Sharif Digital Repository

Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular... 

In this study the bioleaching of a low-grade uranium ore containing 480 ppm uranium has been reported. The studies involved extraction of uranium using Acidithiobacillus ferrooxidans derived from the uranium mine samples. The maximum specific growth rate (μ max) and doubling time (t d) were obtained 0.08 h-1 and 8.66 h, respectively. Parameters such as Fe2+ concentration, particle size, temperature and pH were optimized. The effect of pulp density (PD) was also studied. Maximum uranium bio-dissolution of 100 ± 5 % was achieved under the conditions of pH 2.0, 5 % PD and 35 °C in 48 h with the particles of d 80 = 100 μm. The optimum concentration of supplementary Fe2+ was dependent to the PD.... 

Natural compounds containing polysaccharide ingredients have been employed as candidates for treatment of skin tissue. Herein, for the first time, electrospinning setup was proposed to fabricate an efficient composite nanofibrous structure of Beta vulgaris (obtained from Beet [Chenopodiaceae or Amaranthaceae]) belonged to polysaccharides and an elastic polymer named nylon 66 for skin tissue engineering. Both prepared scaffolds including noncomposite and composite types were studied by Scanning electron microscope (SEM), Fourier transform infrared (FTIR) spectroscopy, mechanical assay, and contact angle. Scanning electron microscope examinations have approved the uniform and homogeneous... 

Since that pathogenic bacteria are major threats to human health, this paper describes the fabrication of an effective and durable sensing platform based on gold nanoparticles/carbon nanoparticles/cellulose nanofibers nanocomposite (AuNPs/CNPs/CNFs) at the surface of glassy carbon electrode for sensitive and selective detection of Staphylococcus aureus (S. aureus). The AuNPs/CNPs/CNFs nanocomposite with the high surface area, excellent conductivity, and good biocompatibility was used for self-assembled of the thiolated specific S. aureus aptamer as a sensing element. The surface morphology of AuNPs/CNPs/CNFs nanocomposite was characterized with field emission scanning electron microscopy... 

Two-dimensional MXenes are the newly emerging family of nanomaterials with competitive performance for nano-device development. Surface functional groups and abundant binding sites make these materials ideal candidates for sensor applications. Herein, we report the successful fabrication of a MXene-based nano-bio device for capturing, sensing, and filtering the Escherichia coli (E. coli) bacteria. Mannose carbohydrate, which binds strongly to E.coli's fimH protein via glucan multivalent interactions, is used as the bio-receptor element. MXene's structure was engineered to guarantee efficient E. coli capturing without mannose detachment. Electrochemical impedance spectroscopy (EIS) and cyclic... 

In this study, WO 3 nanocrystallites were first produced by laser ablation of W target in deionised water. To synthesize palladium, a PdCl 2 solution (0.2 g/L) was added to the liquid. Transmission electron microscope revealed successful synthesis of tungsten oxide nanocrystallites along with the production of Pd and core-shell Pd/WO3 nanoparticles. Gasochromic behavior was examined by hydrogen bubbling into Pd/WO 3 liquid in which a transition to blue absorbing state was observed. Optical absorption spectra of the colored liquid represented different sharp small polaron absorbing peaks below 3 eV and the peaks intensity was observed to be varied with Pd:WO 3 ratio. Time variations of... 

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... 

In recent years, applications of dielectrophoresis-based platforms have been recognized as effective and dependable approach to separate cells and bioparticles, suspended in different carrier fluids, based on particle size and electrical properties. In this study, a microfluidic device was fabricated by an unprecedented electrode pattern, and several experiments were performed to enrich samples including either of yeast, Escherichia coli, or latex particles. A chemical deposition-based method was employed for fabrication of microelectrodes, inducing nonuniform electric field required for dielectrophoresis-based separation. One major advantage of our employed method is low fabrication cost,... 

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison... 

Background: Numerous studies have described the neuroprotective effect of lithium in spinal cord injury in addition to its ameliorative impact on pain sensation. In the present study, we aim to examine the efficacy of 85 mg/kg as well as 50 mg/kg dosage of the lithium chloride (LiCl) through oral consumption in spinal cord injured rats and their effect on gene expression of three candidate genes, corresponding to the hyper-sensitization. Methods: Adult Wistar (male) rats were divided into four experimental groups: control; oral administration of LiCl with 85 mg/kg and 50 mg/kg dosage; and 10 % sucrose receiver as the vehicle. BBB and heat plantar tests were performed weekly throughout four... 

Paenibacillus polymyxa ATCC 21830 was used for the production of curdlan gum for first time. A Box-Behnken experimental design was applied to optimize six variables of batch fermentation culture each at three levels. Statistical analyses were employed to investigate the direct and interactive effects of variables on curdlan production. Optimum cultural conditions were temperature (50. °C), pH (7), fermentation time (96. h), glucose (100. g/L), yeast extract (3. g/L) and agitation speed (150. rpm). The yield of curdlan production was 6.89. g/L at optimum condition medium. Response surface methodology (RSM) and artificial neural network (ANN) were used to model cultural conditions of curdlan... 

An effect-directed analysis (EDA) of fresh and artificially weathered (evaporated, photooxidized) samples of North Sea crude oil and residual heavy fuel oil is presented. Aliphatic, aromatic, and polar oil fractions were tested for the presence of aryl hydrocarbon receptor (AhR) agonist and androgen receptor (AR) antagonist, demonstrating for the first time the AR antagonist effects in the aromatic and, to a lesser extent, polar fractions. An extension of the typical EDA strategy to include an N-way partial least-squares (N-PLS) model capable of relating the comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) data set to the bioassay data... 

Microbial enhanced oil recovery (MEOR) refers to the process of using bacterial activities for more oil recovery from oil reservoirs mainly by interfacial tension reduction and wettability alteration mechanisms. Investigating the impact of these two mechanisms on enhanced oil recovery during MEOR process is the main objective of this work. Different analytical methods such as oil spreading and surface activity measurements were utilized to screen the biosurfactant-producing bacteria isolated from the brine of a specific oil reservoir located in the southwest of Iran. The isolates identified by 16S rDNA and biochemical analysis as Enterobacter cloacae (Persian Type Culture Collection (PTCC)... 

Carbosilane dendrimers are a particular type of dendrimer structure that has been used as delivery vehicles for drugs and nucleic acids. They have a defined structure according to their generation number, and their terminal groups can be rendered cationic or anionic. The cationic charges can address the limitation of electrostatic repulsion between the negatively charged phosphate groups of nucleic acids and negatively charged cell membranes. Specific drugs can be loaded into the central part of the dendrimer or attached at the exterior, and the overall positive charge may improve the efficacy of anti-inflammatory drugs. One promising feature of dendrimers is their non-toxicity both in vitro... 

Porphyrins are organic compounds that continue to attract much theoretical interest, and have been called the “pigments of life”. They have a wide role in photodynamic and sonodynamic therapy, along with uses in magnetic resonance, fluorescence and photoacoustic imaging. There is a vast range of porphyrins that have been isolated or designed, but few of them have real clinical applications. Due to the hydrophobic properties of porphyrins, and their tendency to aggregate by stacking of the planar molecules they are difficult to work with in aqueous media. Therefore encapsulating them in nanoparticles (NPs) or attachment to various delivery vehicles have been used to improve delivery... 

Introduction: In recent years, the use of cost-effective, multifunctional, environmentally friendly and simple prepared nanomaterials/nanoparticles have been emerged considerably. In this manner, different synthesizing methods were reported and optimized, but there is still lack of a comprehensive method with multifunctional properties. Materials and Methods: In this study, we aim to synthesis the copper oxide nanoparticles using Achillea millefolium leaf extracts for the first time. Catalytic activity was investigated by in situ azide alkyne cycloaddition click and also A3 coupling reaction, and optimized in terms of temperature, solvent, and time of the reaction. Furthermore, the... 

Diatoms are unicellular microalga found in soil and almost every aquatic environment (marine and fresh water). Biogenic silica and diatoms are attractive for biotechnological and industrial applications, especially in the field of biomedicine, industrial/synthetic manufacturing processes, and biomedical/pharmaceutical sciences. Deposition of silica by diatoms allows them to create micro- or nanoscale structures which may be utilized in nanomedicine and especially in drug/gene delivery. Diatoms with their unique architectures, good thermal stability, suitable surface area, simple chemical functionalization/modification procedures, ease of genetic manipulations, optical/photonic... 

Currently, Alzheimer's disease (AD) accounts for more than half of all dementia cases. Although genetics, age, and environmental factors affect the disease, the cause of AD is not yet fully known. Various drugs have been proposed for the prevention and treatment of AD, but the delivery of these therapeutic agents to the brain is difficult. The blood–brain barrier prevents systemic drugs from accessing the central nervous system and designing a suitable system to overcome this barrier has attracted much attention. The intranasal pathway, given its proximity to the brain, provides a great opportunity for drug delivery. Understanding the physiological characteristics of the nose can be useful... 

With significant advancements in research technologies, and an increasing global population, microfluidic and nanofluidic systems (such as point-of-care, lab-on-a-chip, organ-on-a-chip, etc) have started to revolutionize medicine. Devices that combine micron and nanotechnologies have increased sensitivity, precision and versatility for numerous medical applications. However, while there has been extensive research on microfluidic and nanofluidic systems, very few have experienced wide-spread commercialization which is puzzling and deserves our collective attention. For the above reasons, in this article, we review research advances that combine micro and nanotechnologies to create the next... 

Overexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression of ssDNA and the related antigens in the population and brisk activity in gene-editing technologies in the treatment/detection may lead to the presence of pCRISPR in the blood. Therefore, the detection and evaluation of their trace concentrations are of...