Sharif Digital Repository

The diverse physical properties of membranes play a critical role in many membrane associated biological processes. Proteins responsible for membrane transport can be affected by the lateral membrane order and lateral segregation of proteins is often controlled by the preference of certain membrane anchors for membrane phases having a physically ordered state. The dynamic properties of coexisting membrane phases are often studied by investigating their thermal behavior. Optical trapping of gold nanoparticles is a useful tool to generate local phase transitions in membranes. The high local temperatures surrounding an irradiated gold nanoparticle can be used to melt a part of a giant... 

Cervical cancer is the second-most-common cause of malignancies in women worldwide, and the oncogenic activity of the human papilloma virus types (HPV) E7 protein has a crucial role in anogenital tumors. In this study, we have designed a therapeutic vaccine based on chitosan nanodelivery systems to deliver HPV-16 E7 DNA vaccine, considered as a tumor specific antigen for immunotherapy of HPV-associated cervical cancer. We have developed a Nano-chitosan (NCS) as a carrier system for intramuscular administration using a recombinant DNA vaccine expressing HPV-16 E7 (NCS-DNA E7 vaccine). NCS were characterized in vitro for their gene transfection ability. Results: The transfection of CS-pEGFP... 

In this study, maghemite (γ-Fe2O3) nanoparticles were produced using gelatin protein as an effective mediator. Size, shape, surface morphology and magnetic properties of the prepared γ-Fe2O3 nanoparticles were characterized using XRD, FT-IR, TEM, SEM and VSM data. The effects of furnace temperature and time of heating together with the amount of gelatin on the produced gelatin-Fe3O4 nanocomposite were examined to prove the fundamental effect of gelatin; both as a capping agent in the nanoscale synthesis and as the director of the spinel γ-Fe2O3 synthesis among possible Fe 2O3 crystalline structures  

Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information... 

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... 

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.... 

With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were... 

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... 

Dilational and shear viscoelasticities are important properties of interfacial layers. These quantities are particularly relevant in all systems which contain a huge internal interfacial area such as foams and emulsions. Therefore, also the 3D rheological behavior of foams or emulsions studied by respective methods is superimposed by the 2D interfacial rheology.We report on recent developments in dilational and shear rheology from an experimental point of view as well as discuss the state of the art of the underlying theories. Examples of most relevant experiments are also presented and discussed. Although not yet extensively investigated, the links between bulk rheology of foams and... 

One of the main factors affecting membrane fouling in MBRs is operational conditions. In this study the influence of aeration rate, filtration mode, and SRT on hollow fiber membrane fouling was investigated using a triple fouling layers perspective. The sludge microbial population distribution was also determined by PCR method. Through various applied operational scenarios the optimal conditions were: aeration rate of 15 LPM; relaxation mode with 40s duration and 8 min. interval; and SRT of 30 days. The similarity between SMP variations in triple fouling layers with its corresponding hydraulic resistance confirmed the effect of SMP on membrane fouling. Among three fouling fractions, the... 

Rhamnolipids (RLs) produced by the opportunistic human pathogen Pseudomonas aeruginosa are considered as potential candidates for the next generation of surfactants. Large-scale production of RLs depends on progress in strain engineering, medium design, operating strategies, and purification procedures. In this work, the rhlAB genes extracted from a mono-RLs-producing strain of P. aeruginosa (ATCC 9027) were introduced to an appropriate safety host Pseudomonas putida KT2440. The capability of the recombinant strain was evaluated in various media. As a prerequisite for optimal medium design, a set of 32 experiments was performed in two steps for screening a number of macro-nutritional... 

Arbuscular mycorrhizal (AM) fungi are non-specific symbionts developing mutual and beneficial symbiosis with most terrestrial plants. Because of the obligatory nature of the symbiosis, the presence of the host plant during the onset and proceeding of symbiosis is necessary. However, AM fungal spores are able to germinate in the absence of the host plant. The fungi detect the presence of the host plant through some signal communications. Among the signal molecules, which can affect mycorrhizal symbiosis are plant hormones, which may positively or adversely affect the symbiosis. In this review article, some of the most recent findings regarding the signaling effects of plant hormones, on... 

Pichia pastoris is used extensively as a production platform for many recombinant proteins. The dissolved oxygen (DO) is one of the most important factors influencing protein production. The influence of the DO on productivity has not been studied independent from the feed rate. In this work, various DO levels were investigated independent from the feed rate. The model system was recombinant P. pastoris under the control of methanol-induced alcohol oxidase promoter, which expressed HRP as the target protein. No significant effect was observed in terms of titer and specific productivity, which is a confirmation of the fact that the DO in a one-compartment system cannot boost productivity for... 

Superparamagnetic zinc ferrite spinel-graphene nanostructures were synthesized as potential therapeutic agents in the magnetic targeted photothermal therapy of cancer and/or drug delivery. The global temperature of the solution and the local temperature at the nanoparticle (NP) surface determine the protein corona composition/content, which in turn affects the biological effects of NPs and the corresponding physiological responses. Therefore, it is rational to hypothesize that spinel-graphene nanostructures may have distinct protein corona compositions and contents, and therapeutic and toxic effects under laser irradiation. To assess this hypothesis, the effects of laser irradiation on the... 

Pemphigus vulgaris is an autoimmune disease, in which the role of Th17 cytokines needs to be further explored. This study was performed to assess serum levels of three interleukins (IL) required for Th17 differentiation (IL-β, IL-6 and IL-23) and two specific Th17 cytokines (IL- 17 and IL-22) in a group of patients with pemphigus vulgaris, at baseline, 3 weeks and 6 months after of treatment. Correlations between anti-desmogleins and cytokines with disease severity as well as the influence of therapy on the above factors were assessed. Forty-three first-admitted pemphigus vulgaris patients with the active disease entered the study, but only 31 completed the study. Forty-five healthy... 

Stochastic simulation is carried out to investigate intracellular viral reaction kinetics and the time evolution of the average particle number ( N̄) and coefficient variation (CV) for genome, template, and structural protein. The coefficient variation of these components is found to be ordered as: CV template > CV structural protein > CVgenome. The average particle number is also calculated via a deterministic approach. The magnitude value of the difference between the stochastic and deterministic approaches is found to be N̄ template ̃ N̄ structural protein > N̄ genome. The Poisson algorithm has been used to investigate the number of particles in the dynamics of intracellular viral... 

One of the most important biological components is lipid nanobio membrane. The lipid membranes of alive cells and their mechanical properties play an important role in biophysical investigations. Some proteins affect the shape and properties of the nanobio membrane while interacting with it. In this study a multiscale approach is experienced: first a 100ns all atom (fine-grained) molecular dynamics simulation is done to investigate the binding of CTX A3, a protein from snake venom, to a phosphatidylcholine lipid bilayer, second, a 5 micro seconds coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment of... 

Introduction: Proximal spinal muscular atrophy (SMA) is one of the most significant neurodegenerative diseases amongst the autosomal-recessive genetic disorders which is caused by the absence of protein survival of motor neuron (SMN). A critical nucleotide difference in SMN2 compared to SMN1 gene leads to an inefficient protein. Hence, homozygous lack of SMN1 provides a progressive disease. Due to the high prevalence, up to now, several molecular diagnostic methods have been used which most of them are lengthy, expensive, and laborious. Methods: In the present study, we exploited a gold nanoprobe-based method for semi-quantitative SMN1 gene dosage analysis compared to SMN2. The assay was... 

Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers,... 

Escherichia coli is widely used host for the intracellular expression of many proteins. However, in some cases also secretion of protein from periplasm was observed. Improvement of both intracellular and extracellular production of recombinant protein in E. coli is an attractive goal in order to reduce production cost and increase process efficiency and economics. Since heat shock proteins in E. coli were reported to be helpful for protein refolding and hindering aggregation, in this work different types of single and periodic heat shocks were tested on lab scale to enhance intracellular and extracellular protein production. A single heat shock prior to induction and different oscillatory...