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21.
Zahra Khoshbin Mohammad Izadyar Mohammad Reza Bozorgmehr Asma Verdian 《Journal of biomolecular structure & dynamics》2020,38(12):3659-3675
AbstractThe aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb2+ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb2+ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb2+. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb2+. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb2+. The density functional theory (DFT) results show that Pb2+ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb2+. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb2+. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma 相似文献
22.
Roshankhah Shiva Abdolmaleki Amir Salahshoor Mohammad Reza 《Molecular biology reports》2020,47(8):6053-6065
Molecular Biology Reports - Mercuric chloride (MC) is a complex substance which is capable to produce free radicals. Middle Eastern Phoenix dactylifera (MEPD) is a flowering plant of palm family... 相似文献
23.
Shahabzadeh Zeinab Darvishzadeh Reza Mohammadi Reza Jafari Morad 《Plant Molecular Biology Reporter》2020,38(2):187-188
Plant Molecular Biology Reporter - The original version of this article unfortunately contained some mistakes in article Title and Table 1. 相似文献
24.
Ahad Ferdowsi Khosroshahi Jafar Soleimani Rad Razie Kheirjou Babak Roshangar Morteza Rashtbar Roya Salehi Mohammad Reza Ranjkesh Leila Roshangar 《Journal of cellular physiology》2020,235(2):1556-1567
The extracellular matrix of different mammalian tissues is commonly used as scaffolds in the field of tissue engineering. One of these tissues, which has frequently been studied due to its structural and biological features, is the small intestine submucosal membrane. These research are mainly done on the porcine small intestine. However, a report has recently been published about a scaffold produced from the submucosal layer of the ovine small intestine. In the present study, ovine small intestine submucosal (OSIS) was decellularized in a modified manner and its histological, morphological, and biomechanical properties were studied. Decellularization was performed in two phases: physical and chemical. In this method, a chloroform-methanol mixture, enzymatic digestion, and a constant dose of sodium dodecyl sulfate (SDS) was used in the least agitation time and its histological property and biocompatibility were evaluated in the presence of adipose tissue-derived stem cells (ADSCs); furthermore, ADSCs were isolated with a simple method (modified physical washing non-enzymatic isolation). The results were showed that the use of OSIS could be effective and operative. Mechanical properties, histological structure and shape, and glycosaminoglycan content were preserved. In the SDS-treated group, more than 90% of the native cells of tissue were deleted, and also in this group, no toxicity was observed and cell proliferation was supported, compared to the untreated group. Therefore, our results indicate that ADSCs seeded on OSIS scaffold could be used as a new approach in regenerative medicine as hybrid or hydrogel application. 相似文献
25.
Mostafa Hasanzadeh Mehrnoosh Mohammadifar Maryam Tavakol Norabadi Samaneh Dashtipoor Navazollah Sahebani Hassan Reza Etebarian 《Archives Of Phytopathology And Plant Protection》2013,46(17):2087-2094
Environmental pollution in addition to direct damage on plant growth, with the destruction of biological control agents, causes indirect damage to plants. The aim of this research was to study the effects of different concentrations (0, 500, 1000, 1500 and 2000 ppm) of heavy metals including Ag, Co, Cu, Fe, Hg, Mn, Pb and Zn on the mycelial growth and to assess the fungicidal or fungistatic effects of these salts on five Nematophagus fungi including Trichoderma harzianum (T8), Trichoderma virens (T21), Trichoderma hamatum (T9), Pochonia chlamydosporia var. chlamydosporia and Arthrobotrys oligospora. The results show that Ag, Co, Cu, Fe and Hg could stop the mycelium growth of all fungi, but Mn, Pb and Zn cannot inhibit the growth of these fungi completely. Among the first group, Hg and Cu stopped the growth of fungi even in 500 ppm. Among these metals that inhibit the growth of fungi, Cu has fungistatic effect and others have fungicide effect. The experiment was conducted in vitro condition, using potato dextrose agar (PDA) under complete randomised design with four replications. The data of mycelium growth were recorded at seven days after inoculation at 25 ± 2°C. 相似文献
26.
Seyyede Sanam Kazemi Shahandashti Reza Maali Amiri Hassan Zeinali Seyyede Sanaz Ramezanpour 《Molecular biology reports》2013,40(2):893-903
Plant cells often increase cold tolerance by reprogramming their genes expression which results in adjusted metabolic alternations, a process enhanced under cold acclimation (CA) phase. In present study, we assessed the changes of membrane fatty acid compositions and defense machine (like antioxidative enzymes) along with damage indexes like electrolyte leakage index (ELI) and malondialdehyde (MDA) during CA, cold stress (CS) and recovery (R) phases in chickpea (Cicer arietinum L.). Results showed an increase in unsaturated fatty acids ratio compare to saturated ones which is a sign of cold tolerance especially after CA phase. Antioxidant enzymes had an important role during CA and R phases while CS affected their activity which can be a sign for associating other metabolites or enzymes activities to create cold tolerance in plants. To investigation of enzymes assay under experimental treatments, the expression pattern of some enzymes including superoxide dismutase (sod), catalase (cat) and lipoxygenase (lox) was studied using quantitative real time PCR. LOX activity has shown a bilateral behavior: a positive relation with membrane damage index in CA and an interesting link with double bond index (DBI) in CS indicating probably its role in secondary metabolites like jasmonic acid signaling pathway. It was suggested that increased DBI and low LOX activity under CS could be a reason for plant cold tolerance. 相似文献
27.
28.
Mohammad Reza Noori-Daloii Nazanin Jalilian Pantea Izadi Maryam Sobhani Zeinab Rabii-Gilani Mir Saeed Yekaninejad 《Molecular biology reports》2013,40(8):4861-4867
Graft versus host disease (GVHD) is a major complication of bone marrow transplantation (BMT). Numerous studies have shown the potential role of cytokine genotypes in the occurrence of GVHD. In this retrospective, case–control study we aimed to investigate the association between 13 cytokine genes and acute GVHD (aGVHD) after HLA-identical sibling BMT in 91 Iranian subjects. Negative association was found between aGVHD and donor IL-10/GCC haplotype or donor IL-4Ra-A allele in the population study. When compared within the leukemia subgroup, we observed positive association between recipient IL-1α ?889/C allele and aGVHD. Also there were negative association between recipient IL-10/CAA haplotype and donor IL-4Ra/A allele and development of aGVHD. Among the different genotypes only donor IL-4Ra and donor IL-12 showed significant association. We conclude that several cytokine polymorphisms are positively and negatively associated with aGVHD in Iranian HLA matched siblings, of which IL-4Ra and IL-12 may play important roles. 相似文献
29.
Armin M. Gamper Reza Rofougaran Simon C. Watkins Joel S. Greenberger Jan H. Beumer Christopher J. Bakkenist 《Nucleic acids research》2013,41(22):10334-10344
The kinase ATR is activated by RPA-coated single-stranded DNA generated at aberrant replicative structures and resected double strand breaks. While many hundred candidate ATR substrates have been identified, the essential role of ATR in the replicative stress response has impeded the study of ATR kinase-dependent signalling. Using recently developed selective drugs, we show that ATR inhibition has a significantly more potent effect than ATM inhibition on ionizing radiation (IR)-mediated cell killing. Transient ATR inhibition for a short interval after IR has long-term consequences that include an accumulation of RPA foci and a total abrogation of Chk1 S345 phosphorylation. We show that ATR kinase activity in G1 phase cells is important for survival after IR and that ATR colocalizes with RPA in the absence of detectable RPA S4/8 phosphorylation. Our data reveal that, unexpectedly, ATR kinase inhibitors may be more potent cellular radiosensitizers than ATM kinase inhibitors, and that this is associated with a novel role for ATR in G1 phase cells. 相似文献
30.
Mohammad Reza Bozorgmehr Jamshidkhan Chamani Ghodsiye Moslehi 《Journal of biomolecular structure & dynamics》2013,31(8):1669-1681
Multi-spectroscopic and density functional theory (DFT) calculations was used to study the interaction between cyclophosphamide (CYP) and aspirin (ASA) with lysozyme (LYS). The experimental results showed that fluorescence quenching of LYS by drug was a result of the formation of drug–LYS complex; static quenching was confirmed to result in fluorescence quenching. Modified Stern–Volmer plots of interaction between CYP and ASA with protein in the binary and ternary systems were used to determine the binding parameters. Molecular distances between the donor (LYS) and acceptor (CYP and ASA) for all systems were estimated according to Forster’s theory. The quantitative analysis obtained by CD spectra suggested that the presence of ASA and CYP decreased the α-helical content of LYS and induced the destabilizing of it. Theoretical studies on the interaction between LYS with ASA and CYP have been carried out using DFT at the B3LYP/6-31G level in the solvent phase. Binding energy of the mentioned complexes was calculated. It showed that tryptophan (Trp) 62 had the most affinity toward ASA and CYP. Analyzing the calculated results revealed that the five member ring of Trp has a key role in interaction of LYS with ASA and CYP. 相似文献