Bioinformatics and protein engineering; presenting a few applications employed in our labs

Bioinformatics uses various algorithms and methods to explorer huge amount of biological data in order to help us to understand biological mechanisms. In our labs research groups use bioinformatics tools to investigate and understand why some biological processes are working and what are the most important features contributing to their functions. Of special importance to our researchers are some enzymes and proteins responsible for salinity and drought stresses and thermostability. Different approaches have been employed but they can be classified as follows: a. statistical analyses to understand the significant differences among normal and desired proteins (halophilic or thermostable), b. feature selection algorithms to define the most important features contributing to desired protein activities, c. neural network modelings and tools to train and test different networks in order to correlate between features and protein characteristics and use these networks to predict desired abilities. The results of some research groups have been presented briefly here.Mansour Ebrahimi, Esmaeil Ebrahimie, Ahmad Tahmasebi, Narjes Rahpeyma Sarvestani, Tahereh Deihim

Effect of red and infrared spectrum low level of laser rays on Rat Seminiferous tubules

Background and Objective: Laser is a source of electromagnetic radiation. Laser therapy has a kind of natural and biological effect on tissue which acts via energy and light power. Todays the use of infrared and red rays from low-power lasers have been established as a routine way for the treatment of diseases. Considering the important role of laser in biological sciences this study was done to compare the effect of red and infrared spectrum low level of laser rays on Rat Seminiferous tubules. Materials and Methods: This experimental study was done on 40 male Rat which divided in four groups including one control and three experimental. In the first experimental group, the right testis of the rats was exposed to a mixture of 300 Hz infra-red ray for 7 minutes and 300 Hz red spectrum for 1 minute daily. In the second experimental group, the right testes were exposed to the 300 Hz infra-red ray for 8 minutes for 40 seconds daily. In the third experimental group, the right testes were exposed to 80 Hz infra-red for 5 minutes and 80 Hz red ray for one minute daily. The controls did not receive any rays. After 15 days, testes were dissected, fixed and stained for histological processing. Thickness of seminiferous tubules and lumen as well as the thickness and area of seminiferous epithelium were measured. The concentration of testosterone was determined with radioimmunoassay. Data was analyzed with SPSS-13 software and ANOVA test. Results: There was a significant difference in the thickness of seminiferous tubules, thickness of lumen space and thickness of epithelium between first (i.e., the mixture of 300 Hz red and infra-red lasers), second (300 Hz infra-red laser) and the third experimental groups (80 Hz red and infra-red lasers) (P<0.05). But no difference was found between the first group and control. The serum testosterone concentration did not show any differences between experimental and control. Conclusion: This study showed that morphologic and morphometric alterations have direct relation with laser energy density

How the nucleus and mitochondria communicate in energy production during stress: nuclear MtATP6, an early-stress responsive gene, regulates the mitochondrial F1F0-ATP synthase complex

A small number of stress-responsive genes, such as those of the mitochondrial F1F0-ATP synthase complex, are encoded by both the nucleus and mitochondria. The regulatory mechanism of these joint products is mysterious. The expression of 6-kDa subunit (MtATP6), a relatively uncharacterized nucleus-encoded subunit of F0 part, was measured during salinity stress in salt-tolerant and salt-sensitive cultivated wheat genotypes, as well as in the wild wheat genotypes, Triticum and Aegilops using qRT-PCR. The MtATP6 expression was suddenly induced 3 h after NaCl treatment in all genotypes, indicating an early inducible stress-responsive behavior. Promoter analysis showed that the MtATP6 promoter includes cis-acting elements such as ABRE, MYC, MYB, GTLs, and W-boxes, suggesting a role for this gene in abscisic acid-mediated signaling, energy metabolism, and stress response. It seems that 6-kDa subunit, as an early response gene and nuclear regulatory factor, translocates to mitochondria and completes the F1F0-ATP synthase complex to enhance ATP production and maintain ion homeostasis under stress conditions. These communications between nucleus and mitochondria are required for inducing mitochondrial responses to stress pathways. Dual targeting of 6-kDa subunit may comprise as a mean of inter-organelle communication and save energy for the cell. Interestingly, MtATP6 showed higher and longer expression in the salt-tolerant wheat and the wild genotypes compared to the salt-sensitive genotype. Apparently, salt-sensitive genotypes have lower ATP production efficiency and weaker energy management than wild genotypes; a stress tolerance mechanism that has not been transferred to cultivated genotypes.Ali Asghar Moghadam, Eemaeil Ebrahimie, Seyed Mohsen Taghavi, Ali Niazi, Mahbobeh Zamani Babgohari, Tahereh Deihimi, Mohammad Djavaheri, Amin Ramezan

Quantitative expression analysis of TaSOS1 and TaSOS4 genes in cultivated and wild wheat plants under salt stress

Salt stress is a mixture of ionic, osmotic, and oxidative stresses. The expression of TaSOS1 (a transmembrane Na(+)/H(+) antiporter) and TaSOS4 [a cytoplasmic pyridoxal (PL) kinase] genes were measured in four different salinity levels and different time courses of salinity exposure using qRT-PCR technique. Mahuti (salt tolerant) and Alamut (salt sensitive) cultivars were used as cultivated wheat, and T. boeticum and Aegilops crassa as wild wheat plants. Salt-induced expression of TaSOS1 in these wild wheat plants indicates the presence of active TaSOS1 gene on the genomes A and D. The TaSOS1 and TaSOS4 transcript levels were found to be downregulated after salt treatment in all cultivars except in A. crassa, which was in contrast with its expression pattern in roots that was being upregulated from a very low-basal expression, after salt treatments. Duncan's Multiple Range Test showed a significant difference between expression in the 200-mM NaCl concentration with the 50 and 100 mM for the TaSOS1 gene, and no significant difference for TaSOS4. Lack of significant correlation between the TaSOS1 and TaSOS4 gene expressions confirms the theory that PLP has no significant effect on the expression of the TaSOS1 gene in wheat leaves.Amin Ramezani, Ali Niazi, Ali Asghar Abolimoghadam, Mahboobeh Zamani Babgohari, Tahereh Deihimi, Mahmod Ebrahimi, Hosein Akhtardanesh, Esmail Ebrahimi