Sharif Digital Repository

The process through which neurons are labeled is a key methodological choice in measuring neuron morphology. However, little is known about how this choice may bias measurements. To quantify this bias we compare the extracted morphology of neurons collected from the same rodent species, experimental condition, gender distribution, age distribution, brain region and putative cell type, but obtained with 19 distinct staining methods. We found strong biases on measured features of morphology. These were largest in features related to the coverage of the dendritic tree (e.g., the total dendritic tree length). Understanding measurement biases is crucial for interpreting morphological data  

The aggregation of an amyloid protein, α-synuclein (α-Syn), has been suggested as a potential cause of Parkinson's and several other neurodegenerative diseases. To explore the possibility of using nanoparticle-based therapeutic agents for the treatment of such diseases, we investigated the influence of surface chemistry and concentration of mesoporous silica nanoparticles (MSNPs) on the fibrillation of recombinant human α-Syn protein in the present work. Bare MSNPs as well as MSNPs of different surface functionalities, including 3-(2-aminoethyl amino) propyltrimethoxysilane (AAS), succinic anhydride (carboxyl), and polyethyleneimine (PEI) were prepared and characterized by electron... 

In this paper, we have proposed, designed, implemented, and characterized a low-cost camera-based microarray scanner which is capable of imaging fluorescently-labeled DNA or Protein microarrays. The proposed system is designed to simultaneously measure two different fluorescent dyes using two parallel channels which increase the overall scan speed. We have shown that the wide dynamic range of system makes it able to detect fluorophore densities from 100-106 molecule/μm2. In each capture, a 5.6 mm × 3.7 mm field is imaged on a 22.3 mm × 14.9 mm (18 megapixels) CMOS sensor. Therefore, the microarray can be scanned with ∼ 1μm2 spatial resolution which is high enough to distinguish borders of... 

Membrane nanotubes, ubiquitous in cellular systems, adopt a spectrum of curvatures and shapes that are dictated by their intrinsic physical characteristics as well as their interactions with the local cellular environment. A high bending flexibility is needed in the crowded cytoplasm where tubes often need to bend significantly in the axial direction at sub-micron length scales. We find the stiffness of spontaneously formed membrane nanotubes by measuring the persistence length of reconstituted membrane nanotubes freely suspended in solution and imaged by fluorescence microscopy. By quantifying the tube diameter we demonstrate for the first time that the persistence length scales linearly... 

Contamination of pistachio nuts with aflatoxin is one of the most significant issues related to pistachio health and expert. A fast pistachio aflatoxin concentration measurement method based on the laser induced fluorescence spectroscopy (LIFS) is proposed. The proposed method from theoretical and experimental points of view is analyzed. In our experiments XeCl Excimer laser is employed as an Ultra Violet (UV) source (λ=308 nm) and a UV-visible (UV-vis) spectrometer is used for fluorescent emission detection. Our setup is employed to measure the concentration of different type of Aflatoxins in pistachio nuts. Measurements results obtained by the LIFS method are compared with those are... 

Producing mature and functional cardiomyocytes (CMs) by in vitro differentiation of induced pluripotent stem cells (iPSCs) using only biochemical cues is challenging. To mimic the biophysical and biomechanical complexity of the native in vivo environment during the differentiation and maturation process, polydimethylsiloxane substrates with 3D topography at the micrometer and sub-micrometer levels are developed and used as cell-culture substrates. The results show that while cylindrical patterns on the substrates resembling mature CMs enhance the maturation of iPSC-derived CMs, sub-micrometer-level topographical features derived by imprinting primary human CMs further accelerate both the... 

Nanoscaled quantum dots (QDs), with unique optical properties have been used for the development of theranostics. Here, InP/ZnS QDs were synthesised and functionalised with folate (QD-FA), D-glucosamine (QD-GA) or both (QD-FA-GA). The bi-functionalised QDs were further conjugated with doxorubicin (QD-FA-GA-DOX). Optimum Indium to fatty acid (In:MA) ratio was 1:3.5. Transmission electron microscopy (TEM) micrographs revealed spherical morphology for the QDs (11 nm). Energy-dispersive spectroscopy (EDS) spectrum confirmed the chemical composition of the QDs. MTT analysis in the OVCAR-3 cells treated with bare QDs, QD-FA, QD-GA, QD-FA-GA and QD-FA-GA-DOX (0.2 mg/mL of QDs) after 24 h indicated... 

Mitochondria is a major regulator of inducing tumor apoptosis and it is as a prime target for chemotherapy. Anticancers need to access specific tumor cells and also pass through different barriers such as outer and inner membranes of mitochondria. Targeted accumulation of paclitaxel (PTX) within the mitochondria was achieved by direct conjugation of PTX with triphenylphosphonium (TPP) as a mitochondrial membrane-permeable cation. PTX-TPP prodrug was synthesized by pH-sensitive ester bond between the hydroxyl function of PTX and the carboxylic function of TPP. This ester bond is only cleaved by the mitochondrial aldehyde dehydrogenase. Prodrug was loaded in the albumin nanoparticles by... 

We report the development of a metastasis-on-a-chip platform to model and track hepatocellular carcinoma (HCC)–bone metastasis and to analyze the inhibitory effect of an herb-based compound, thymoquinone (TQ), in hindering the migration of liver cancer cells into the bone compartment. The bioreactor consisted of two chambers, one accommodating encapsulated HepG2 cells and one bone-mimetic niche containing hydroxyapatite (HAp). Above these chambers, a microporous membrane was placed to resemble the vascular barrier, where medium was circulated over the membrane. It was observed that the liver cancer cells proliferated inside the tumor microtissue and disseminated from the HCC chamber to the... 

In the present study, the feasibility of electrospun polyethersolfone (PES) nanofibrous membrane as the solid substrate for microfluidic based immunoassays to enhance the density of immobilized antibody on the surface of membrane was assessed. Conversely, the efficacy of antibody immobilization was compared by two different strategies as 1-Ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC)/N-Hydroxysuccinimide (NHS) coupling chemistry and hydrophobic interaction. Compared to conventional immunoassays carried out in plates or gels, microfluidic based immunoassays grant a lot of advantages such as a consumption of little samples and reagents, shorter analysis time, and higher efficiency.... 

Engineered nanoparticles are increasingly being considered for use as biosensors, imaging agents and drug delivery vehicles. Their versatility in design and applications make them an attractive proposition for new biological and biomedical approaches. Despite the remarkable speed of development in nanoscience, relatively little is known about the interaction of nanoscale objects with living systems. In a biological fluid, proteins associate with nanoparticles, and the amount and the presentation of the proteins on their surface could lead to a different in vivo response than an uncoated particle. Here, in addition to protein adsorption, we are going to introduce concept of cell "vision",... 

A new method for fluorescent microscopy has been proposed. Proposed method uses indirect excitation of fluorophores with nanometer localized illuminating source. Localized source is created at corners of gold nanotriangles which are deposited on glass substrate. Actually the combination of gold nanotriangle (deposited on glass) acts as active substrate (where species will be placed) for our proposed method. The structure will be scanned with a focused beam of laser (or combination of beams). Due to electric field enhancement in corners and edges of nanotringle (because of surface plasmons), third order nonlinear effect will be enhanced accordingly. Enhancement in third order nonlinearity... 

In this paper we introduce novel strategy for antibody immobilization using high surface area electrospun nanofibrous membrane based on ethyl-3-(3-dimethylaminopropyl)-carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling chemistry. To present the high performance of proposed biosensors, anti-staphylococcus enterotoxin B (anti-SEB) was used as a model to demonstrate the utility of our proposed system. Polymer solution of polyethersolfone was used to fabricate fine nanofibrous membrane. Moreover, industrial polyvinylidene fluoride membrane and conventional microtiter plate were also used to compare the efficiency of antibody immobilization. Scanning electron microscopy images were taken to... 

In the last decades, numerous attempts have been made to prevent microbial pollution spreading, using antibacterial agents. Zeolitic imidazolate framework-8 (ZIF-8) belongs to a subgroup of metal organic frameworks (MOFs) merits of attention due to the zinc ion clusters and its effective antibacterial activity. In this work, Ag-doped magnetic microporous γ-Fe2O3@SiO2@ZIF-8-Ag (FSZ-Ag) was successfully synthesized by a facile methodology in room temperature and used as an antibacterial agent against the growth of the Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus bacteria. Several characterization methods were applied to analyze the properties of the materials, and the... 

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...