Sadeghzadeh, N ; Vossoughi, M ; Hosseinzadeh, S ; Sharif University of Technology
    Wiley-Liss Inc  2019
    Abstract
    While the differentiation factors have been widely used to differentiate mesenchymal stem cells (MSCs) into various cell types, they can cause harm at the same time. Therefore, it is beneficial to propose methods to differentiate MSCs without factors. Herein, magnetoelectric (ME) nanofibers were synthesized as the scaffold for the growth of MSCs and their differentiation into neural cells without factors. This nanocomposite takes the advantage of the synergies of the magnetostrictive filler, CoFe 2 O 4 nanoparticles (CFO), and piezoelectric polymer, polyvinylidene difluoride (PVDF). Graphene oxide nanosheets were decorated with CFO nanoparticles for a proper dispersion in the polymer through... 

    MicroRNA profiling reveals important functions of miR-125b and let-7a during human retinal pigment epithelial cell differentiation

    , Article Experimental Eye Research ; Volume 190 , 2020 Shahriari, F ; Satarian, L ; Moradi, S ; Sharifi Zarchi, A ; Günther, S ; Kamal, A ; Totonchi, M ; Mowla, S. J ; Braun, T ; Baharvand, H ; Sharif University of Technology
    Academic Press  2020
    Abstract
    Retinal pigment epithelial (RPE) cells are indispensable for eye organogenesis and vision. To realize the therapeutic potential of in vitro-generated RPE cells for cell-replacement therapy of RPE-related retinopathies, molecular mechanisms of RPE specification and maturation need to be investigated. So far, many attempts have been made to decipher the regulatory networks involved in the differentiation of human pluripotent stem cells into RPE cells. Here, we exploited a highly-efficient RPE differentiation protocol to determine global expression patterns of microRNAs (miRNAs) during human embryonic stem cell (hESC) differentiation into RPE using small RNA sequencing. Our results revealed a... 

    Metabolomics fingerprinting of the human seminal plasma of asthenozoospermic patients

    , Article Molecular Reproduction and Development ; Vol. 81, Issue. 1 , 2014 , pp. 84-86 ; ISSN: 1098-2795 Gilany, K ; Moazeni-Pourasil, R. S ; Jafarzadeh, N ; Savadi-Shiraz, E ; Sharif University of Technology
    Abstract
    It is estimated that 20% of couples are infertile, and half of these infertility cases are linked to men. One of conditions that can affect male fertility is asthenozoospermia. We applied Raman spectroscopy to the analysis of the metabolome of the human seminal plasma, and used chemometrics on the patterns of Raman spectra obtained. Significant changes were observed in the metabolome of the human seminal plasma of asthenozoospermic patients  

    Cytotoxicity of protein corona-graphene oxide nanoribbons on human epithelial cells

    , Article Applied Surface Science ; Volume 320 , 30 November , 2014 , Pages 596-601 ; ISSN: 01694332 Mbeh, D. A ; Akhavan, O ; Javanbakht, T ; Mahmoudi, M ; Yahia, L ; Sharif University of Technology
    Abstract
    Graphene oxide nanoribbons (GONRs) were synthesized using an oxidative unzipping of multi-walled carbon nanotubes. The interactions of the GONRs with various concentrations of fetal bovine serum or human plasma serum indicated that the GONRs were functionalized substantially by the albumin originated from the two different protein sources. Then, concentration-dependent cytotoxicity of the protein-functionalized GONRs on human epithelial cells was studied. Although the GONRs with concentrations ≤50 μg/mL did not exhibit significant cytotoxicity on the cells (with the cell viability >85%), the concentration of 100 μg/mL exhibited significant cytotoxicity including prevention of cell... 

    Engineering 3D parallelized microfluidic droplet generators with equal flow profiles by computational fluid dynamics and stereolithographic printing

    , Article Lab on a Chip ; Volume 20, Issue 3 , 2020 , Pages 490-495 Kamperman, T ; Teixeira, L. M ; Salehi, S. S ; Kerckhofs, G ; Guyot, Y ; Geven, M ; Geris, L ; Grijpma, D ; Blanquer, S ; Leijten, J ; Sharif University of Technology
    Royal Society of Chemistry  2020
    Abstract
    Microfluidic droplet generators excel in generating monodisperse micrometer-sized droplets and particles. However, the low throughput of conventional droplet generators hinders their clinical and industrial translation. Current approaches to parallelize microdevices are challenged by the two-dimensional nature of the standard fabrication methods. Here, we report the facile production of three-dimensionally (3D) parallelized microfluidic droplet generators consisting of stacked and radially multiplexed channel designs. Computational fluid dynamics simulations form the design basis for a microflow distributor that ensures similar flow rates through all droplet generators. Stereolithography is... 

    Metabolic profiling of seminal plasma from teratozoospermia patients

    , Article Journal of Pharmaceutical and Biomedical Analysis ; Volume 178 , January , 2020 Mehrparvar, B ; Chashmniam, S ; Nobakht, F ; Amini, M ; Javidi, A ; Minai Tehrani, A ; Arjmand, B ; Gilany, K ; Sharif University of Technology
    Elsevier B. V  2020
    Abstract
    Teratozoospermia is one of conditions that can cause male infertility. The mechanism of teratozoospermia remains unclear. The knowledge of the metabolites in human seminal plasma (HSP) is meaningful for the pathological study of teratozoospermia. Analysis of changed metabolites in HSP can help understand the cellular mechanism, find the novel biomarkers and subsequently design a diagnosis test. In this study, the analysis of samples performed by proton nuclear magnetic resonance spectroscopy (1H NMR spectroscopy) to identify the various metabolites, with the aim of finding metabolic profiles and biomarkers related to male infertility. Eighteen de-regulated metabolites were identified in... 

    Whole-genome analysis of de novo somatic point mutations reveals novel mutational biomarkers in pancreatic cancer

    , Article Cancers ; Volume 13, Issue 17 , 2021 ; 20726694 (ISSN) Ghareyazi, A ; Mohseni, A ; Dashti, H ; Beheshti, A ; Dehzangi, A ; Rabiee, H. R ; Alinejad Rokny, H ; Sharif University of Technology
    MDPI  2021
    Abstract
    It is now known that at least 10% of samples with pancreatic cancers (PC) contain a causative mutation in the known susceptibility genes, suggesting the importance of identifying cancer-associated genes that carry the causative mutations in high-risk individuals for early detection of PC. In this study, we develop a statistical pipeline using a new concept, called gene-motif, that utilizes both mutated genes and mutational processes to identify 4211 3-nucleotide PC-associated gene-motifs within 203 significantly mutated genes in PC. Using these gene-motifs as distinguishable features for pancreatic cancer subtyping results in identifying five PC subtypes with distinguishable phenotypes and... 

    Design and fabrication of injectable microcarriers composed of acellular cartilage matrix and chitosan

    , Article Journal of Biomaterials Science, Polymer Edition ; Volume 29, Issue 6 , 2018 , Pages 683-700 ; 09205063 (ISSN) Sivandzade, F ; Mashayekhan, S ; Sharif University of Technology
    Taylor and Francis Inc  2018
    Abstract
    Cartilage is an avascular tissue with limited self-repair ability. Since the methods for treatment of cartilage defects have not been effective, new therapies based on tissue engineering are considered over the recent years. In this study, human cartilage tissue was decellularized and porous injectable microcarriers (MCs) composed of acellular extracellular matrix (ECM) of cartilage tissue and chitosan (CS), with different ECM weight ratios, were fabricated by electrospraying technique to be used in the treatment of articular cartilage defects. Various properties of ECM/CS MCs such as microstructure, mechanical strength, water uptake behaviour, and biodegradability rate were investigated.... 

    Stereolithography 3D bioprinting method for fabrication of human corneal stroma equivalent

    , Article Annals of Biomedical Engineering ; Volume 48, Issue 7 , June , 2020 , Pages 1955-1970 Mahdavi, S. S ; Abdekhodaie, M. J ; Kumar, H ; Mashayekhan, S ; Baradaran Rafii, A ; Kim, K ; Sharif University of Technology
    Springer  2020
    Abstract
    Abstract: 3D bioprinting technology is a promising approach for corneal stromal tissue regeneration. In this study, gelatin methacrylate (GelMA) mixed with corneal stromal cells was used as a bioink. The visible light-based stereolithography (SLA) 3D bioprinting method was utilized to print the anatomically similar dome-shaped structure of the human corneal stroma. Two different concentrations of GelMA macromer (7.5 and 12.5%) were tested for corneal stroma bioprinting. Due to high macromer concentrations, 12.5% GelMA was stiffer than 7.5% GelMA, which made it easier to handle. In terms of water content and optical transmittance of the bioprinted scaffolds, we observed that scaffold with... 

    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) Dezfuli, S. N ; 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... 

    Fabrication of porous scaffolds with decellularized cartilage matrix for tissue engineering application

    , Article Biologicals ; Volume 48 , 2017 , Pages 39-46 ; 10451056 (ISSN) Nasiri, B ; Mashayekhan, S ; Sharif University of Technology
    Academic Press  2017
    Abstract
    Due to the avascular nature of articular cartilage, damaged tissue has little capacity for spontaneous healing. Three-dimensional scaffolds have potential for use in tissue engineering approach for cartilage repair. In this study, bovine cartilage tissue was decellularized and chemically crosslinked hybrid chitosan/extracellular matrix (ECM) scaffolds were fabricated with different ECM weight ratios by simple freeze drying method. Various properties of chitosan/ECM scaffolds such as microstructure, mechanical strength, swelling ratio, and biodegradability rate were investigated to confirm improved structural and biological characteristics of chitosan scaffolds in the presence of ECM. The... 

    Anti-HER2 VHH targeted magnetoliposome for intelligent magnetic resonance imaging of breast cancer cells

    , Article Cellular and Molecular Bioengineering ; Volume 10, Issue 3 , 2017 , Pages 263-272 ; 18655025 (ISSN) Khaleghi, S ; Rahbarizadeh, F ; Ahmadvand, D ; Madaah Hosseini, H. R ; Sharif University of Technology
    Abstract
    The combination of liposomes with magnetic nanoparticles, because of their strong effect on T2 relaxation can open new ways in the innovative cancer therapy and diagnosis. In order to design an intelligent contrast agent in MRI, we chose anti-HER2 nanobody the smallest fully functional antigen-binding fragments evolved from the variable domain, the VHH, of a camel heavy chain-only antibody. These targeted magnetoliposomes bind to the HER2 antigen which is highly expressed on breast and ovarian cancer cells so reducing the side effects as well as increasing image contrast and effectiveness. Cellular iron uptake analysis and in vitro MRI of HER2 positive cells incubated with targeted... 

    Construction of scaffolds composed of acellular cardiac extracellular matrix for myocardial tissue engineering

    , Article Biologicals ; Volume 53 , 2018 , Pages 10-18 ; 10451056 (ISSN) Esmaeili Pourfarhangi, K ; Mashayekhan, S ; Ghanbari Asl, S ; Hajebrahimi, Z ; Sharif University of Technology
    Academic Press  2018
    Abstract
    High rates of mortality and morbidity stemming from cardiovascular diseases unveil extreme limitations in current therapies despite enormous advances in medical and pharmaceutical sciences. Following myocardial infarction (MI), parts of myocardium undergo irreversible remodeling and is substituted by a scar tissue which eventually leads to heart failure (HF). To address this issue, cardiac patches have been utilized to initiate myocardial regeneration. In this study, a porous cardiac patch is fabricated using a mixture of decellularized myocardium extracellular matrix (ECM) and chitosan (CS). Results of rheological measurements, SEM, biodegradation test, and MTT assay showed that the... 

    Atorvastatin treatment softens human red blood cells: an optical tweezers study

    , Article Biomedical Optics Express ; Volume 9, Issue 3 , 2018 ; 21567085 (ISSN) Sheikh Hasani, V ; Babaei, M ; Azadbakht, A ; Pazoki Toroudi, H ; Mashaghi, A ; Moosavi Movahedi, A. A ; Seyed Reihani, .N ; Sharif University of Technology
    OSA - The Optical Society  2018
    Abstract
    Optical tweezers are proven indispensable single-cell micro-manipulation and mechanical phenotyping tools. In this study, we have used optical tweezers for measuring the viscoelastic properties of human red blood cells (RBCs). Comparison of the viscoelastic features of the healthy fresh and atorvastatin treated cells revealed that the drug softens the cells. Using a simple modeling approach, we proposed a molecular model that explains the drug-induced softening of the RBC membrane. Our results suggest that direct interactions between the drug and cytoskeletal components underlie the drug-induced softening of the cells. © 2018 Optical Society of America