ABSTRACT
Prediction of interaction sites within the membrane protein complexes using the sequence data is of a great importance, because it would find applications in modification of molecules transport through membrane, signaling pathways and drug targets of many diseases. Nevertheless, it has gained little attention from the protein structural bioinformatics community. In this study, a wide variety of prediction and classification tools were applied to distinguish the residues at the interfaces of membrane proteins from those not in the interfaces. The tuned SVM model achieved the high accuracy of 86.95% and the AUC of 0.812 which outperforms the results of the only previous similar study. Nevertheless, prediction performances obtained using most employed models cannot be used in applied fields and needs more effort to improve. Considering the variety of the applied tools in this study, the present investigation could be a good starting point to develop more efficient tools to predict the membrane protein interaction site residues
ABSTRACT
This study investigated the possible synergistic effect of simultaneous treatment of bone morphogenic protein [BMP]-4 as a chemical stimulator and static magnetic field [SMF] as a physical stimulator on viability percent and proliferation rate in rat bone marrow stem cells. Passage 5 cells were trypsinized, and a cell suspension prepared after which the cells were counted and cultured in 25 cm[2] flasks. Cells were incubated for one day and washed with phosphate-buffered saline. We added BMP-4 at the optimum concentration of 25 ng/ml at different times [24, 48 and 96 h] into the medium. The cells were exposed at an optimum intensity of 4 mT of the SMF at different exposure times [24, 48, and 96 h]. Subsequently cells were washed with phosphate-buffered saline, trypsinized, and separate cell suspensions were prepared from each flask. We investigated the viability and proliferation rates of treated cells by staining them with Trypan blue and performed cell counts with an optical microscope. The mean numbers of whole cells and living cells were considered to be the proliferation and survival rates, respectively. Increased SMF exposure and BMP-4 increased the viability percent and change in proliferation rate in the treated groups compared with their corresponding controls. The maximum increased viability was observed in the group that was treated with BMP-4 for 96 h. Our results have supported the hypothesis that SMF alters the viability and proliferation rate of treated BMSCs, which was enhanced when the cells were treated simultaneously with SMF and BMP-4
ABSTRACT
The environmental exposure to Magnetic Fields [MFs] may interact with biological systems. MFs are generated from various sources such as power lines, electric appliances at homes and offices, electrified transportation systems including urban railway systems and diagnostic devices such as Magnetic Resonance Imaging [MRI]. There are some scientific evidences that imply the exposure to MFs are hazardous to our health and increases the rate of some cancers like leukemia. The biological consequences of exposure to MFs have been investigated from a variety of endpoints. However, most studies have been performed in vitro and have examined effects on cellular processes and its malfunction; such studies can be used as evidence of effects in vivo. In this study Bone Marrow Stem Cells were grown in the absence and in the presence of a 15 mT Static Magnetic Field for 5 hours in order to determine any changes in cell cycle progression using the count of cells in different phases. The count of cells in a special phase of cell cycle indicates the length of that phase. The Static Magnetic Field was performed using a locally designed MF generator. A significant increase in the number of cells in G0/G1 was observed in comparison with the controls. Also the number of cells in G0/G1 in the cells treated with Hydrogen-Peroxide, as an oxidative agent, was significantly increased in Static MF. Genetic material damages or mal-function of related proteins may cause these halts. Mfs have not enough energy to affect the biological molecules directly but the mechanism of free radical mediators is probable. These kinds of damages [direct or indirect] can permanently bring the cell cycle to a halt