International Journal of Environmental Research, 2013
Problematic dyes extensively used in different industries such as textile, paper, food, plasticsa... more Problematic dyes extensively used in different industries such as textile, paper, food, plasticsand cosmetics have undesirable environmental effects. White rot fungi demonstrating effective extracellularenzyme system, which is capable of degrading dyes and various xenobiotics. The aim of this study was tooptimize decolorization of reactive blue 19 (RB19) dye using Phanerochaetechrysosporium. A Box-Behnkendesign and Response Surface Methodology (RSM) were used to study the effect of independentvariables, namely glycerol concentration (15, 20 and 25 g/L), temperature (27, 30 and 40oC) and pH (5.5, 6.0 and 6.5) on color removal efficiency in aqueous solution. From RSM-generated model, the optimum conditions for RB19 decolorization were identified to be at temperature of 20oC, glycerol concentration of 120/L and pH: 6.5. At the optimum conditions, predicted decolorization was 98 percent. The confirmatory experiments were conducted, which confirmed the results by 99.8 percent color remov...
Efforts to express lipase in the periplasmic space of Escherichia coli have so far been unsuccess... more Efforts to express lipase in the periplasmic space of Escherichia coli have so far been unsuccessful and most of the expressed recombinant lipases accumulate in the insoluble cell fraction. To evaluate the role of native and heterologous signal peptides in translocation of the lipase across the inner membrane of E. coli, the lipase gene (btl2) was cloned downstream of the native Bacillus signal peptide and also in fusion with the pelB, ansB and ansB/asp signal peptides. For this purpose, four recombinant expression vectors (pYRK P .P, pYRK P .N, pYRK P. A and pYRK P .AA) were constructed and expressed in E. coli. Osmotic shock analysis showed that recombinant lipase was overexpressed as inclusion bodies in E. coli. The lipase inclusion bodies were subsequently solublized, refolded and purified using single column ion-exchange chromatography. To evaluate localization of lipase in the cell, the purified lipases were subjected to capillary isoelectric focusing and tandem mass spectrometry. Results showed that all signal peptides were able to direct the lipase from the cytoplasm into the periplasmic space of E. coli, because the periplasmic space of E. coli is not suitable for lipase folding, the translocated lipase aggregates in this space as inclusion bodies.
The mature core protein of the Hepatitis C virus (HCVC173) carrying pelB as a signal peptide (Pel... more The mature core protein of the Hepatitis C virus (HCVC173) carrying pelB as a signal peptide (PelB::core) was overexpressed in Escherichia coli as 18% and 23.3% of the host's total protein, in flask and fermentor cultivation, respectively. A final specific yield of 25 ± 1 mg HCVC173/g dry cell weight and an overall productivity of 51±1 mg HCVC173/l/h were obtained in the stirred-tank fermentor. The recombinant PelB::core protein was overexpressed as the inclusion body (IB) form, higher than the expected level when compared to the HCVC173, which was also showed by the analysis of secondary structure of mRNAs and calculation of the Codon Adaptation Index of the gene. The results showed that the combined effects of protein fusion and the signal sequence significantly enhanced the production of recombinant mature HCVC173 in E. coli. Therefore, the fusion form of the mature HCV core protein and the conditions defined in this study provide an alternative strategy for HCVC173 production in high cell density culture of E. coli.
Introduction:Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromati... more Introduction:Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromatic hydrocarbons properties, could be derived from fatty acids of the cells of the animals, plants, algae and bacteria. So, a wide range of approaches have been considered to increase the oil production in biodiesel resources. In this regard, biotechnology approaches can provide new solutions based on application of molecular mechanisms. Materials and methods: A comprehensive survey on molecular mechanisms and key enzymes which are involved in the production and accumulation of the lipids in biodiesel resources have been considered based on literature study and in-silico investigation. In-silico investigation has been performed via InterProScan 5، Motif scan، Conserved Domain، ProtParam، TMHMM، GC content calculator، NetNGlyc، NetPhos، Sulfinator، Protein Blastand MEGA6 programs for characterizing the structure, functions and homology survey of the selected sequences. Results: Our survey l...
All Data which reveal the all functional elements in human coagulation factor VIII gene are prese... more All Data which reveal the all functional elements in human coagulation factor VIII gene are presented.
Background: Silver nanoparticles can consider as an alternative source for some antibiotic usages... more Background: Silver nanoparticles can consider as an alternative source for some antibiotic usages<br> due to those effective antibacterial activity and eco-friendly characteristics.<br> Objective: This in vitro study was done to evaluate the inhibitory effect of extracellular synthesized<br> of silver nanoparticles using inexpensive cellulosic materials and supernatant culture of Isoptericola<br> variabilis sp. IRSH1 against Staphylococcus aureus and Pseudomonas aeruginosa.<br> Methods: Silver nanoparticles were produced by extracellular biosynthesis using supernatant<br> culture of a novel thermotolerant Isoptericola variabilis sp.IRSH1 and characterized. The<br> antibacterial activities of the synthesized silver nanoparticles were examined by the standard KirbyBauer disc diffusion method against Staphylococcus aureus and Pseudomonas aeruginosa on<br> Muller-Hinton agar plates.<br> Findings: The silver nanoparticles were produce...
Endo-1,4-β-glucanase is one of three cellulolytic enzymes in a triplet catalytic system that are ... more Endo-1,4-β-glucanase is one of three cellulolytic enzymes in a triplet catalytic system that are required for extracellular cellulose hydrolysis. Thermostable endo-1,4-β-glucanase is important and is included in a considerable portion of industrial enzymes. Hot springs are extreme niches which are important sources of the bacteria producing thermostable enzymes. Accordingly in this study, sampling was performed from four hot springs in the north and northwest of Iran and the screening and identification of acid-stable and thermostable of endo 1,4 -β-glucanase producing bacteria was investigated. Endo1,4β-glucanase activity of these isolated strains were determined by qualitative Congo-Red staining as well as quantitative Carboxymethyl cellulose/Dinitrosalicylic acid methods as indicators of cellulase production. Three isolates out of twelve initially selected bacteria showed noticeable endo 1,4-β-glucanase activity, including Paenibacillus sp. ASh 4 , Bacillus sp. AGh1 and Bac...
Background: Characterizing the structure and function of superoxide dismutase (SOD), as an antiox... more Background: Characterizing the structure and function of superoxide dismutase (SOD), as an antioxidant enzyme providing opportunities for its application in food supplements. Objectives: In this study, the features of the Manganese-SOD of Lactococcus Lactis (SDLL), subsp. Cremoris MG1363, as probiotic bacteria, were determined on the basis of the computational methods. Materials and Methods: The protein’s physicochemical properties and the prediction of its secondary structure were determined via the ProtParam server and the GOR program respectively. Moreover, the 3D structures of the proteins were constructed via the MODELLER on the basis of the homology method and the threading algorithm MUSTER. On the other hand, the structural stability of the models was assayed under the quasi-physiological conditions by the GROMACS program via the GROMOS96 43a1 force field in Linux system. Finally, using the Molecular Docking Studies, the functionality features of the models were predicted thr...
Abstract Biocompatible, biostable aramid, and nanocomposites are commonly used for implanted devi... more Abstract Biocompatible, biostable aramid, and nanocomposites are commonly used for implanted devices because of their water and gas permeability that protects electronic circuit of the device against the moisture environment as well as the ions that exist in the human body. Aramid composites have attracted significant attention in the applications of soft tissue engineering due to the nature of biodegradability and tunable mechanical features. The nanosized webs and hybrid films of chitosan/m-aramid have been successfully used due to their antimicrobial properties. In this chapter, a state-of-the art review of biocompatible and biostable aramide and composites is presented. Recent progress and developments of composite processing methodologies and chemical modification techniques are also discussed.
Applied microbiology and biotechnology, Jan 3, 2018
The celH gene from Clostridium thermocellum encodes a protein containing 900 residues and three c... more The celH gene from Clostridium thermocellum encodes a protein containing 900 residues and three components, including Cel5E, Lic26a, and carbohydrate-binding domains. Cel5E is a member of the glycoside hydrolase-5 family and is a bifunctional xylanase/cellulase enzyme. We targeted a semi-hydrophobic pocket near the Cel5E active site and theoretically screened mutated variants for enhanced levels of thermal stability. Cel5E mutations were inserted into celH by overlapping polymerase chain reaction, followed by expression of wild-type and mutant enzymes in Escherichia coli BL21 (DE3) and purification by affinity chromatography. Thermal-stabilizing mutations were subjected to molecular dynamics simulation, and measurement of the in vacuo potential energy, van der Waals forces, electrostatic interactions, and net nonbonded potential energies obtained an overall binding affinity of - 64.964 KJ/mol for wild-type Cel5E and - 176.148, - 200.921, and - 120.038 KJ/mol for the N94F, N94W, and ...
Introduction: Evaluation of symbiosis between Arbuscular mycorrhizal fungi (AMF) and Saffron (Cro... more Introduction: Evaluation of symbiosis between Arbuscular mycorrhizal fungi (AMF) and Saffron (Crocus Sativus L.) is important because this strategic plant encounters with many environmental stresses such as climatic and edaphic stresses during seasons and the AMF can let the crops increase their productivity along with the improvement of their resistance to stress factors and pathogens Materials and methods: The spores of AMF around rhizosphere of saffron were studied in three fields of Gonabad, Khorasan province, Iran (2013-14). Moreover, the colonization of mycorrhizal fungi with saffron and sorghum trap were studied in three regions using morphologic and molecular methods by nested PCR and amplification of small subunit of rRNA gene fragments. Results: Three species of arbuscular mycorrhizal fungi, Scutellospora dipurpurescens, Funneliformis caledonius and Rhizophagus aggregatus were identified in the soil around rhizosphere of the saffron of three regions. The colonization of so...
Background: Considering natural thermal stability, Geobacillus stearothermophilus amylase and Cel... more Background: Considering natural thermal stability, Geobacillus stearothermophilus amylase and Cel5E from Clostridium thermocellum are good candidates for industrial applications. To be compatible with the industrial applications, this enzyme should be stable in the high temperatures, so any improvement in their thermal stability is valuable. Objectives: Using in silico approach and identifying point mutations in the structure amylase of G. stearothermophilus and Cel5E from C. termocellum we tried to increase thermal stability of the enzymes along with their catalytic activity to reach a new industrial amylase with higher thermostability and an improved function. Materials and Methods: In this study we predicted the 3D structure of the enzymes, then simulated the molecular docking study using MolDock, PLANTS, and Lamarkian genetic algorithm as scoring functions for the docking and in silico engineering of the protein aiming to increase the thermal stability and catalytic activity. Results: A series of thermal stability increasing point mutations were exerted around the active site of the enzyme, then by docking procedure, the binding affinity was measured and finally a list of mutations which theoretically improved the increased thermal stability as well as catalytic activity were proposed. Conclusions: Based on the in silico results obtained the modified enzymes seems to be suitable candidates for considering in both laboratory and industrial scales.
Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 2015
This study aimed to isolate and evaluate the cellulase activity of cellulolytic bacteria in hot s... more This study aimed to isolate and evaluate the cellulase activity of cellulolytic bacteria in hot springs of Dehloran, Ilam province, Iran. Water and sludge samples were collected from the hot springs and the bacterial enrichment was performed in a medium containing rice barn and carboxymethyl cellulose (CMC). The cultures were incubated at 50 °C in aerobic conditions. The bacteria were isolated on CMC agar (1%) medium. Cellulase assay of the isolates was measured by the evaluation of endoglucanase enzyme activity, which is also called as carboxymethyl cellulase (CMCase). The isolated thermotolerant bacteria were then identified and optimized for the production of CMCase. Moreover, stabilizing elements of the enzyme were identified with in silico approach. The chosen isolate was identified as Isoptericola variabilis sp. IDAH9. The identified strain produced the most thermostable CMCase at a concentration of 5.6 g/L of ammonium sulfate, 9 g/L CMCase or 12 g/L rice bran, 0/6% Tween-80, ...
Introduction: Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromat... more Introduction: Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromatic hydrocarbons properties, could be derived from fatty acids of the cells of the animals, plants, algae and bacteria. So, a wide range of approaches have been considered to increase the oil production in biodiesel resources. In this regard, biotechnology approaches can provide new solutions based on application of molecular mechanisms. Materials and methods: A comprehensive survey on molecular mechanisms and key enzymes which are involved in the production and accumulation of the lipids in biodiesel resources have been considered based on literature study and in-silico investigation. In-silico investigation has been performed via InterProScan 5 ، Motif scan ، Conserved Domain ،ProtParam ، TMHMM ، GC content calculator ، NetNGlyc ، NetPhos ، Sulfinator ، Protein Blastand MEGA6 programs for characterizing the structure, functions and homology survey of the selected sequences. Results: Our survey led to the introduced diacyl glycerol acyl transferase (DGAT), waxester synthase/diacyl glycerol acyltransferase (WS/DGAT), oleosin, MLDP and TadA as the effective enzymes and proteins in lipid production and accumulation in selected biodiesel organisms. An investigation on the structure of the corresponding genes of the selected enzymes, led to reveal their various features in the length, GC content as well as in intronic properties. On the other hand, this characterizing on the selected enzymes and proteins disclosed post-translational modifications in all of them, as well as their localization in the cells. Moreover MBOAT, DAGAT, UPF0089, Oleosin and apolipo protein have been revealed in their context as critical domains. On the other hand, homology survey of the selected enzymes and proteins led to introduce the Verniciafordii, Ricinuscommunis, Dunaliella parva , Thalassiosira pseudonana, Saitoella complicata, Rhodococcus imtechensis and Rhodococcus wratislaviensis species, as new sources of biodiesel with possible capability for lipid production. Discussion and conclusion: Overall, this survey provides a series of motifs and domains in biodiesel process, as well as introducing several organisms with potency in biodiesel production, which could be more examined in an experimental condition.
International Journal of Environmental Research, 2013
Problematic dyes extensively used in different industries such as textile, paper, food, plasticsa... more Problematic dyes extensively used in different industries such as textile, paper, food, plasticsand cosmetics have undesirable environmental effects. White rot fungi demonstrating effective extracellularenzyme system, which is capable of degrading dyes and various xenobiotics. The aim of this study was tooptimize decolorization of reactive blue 19 (RB19) dye using Phanerochaetechrysosporium. A Box-Behnkendesign and Response Surface Methodology (RSM) were used to study the effect of independentvariables, namely glycerol concentration (15, 20 and 25 g/L), temperature (27, 30 and 40oC) and pH (5.5, 6.0 and 6.5) on color removal efficiency in aqueous solution. From RSM-generated model, the optimum conditions for RB19 decolorization were identified to be at temperature of 20oC, glycerol concentration of 120/L and pH: 6.5. At the optimum conditions, predicted decolorization was 98 percent. The confirmatory experiments were conducted, which confirmed the results by 99.8 percent color remov...
Efforts to express lipase in the periplasmic space of Escherichia coli have so far been unsuccess... more Efforts to express lipase in the periplasmic space of Escherichia coli have so far been unsuccessful and most of the expressed recombinant lipases accumulate in the insoluble cell fraction. To evaluate the role of native and heterologous signal peptides in translocation of the lipase across the inner membrane of E. coli, the lipase gene (btl2) was cloned downstream of the native Bacillus signal peptide and also in fusion with the pelB, ansB and ansB/asp signal peptides. For this purpose, four recombinant expression vectors (pYRK P .P, pYRK P .N, pYRK P. A and pYRK P .AA) were constructed and expressed in E. coli. Osmotic shock analysis showed that recombinant lipase was overexpressed as inclusion bodies in E. coli. The lipase inclusion bodies were subsequently solublized, refolded and purified using single column ion-exchange chromatography. To evaluate localization of lipase in the cell, the purified lipases were subjected to capillary isoelectric focusing and tandem mass spectrometry. Results showed that all signal peptides were able to direct the lipase from the cytoplasm into the periplasmic space of E. coli, because the periplasmic space of E. coli is not suitable for lipase folding, the translocated lipase aggregates in this space as inclusion bodies.
The mature core protein of the Hepatitis C virus (HCVC173) carrying pelB as a signal peptide (Pel... more The mature core protein of the Hepatitis C virus (HCVC173) carrying pelB as a signal peptide (PelB::core) was overexpressed in Escherichia coli as 18% and 23.3% of the host's total protein, in flask and fermentor cultivation, respectively. A final specific yield of 25 ± 1 mg HCVC173/g dry cell weight and an overall productivity of 51±1 mg HCVC173/l/h were obtained in the stirred-tank fermentor. The recombinant PelB::core protein was overexpressed as the inclusion body (IB) form, higher than the expected level when compared to the HCVC173, which was also showed by the analysis of secondary structure of mRNAs and calculation of the Codon Adaptation Index of the gene. The results showed that the combined effects of protein fusion and the signal sequence significantly enhanced the production of recombinant mature HCVC173 in E. coli. Therefore, the fusion form of the mature HCV core protein and the conditions defined in this study provide an alternative strategy for HCVC173 production in high cell density culture of E. coli.
Introduction:Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromati... more Introduction:Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromatic hydrocarbons properties, could be derived from fatty acids of the cells of the animals, plants, algae and bacteria. So, a wide range of approaches have been considered to increase the oil production in biodiesel resources. In this regard, biotechnology approaches can provide new solutions based on application of molecular mechanisms. Materials and methods: A comprehensive survey on molecular mechanisms and key enzymes which are involved in the production and accumulation of the lipids in biodiesel resources have been considered based on literature study and in-silico investigation. In-silico investigation has been performed via InterProScan 5، Motif scan، Conserved Domain، ProtParam، TMHMM، GC content calculator، NetNGlyc، NetPhos، Sulfinator، Protein Blastand MEGA6 programs for characterizing the structure, functions and homology survey of the selected sequences. Results: Our survey l...
All Data which reveal the all functional elements in human coagulation factor VIII gene are prese... more All Data which reveal the all functional elements in human coagulation factor VIII gene are presented.
Background: Silver nanoparticles can consider as an alternative source for some antibiotic usages... more Background: Silver nanoparticles can consider as an alternative source for some antibiotic usages<br> due to those effective antibacterial activity and eco-friendly characteristics.<br> Objective: This in vitro study was done to evaluate the inhibitory effect of extracellular synthesized<br> of silver nanoparticles using inexpensive cellulosic materials and supernatant culture of Isoptericola<br> variabilis sp. IRSH1 against Staphylococcus aureus and Pseudomonas aeruginosa.<br> Methods: Silver nanoparticles were produced by extracellular biosynthesis using supernatant<br> culture of a novel thermotolerant Isoptericola variabilis sp.IRSH1 and characterized. The<br> antibacterial activities of the synthesized silver nanoparticles were examined by the standard KirbyBauer disc diffusion method against Staphylococcus aureus and Pseudomonas aeruginosa on<br> Muller-Hinton agar plates.<br> Findings: The silver nanoparticles were produce...
Endo-1,4-β-glucanase is one of three cellulolytic enzymes in a triplet catalytic system that are ... more Endo-1,4-β-glucanase is one of three cellulolytic enzymes in a triplet catalytic system that are required for extracellular cellulose hydrolysis. Thermostable endo-1,4-β-glucanase is important and is included in a considerable portion of industrial enzymes. Hot springs are extreme niches which are important sources of the bacteria producing thermostable enzymes. Accordingly in this study, sampling was performed from four hot springs in the north and northwest of Iran and the screening and identification of acid-stable and thermostable of endo 1,4 -β-glucanase producing bacteria was investigated. Endo1,4β-glucanase activity of these isolated strains were determined by qualitative Congo-Red staining as well as quantitative Carboxymethyl cellulose/Dinitrosalicylic acid methods as indicators of cellulase production. Three isolates out of twelve initially selected bacteria showed noticeable endo 1,4-β-glucanase activity, including Paenibacillus sp. ASh 4 , Bacillus sp. AGh1 and Bac...
Background: Characterizing the structure and function of superoxide dismutase (SOD), as an antiox... more Background: Characterizing the structure and function of superoxide dismutase (SOD), as an antioxidant enzyme providing opportunities for its application in food supplements. Objectives: In this study, the features of the Manganese-SOD of Lactococcus Lactis (SDLL), subsp. Cremoris MG1363, as probiotic bacteria, were determined on the basis of the computational methods. Materials and Methods: The protein’s physicochemical properties and the prediction of its secondary structure were determined via the ProtParam server and the GOR program respectively. Moreover, the 3D structures of the proteins were constructed via the MODELLER on the basis of the homology method and the threading algorithm MUSTER. On the other hand, the structural stability of the models was assayed under the quasi-physiological conditions by the GROMACS program via the GROMOS96 43a1 force field in Linux system. Finally, using the Molecular Docking Studies, the functionality features of the models were predicted thr...
Abstract Biocompatible, biostable aramid, and nanocomposites are commonly used for implanted devi... more Abstract Biocompatible, biostable aramid, and nanocomposites are commonly used for implanted devices because of their water and gas permeability that protects electronic circuit of the device against the moisture environment as well as the ions that exist in the human body. Aramid composites have attracted significant attention in the applications of soft tissue engineering due to the nature of biodegradability and tunable mechanical features. The nanosized webs and hybrid films of chitosan/m-aramid have been successfully used due to their antimicrobial properties. In this chapter, a state-of-the art review of biocompatible and biostable aramide and composites is presented. Recent progress and developments of composite processing methodologies and chemical modification techniques are also discussed.
Applied microbiology and biotechnology, Jan 3, 2018
The celH gene from Clostridium thermocellum encodes a protein containing 900 residues and three c... more The celH gene from Clostridium thermocellum encodes a protein containing 900 residues and three components, including Cel5E, Lic26a, and carbohydrate-binding domains. Cel5E is a member of the glycoside hydrolase-5 family and is a bifunctional xylanase/cellulase enzyme. We targeted a semi-hydrophobic pocket near the Cel5E active site and theoretically screened mutated variants for enhanced levels of thermal stability. Cel5E mutations were inserted into celH by overlapping polymerase chain reaction, followed by expression of wild-type and mutant enzymes in Escherichia coli BL21 (DE3) and purification by affinity chromatography. Thermal-stabilizing mutations were subjected to molecular dynamics simulation, and measurement of the in vacuo potential energy, van der Waals forces, electrostatic interactions, and net nonbonded potential energies obtained an overall binding affinity of - 64.964 KJ/mol for wild-type Cel5E and - 176.148, - 200.921, and - 120.038 KJ/mol for the N94F, N94W, and ...
Introduction: Evaluation of symbiosis between Arbuscular mycorrhizal fungi (AMF) and Saffron (Cro... more Introduction: Evaluation of symbiosis between Arbuscular mycorrhizal fungi (AMF) and Saffron (Crocus Sativus L.) is important because this strategic plant encounters with many environmental stresses such as climatic and edaphic stresses during seasons and the AMF can let the crops increase their productivity along with the improvement of their resistance to stress factors and pathogens Materials and methods: The spores of AMF around rhizosphere of saffron were studied in three fields of Gonabad, Khorasan province, Iran (2013-14). Moreover, the colonization of mycorrhizal fungi with saffron and sorghum trap were studied in three regions using morphologic and molecular methods by nested PCR and amplification of small subunit of rRNA gene fragments. Results: Three species of arbuscular mycorrhizal fungi, Scutellospora dipurpurescens, Funneliformis caledonius and Rhizophagus aggregatus were identified in the soil around rhizosphere of the saffron of three regions. The colonization of so...
Background: Considering natural thermal stability, Geobacillus stearothermophilus amylase and Cel... more Background: Considering natural thermal stability, Geobacillus stearothermophilus amylase and Cel5E from Clostridium thermocellum are good candidates for industrial applications. To be compatible with the industrial applications, this enzyme should be stable in the high temperatures, so any improvement in their thermal stability is valuable. Objectives: Using in silico approach and identifying point mutations in the structure amylase of G. stearothermophilus and Cel5E from C. termocellum we tried to increase thermal stability of the enzymes along with their catalytic activity to reach a new industrial amylase with higher thermostability and an improved function. Materials and Methods: In this study we predicted the 3D structure of the enzymes, then simulated the molecular docking study using MolDock, PLANTS, and Lamarkian genetic algorithm as scoring functions for the docking and in silico engineering of the protein aiming to increase the thermal stability and catalytic activity. Results: A series of thermal stability increasing point mutations were exerted around the active site of the enzyme, then by docking procedure, the binding affinity was measured and finally a list of mutations which theoretically improved the increased thermal stability as well as catalytic activity were proposed. Conclusions: Based on the in silico results obtained the modified enzymes seems to be suitable candidates for considering in both laboratory and industrial scales.
Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 2015
This study aimed to isolate and evaluate the cellulase activity of cellulolytic bacteria in hot s... more This study aimed to isolate and evaluate the cellulase activity of cellulolytic bacteria in hot springs of Dehloran, Ilam province, Iran. Water and sludge samples were collected from the hot springs and the bacterial enrichment was performed in a medium containing rice barn and carboxymethyl cellulose (CMC). The cultures were incubated at 50 °C in aerobic conditions. The bacteria were isolated on CMC agar (1%) medium. Cellulase assay of the isolates was measured by the evaluation of endoglucanase enzyme activity, which is also called as carboxymethyl cellulase (CMCase). The isolated thermotolerant bacteria were then identified and optimized for the production of CMCase. Moreover, stabilizing elements of the enzyme were identified with in silico approach. The chosen isolate was identified as Isoptericola variabilis sp. IDAH9. The identified strain produced the most thermostable CMCase at a concentration of 5.6 g/L of ammonium sulfate, 9 g/L CMCase or 12 g/L rice bran, 0/6% Tween-80, ...
Introduction: Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromat... more Introduction: Biodiesel as a biofuel, with renewable, biodegradable and free of polycyclic aromatic hydrocarbons properties, could be derived from fatty acids of the cells of the animals, plants, algae and bacteria. So, a wide range of approaches have been considered to increase the oil production in biodiesel resources. In this regard, biotechnology approaches can provide new solutions based on application of molecular mechanisms. Materials and methods: A comprehensive survey on molecular mechanisms and key enzymes which are involved in the production and accumulation of the lipids in biodiesel resources have been considered based on literature study and in-silico investigation. In-silico investigation has been performed via InterProScan 5 ، Motif scan ، Conserved Domain ،ProtParam ، TMHMM ، GC content calculator ، NetNGlyc ، NetPhos ، Sulfinator ، Protein Blastand MEGA6 programs for characterizing the structure, functions and homology survey of the selected sequences. Results: Our survey led to the introduced diacyl glycerol acyl transferase (DGAT), waxester synthase/diacyl glycerol acyltransferase (WS/DGAT), oleosin, MLDP and TadA as the effective enzymes and proteins in lipid production and accumulation in selected biodiesel organisms. An investigation on the structure of the corresponding genes of the selected enzymes, led to reveal their various features in the length, GC content as well as in intronic properties. On the other hand, this characterizing on the selected enzymes and proteins disclosed post-translational modifications in all of them, as well as their localization in the cells. Moreover MBOAT, DAGAT, UPF0089, Oleosin and apolipo protein have been revealed in their context as critical domains. On the other hand, homology survey of the selected enzymes and proteins led to introduce the Verniciafordii, Ricinuscommunis, Dunaliella parva , Thalassiosira pseudonana, Saitoella complicata, Rhodococcus imtechensis and Rhodococcus wratislaviensis species, as new sources of biodiesel with possible capability for lipid production. Discussion and conclusion: Overall, this survey provides a series of motifs and domains in biodiesel process, as well as introducing several organisms with potency in biodiesel production, which could be more examined in an experimental condition.
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