Nanobiotechnology
Foozieh Moghadami; Mahdi Kalantari; Fatemeh Hajmoradi
Volume 1, Issue 1 , March 2025, Pages 1-10
Abstract
Background: The membrane-bound sorbitol dehydrogenase is a member of the flavoprotein dehydrogenase–cytochrome complex located in the respiratory chain of the genus of Gluconobacter oxidizes D-sorbitol to L-sorbose, the vitamin C intermediate production, with high specificity. In this research, ...
Read More
Background: The membrane-bound sorbitol dehydrogenase is a member of the flavoprotein dehydrogenase–cytochrome complex located in the respiratory chain of the genus of Gluconobacter oxidizes D-sorbitol to L-sorbose, the vitamin C intermediate production, with high specificity. In this research, the silver nanoparticles effect on L-sorbose production and the sorbitol dehydrogenase activity by Gluconobacter oxydans were investigated through response surface methodology.Methods: The silver nanoparticles effect on L-sorbose production was studied in a 2.5 L laboratory-scale bioreactor. The central composite design was employed for evaluation of the silver nanoparticles effect on sorbitol dehydrogenase activity at different pH and temperatures. The sorbitol dehydrogenase of Gluconobacter oxydans activity was evaluated in the membrane fractions by colorimetric method.Results: The results showed that the addition of 50 mg/L of silver nanoparticles into the culture medium caused a decrease of 2.3 and 1.7 times in L-sorbose production and dry cell weight, respectively. Studying the sorbitol dehydrogenase activity through response surface methodology showed that the highest and lowest activity were observed when 0 and 100 mg/L of silver nanoparticles were added into the culture medium, respectively (35 and 1.5 U/L). The temperature and pH showed a direct effect on the sorbitol dehydrogenase. The effects of the three parameters of temperature, pH, and nanoparticle concentration were linear. The parameters of temperature and silver nanoparticles concentrations showed a positive interaction.Conclusion: It could be concluded that silver nanoparticles decreased the L-sorbose production by Gluconobacter oxydans through inhibiting the membrane-bound sorbitol dehydrogenase activity and cell growth.
Bioinformatics
Saber Samadiafshar; Ali Nikakhtar; Sahel Samadiafshar; Nadia Garmsiri; Farnia Garmsiri; Roghayeh Azizi; Somayaeh - Farahmand
Volume 1, Issue 1 , March 2025, Pages 11-16
Abstract
Background: Kidney renal clear cell carcinoma account for 2-3% of the global cancer burden and has the highest death rate of any genitourinary malignancy. Apoptosis is one of the natural immune cycles that fight against cancers. MicroRNAs are small non-coding RNA molecules that can influence the function ...
Read More
Background: Kidney renal clear cell carcinoma account for 2-3% of the global cancer burden and has the highest death rate of any genitourinary malignancy. Apoptosis is one of the natural immune cycles that fight against cancers. MicroRNAs are small non-coding RNA molecules that can influence the function of proteins.Methods: The functional cycles of four microRNAs (133b, 155, 185, 217) involved in kidney cancer apoptosis were identified. Then, the effects of 7 selected medications which is routinely used by specialist doctors to treat cancer (Cabozantinib, Doxorubicin, Everolimus, Nelarabine, Sorafenib, Sunitinib, and Temsirolimus) on the target proteins were evaluated with dynamic techniques and molecular docking. Docking with powerful servers was evaluated in terms of the possibility of occurrence. Finally, the chemical and medicinal properties (Admet), toxicity, mutagenicity, and site of action of the selected drugs were predicted in silico.Results: The results indicated that drug Sunitinib had the best binding energy with 5 target proteins (VHL= -5, VEGF-A= -7.1, BACH1= -7.4, CUL4B= -5.1, JAK-2= -8 (kcal/mol)) and showed acceptable results in terms of molecular weight (398.5 Dalton), site of action (Mitochondria), and mutagenicity (0.5200 (negative)).Conclusion: The identified evidence demonstrates the positive efficacy and effectiveness of sunitinib in various kidney carcinomas. Targeted therapies are steps towards the targeted increase of apoptosis and the control of cell proliferation and migration, which enable the correct treatment of renal clear cell carcinoma and the prescribing of drugs that cause the least secondary damage to patients.
Bioinformatics
Somayeh Farahmand; Marzieh Dehghan Shasaltaneh; Faezeh Fatemi; Mahnaz Shojapour
Volume 1, Issue 1 , March 2025, Pages 17-31
Abstract
Iron-rusticyanin reductase (Cyc2) is the first protein in the respiratory chain of Acidithiobacillus ferrooxidans (Af), which plays a crucial role in electron transfer. Cytochrome c (cytC) is located in the bacterial outer membrane (OM) and functions as the first electron carrier inside the respiratory ...
Read More
Iron-rusticyanin reductase (Cyc2) is the first protein in the respiratory chain of Acidithiobacillus ferrooxidans (Af), which plays a crucial role in electron transfer. Cytochrome c (cytC) is located in the bacterial outer membrane (OM) and functions as the first electron carrier inside the respiratory ferrous iron oxidation pathway is encoded by the Cyc2 gene. The present computational research examines the effect of a novel Cyc2 mutation (F312Y) to enhance conformational flexibility of the mentioned protein for target recognition. Molecular dynamic simulations (MD) of wild and mutant types of Cyc2 protein were carried out. By analyzing RMSD, RMSF, SASA, Rg, H Bond, DSSP, PCA, ED, DCCM, FEL and EM the conformational variations of mutated protein were studied. The results of the RMSF analysis represent an increase in the flexibility of the ligand after mutant. Eventually, the flexibility of the active site probably improves electron transfer by increasing the amount of Eo at the mutation point. Our results confirm that the mutated protein retains its stability during the simulation. With the conversion of Phenylalanine 312 into Tyrosine, an alpha-amino acid with hydrophobic and nonpolar side chains changes to a polar side group with an extra -OH group. This resulted in more intracellular hydrogen bonds. Furthermore, the mutant variant was more stable than the wild-type. Findings from the present study indicate that an interface between the F312Y mutation and rusticyanin activation could improve the electron transfer rate and yield fruitful insight into site-specific mutagenesis studies.
Evolutionary Biology
Amir Abbas Minaeifar
Volume 1, Issue 1 , March 2025, Pages 33-44
Abstract
Cousinia is the one of largest genera in Asteraceae family, after Astragalus, Cousinia is the largest genus, with over than 270 species and 43 sections in Iran. Morphological studies and micro-morphological studies of the leaf characters were performed in 31 species of the genus Cousinia (sections Albidae, ...
Read More
Cousinia is the one of largest genera in Asteraceae family, after Astragalus, Cousinia is the largest genus, with over than 270 species and 43 sections in Iran. Morphological studies and micro-morphological studies of the leaf characters were performed in 31 species of the genus Cousinia (sections Albidae, Cousinia and Stenocephalae) growing in Iran. In total 17 morphological characters and 11 micro-morphological characters of the leaf epidermises were scored. UPGMA clustering and PCA ordination based on morphological characters almost separated the three sections. However, the same analyses based on micro-morphological characters did not completely agree with morphological results. Combined analyses of micro and morphological characters suggest that C. chlorocephala has closer affinity with the section Stenocephalae. It seems use of both micro-morphological and morphological characters for analysis, show species relationship clear than only morphological result data analysis. According to the results of the relationship of the species using the total characteristics of the grouping of this taxon, it needs to be revised again and molecular studies in this field are needed for more certainty.
Cell Biology
Naeimeh Dehghani; Hamed Daneshpazhouh
Volume 1, Issue 1 , March 2025, Pages 45-54
Abstract
Background: This study aimed to investigate the effect of docetaxel on the expression level of mitochondria- related genes including mitochondrial transcription A (TFAM) and mitochondrial-encoded cytochrome c oxidase subunit 1 (MT-COX 1) in mouse MII oocytes following vitrification by cryotop.Methods: ...
Read More
Background: This study aimed to investigate the effect of docetaxel on the expression level of mitochondria- related genes including mitochondrial transcription A (TFAM) and mitochondrial-encoded cytochrome c oxidase subunit 1 (MT-COX 1) in mouse MII oocytes following vitrification by cryotop.Methods: Oocytes were selected by simple random sampling and distributed amongst five experimental groups (control (n=126), docetaxel (n=132), docetaxel + cryoprotectant agent (CPA) (n=134), docetaxel+ Vitrification (n=132), and vitrification (n=123)). In this experimental study, the survival and fertilization of methaphase II (MII) mouse oocytes were assessed after vitrification by cryotop. In the second experiment, the effects of docetaxel on the expression of TFAM and COX1 genes were determined in vitrified-warmed oocytes by real-time RT-PCR. Each experimental group was compared with the control group.Results: The results showed a significant reduction in the survival rate of each group in comparison with the controls (P<0.05). The survival rate was significantly lower in both vitrification groups (Docetaxel+ vitrification, vitrification) than in non-vitrification groups (fresh control and Docetaxel) (P<0.05). The survival rate of vitrified/warmed oocytes was significantly higher in the Docetaxel+ vitrification group compared with the vitrification group (P=0.005). There were significant differences in the fertilization rate between the docetaxel group with the other groups (P<0.05). There were significant differences between the expression level of Cox1 gene in the control group with docetaxel and vitrification groups (P<0.05). the results showed that the expression level of COX1, TFAM genes was significantly high in CPA, vitrification group (P<0.05) and pretreatment of oocytes with docetaxel can decrease the expression level of cox1, TFAM genes in the vitrified group (vitrification) and non-vitrified group (CPA) (P<0.05).Conclusions: This study indicates that vitrification of mouse MII oocytes can lead to an increase in mitochondrial gene expressions (specifically TFAM and COX1). However, the pretreatment of oocytes with docetaxel is observed to result in a decrease in mitochondrial gene expression.
