First and foremost, I am a chemical engineering expert. Recently, I do research in the field of environmental biotechnology on topics such as biodegradation and waste conversion to value added products.
ABSTRACT Fungal delignification can be considered as a feasible process to pre-treat lignocellulo... more ABSTRACT Fungal delignification can be considered as a feasible process to pre-treat lignocellulosic biomass in biofuel production, if its performance is improved in terms of efficiency thorough a few modifications. In this study, Trichoderma viride was utilized to investigate the effect of wet-milling, addition of surfactant (Tween 80) and optimization of operating factors such as temperature, biomass to liquid medium ratio and glucose concentration on biodelignification of rice straw. Next, the enzymatic hydrolysis of pretreated biomass was studied at various pretreatment times. Results revealed that the wet milling and addition of surfactant increases the lignin removal about 15% and 11%, respectively. The optimization of operating factors resulted in high lignin removal efficiency equal to 74% in a 30 day pretreatment. The maximum enzymatic saccharification of pretreated biomass at optimum conditions was obtained equal to 56%. Conversion of cellulose to reducing sugars during the pretreatment stage was 21% which suggests that higher saccharification efficiency could be achieved in a simultaneous pretreatment and saccharification process.
International Journal of Biological Macromolecules, 2015
Production of xanthan gum using immobilized cells of Xanthomonas campestris and Xanthomonas pelar... more Production of xanthan gum using immobilized cells of Xanthomonas campestris and Xanthomonas pelargonii grown on glucose or hydrolyzed starch as carbon sources was investigated. Calcium alginate (CA) and calcium alginate-polyvinyl alcohol-boric acid (CA-PVA) beads were used for the immobilization of cells. Xanthan titers of 8.2 and 9.2g/L were obtained for X. campestris cells immobilized in CA-PVA beads using glucose and hydrolyzed starch, respectively, whereas those for X. pelargonii were 8 and 7.9 g/L, respectively. Immobilized cells in CA-PVA beads were successfully employed in three consecutive cycles for xanthan production without any noticeable degradation of the beads whereas the CA beads were broken after the first cycle. The results of this study suggested that immobilized cells are advantageous over the free cells for xanthan production. Also it was shown that the cells immobilized in CA-PVA beads are more efficient than cells immobilized in CA beads for xanthan production.
ABSTRACT Rock samples from the Asmary outcrop formation of the Ahwaz oil rich zone with a porosit... more ABSTRACT Rock samples from the Asmary outcrop formation of the Ahwaz oil rich zone with a porosity of 16% and permeability of 1 md and MIS crude oil with an API value of 42.5 and moderate asphaltene content of 3%, were used to study the effect of the incubation time and flow rate of the displacing fluid in MEOR operations. Five species of rod shaped, gram positive, thermophile and facultative bacteria were isolated and purified from the crude. Due to the high sweep efficiency prevailing in the core flooding system, the effect of the displacing brine flow rate on the oil recovery efficiency was found not to be significant. On the other hand, a 100% increase in incubation time from 7 to 14 days resulted in an increase from 3% to 4% in the total cumulative production. Application of a cyclic operation was not effective in promoting the efficiency of the MEOR operation, probably due to the stronger effect of flooding on the removal of valuable metabolites, as compared to undesired ones, before the stationary phase of the microbial kinetics. While qualitative measurements did not show a strong change in the water-rock contact angle, more than a 4-fold increase in capillary number occurred after microbial treatment, implying that reduction of interfacial tension was the stronger mechanism of oil recovery in this work.
To reclaim the surfactant molecules from oil in water emulsions, an electroflotation technique wa... more To reclaim the surfactant molecules from oil in water emulsions, an electroflotation technique was utilized. A two staged separation mechanism was suggested to describe the process and its theoretical aspects were explained in detail. The effects of operating parameters such as flotation time and current density on recovery efficiency of surfactants from emulsions stabilized by ionic (sodium dodecyl sulphate: SDS) and non ionic (Tween 80) surfactants were investigated using a simple electroflotation column. The results revealed that the surfactant recovery efficiencies for all of the experiments were higher than 70% after 30 minutes treatment. Consequently, the presented method could be considered as an effective process in recycling the valuable surfactants from the emulsions existing in industrial wastes.
AIM: The main goal of the present study was to examine the possibility of using starch as the mai... more AIM: The main goal of the present study was to examine the possibility of using starch as the main substrate for microbial production of xanthan gum by Xanthomonas campestris and Xanthomonas pelargonii. METHODS: The bacteria were cultivated on starch hydrolyzate and glucose (as a reference) at three different sugar concentrations of 20, 30, and 40 g/L. Samples were taken at different time intervals (24, 48, and 72 h) from cultivation broth and concentration of xanthan was determined. General linear regression method was employed to analyze the results. RESULTS: For starch hydrolyzate and glucose, the highest xanthan concentration of 8.7 and 7.8 g/L, respectively, was achieved at 40 g/l of substrate concentration after 48 h for Xanthomonas campestris. For all substrate concentrations, maximum xanthan production was obtained after 48 h while prolonged cultivation time (72 h) reduced the concentration significantly. Generally, differences between product yields obtained in cultures con...
Human growth hormone (hGH) is synthesized and stored by somatotroph cells of the anterior pituita... more Human growth hormone (hGH) is synthesized and stored by somatotroph cells of the anterior pituitary gland and can effect on body metabolism. This protein can be used to treat hGH deficiency, Prader-Willi syndrome and Turner syndrome. The limitations in current technology for soluble recombinant protein production, such as inclusion body formation, decrease its usage for therapeutic purposes. To achieve high levels of soluble form of recombinant human growth hormone (rhGH) we used suitable host strain, appropriate induction temperature, induction time and culture media composition. For this purpose, 32 experiments were designed using Taguchi method and the levels of produced proteins in all 32 experiments were evaluated primarily by ELISA and dot blotting and finally the purified rhGH protein products assessed by SDS-PAGE and Western blotting techniques. Our results indicate that media, bacterial strains, temperature and induction time have significant effects on the production of rhGH. The low cultivation temperature of 25°C, TB media (with 3% ethanol and 0.6M glycerol), Origami strain and a 10-h induction time increased the solubility of human growth hormone.
Physical chemistry chemical physics : PCCP, Jan 22, 2015
Bio-electrosynthesis is one of the significant developments in reverse microbial fuel cell techno... more Bio-electrosynthesis is one of the significant developments in reverse microbial fuel cell technology which is potentially capable of creating organic compounds by combining CO2 with H2O. Accordingly, the main objective in the current study was to present a model of microbial electrosynthesis for producing organic compounds (acetate) based on direct conduction of electrons in biofilms. The proposed model enjoys a high degree of rigor because it can predict variations in the substrate concentration, electrical potential, current density and the thickness of the biofilm. Additionally, coulombic efficiency was investigated as a function of substrate concentration and cathode potential. For a system containing CO2 as the substrate and Sporomusa ovata as the biofilm forming microorganism, an increase in the substrate concentration at a constant potential can lead to a decrease in coulombic efficiency as well as an increase in current density and biofilm thickness. On the other hand, an i...
Journal of peptide science : an official publication of the European Peptide Society, 2015
The world is entering the third decade of the acquired immunodeficiency syndrome (AIDS) pandemic.... more The world is entering the third decade of the acquired immunodeficiency syndrome (AIDS) pandemic. The primary cause of the disease has known to be human immunodeficiency virus type I (HIV-1). Recently, peptides are shown to have high potency as drugs in the treatment of AIDS. Therefore, in the present study, we have developed a method to predict anti-HIV-1 peptides using support vector machine (SVM) as a powerful machine learning algorithm. Peptide descriptors were represented based on the concept of Chou's pseudo-amino acid composition (PseAAC). HIV-1 P24-derived peptides were examined to predict anti-HIV-1 activity among them. The efficacy of the prediction was then validated in vitro. The mutagenic effect of validated anti-HIV-1 peptides was further investigated by the Ames test. Computational classification using SVM showed the accuracy and sensitivity of 96.76% and 98.1%, respectively. Based on SVM classification algorithm, 3 out of 22 P24-derived peptides were predicted to...
High-mobility group proteins are a superfamily of DNA-binding proteins that bind to the DNA minor... more High-mobility group proteins are a superfamily of DNA-binding proteins that bind to the DNA minor groove and bend it, whereas most of the transcription factors such as centromere protein B (CENP-B), octamer (Oct)-1, growth factor independence 1 (Gfi-1), and WRKY bind to the major groove of DNA. Classification of proteins using their DNA-binding features is the aim of this study. Nuclear localization signals play more important roles in entering DNA-binding proteins to nucleus and doing their functions; therefore, they have been considered as a feature which is important for DNA-binding manner in proteins. Nuclear localization signals (NLSs) were predicted by two prediction web servers, and then, their sequence ordered features were extracted by Chou's pseudo amino acid composition (PseAAC) and ProtParam. Multilayer perceptron was used as an artificial neural network for analyzing the features by calculating the correlation coefficient and 30-fold cross-validation. Another used d...
ABSTRACT Dibenzothiophene (DBT) is a recalcitrant organic sulfur compound which remains in the cr... more ABSTRACT Dibenzothiophene (DBT) is a recalcitrant organic sulfur compound which remains in the crude oil after hydrodesulfurization (HDS) process and can be removed by biodesulfurization (BDS). The objective of this study was the isolation of novel strain capable more BDS rate and optimization of DBT removal by both growing and resting cells. Response surface Methodology (RSM) was applied for evaluating the interactive effects of three independent factors including DBT concentration, temperature and pH. The three factors Box-Benken design with three center points was performed to generate the optimum condition for DBT removal by growing cells in aqueous medium and resting cells in biphasic medium. Among the isolated bacteria from oil-contaminated soil, a gram-positive, non-spore forming isolate designated PD1 showed the high BDS rate and capable to convert the DBT to 2-hydroxybiphenyl (2-HBP) as the final product. Analysis of variance (ANOVA) demonstrated that all of the studied parameters in the growing cells system showed significant effect on BDS rate, while in the resting cells effect of pH was not significant (P > 0.05). Maximum 2-HBP production (0.21 mM) by growing cells of PD1 strain was obtained at 0.38 mM initial DBT concentration, pH 6.88 and temperature of 27.57°C. For resting cells, maximum BDS activity of PD1 strain was determined as 0.46 μM 2-HBP/min g DCW at optimum pH 6.29, temperature of 26.13°C and DBT concentration of 7.73 mM. The BDS efficiency of Rhodococcus erythropolis PD1 (NCBI Gene Bank Accession no. JX625154) was increased by setting each factor at the optimum level.
ABSTRACT Fungal delignification can be considered as a feasible process to pre-treat lignocellulo... more ABSTRACT Fungal delignification can be considered as a feasible process to pre-treat lignocellulosic biomass in biofuel production, if its performance is improved in terms of efficiency thorough a few modifications. In this study, Trichoderma viride was utilized to investigate the effect of wet-milling, addition of surfactant (Tween 80) and optimization of operating factors such as temperature, biomass to liquid medium ratio and glucose concentration on biodelignification of rice straw. Next, the enzymatic hydrolysis of pretreated biomass was studied at various pretreatment times. Results revealed that the wet milling and addition of surfactant increases the lignin removal about 15% and 11%, respectively. The optimization of operating factors resulted in high lignin removal efficiency equal to 74% in a 30 day pretreatment. The maximum enzymatic saccharification of pretreated biomass at optimum conditions was obtained equal to 56%. Conversion of cellulose to reducing sugars during the pretreatment stage was 21% which suggests that higher saccharification efficiency could be achieved in a simultaneous pretreatment and saccharification process.
International Journal of Biological Macromolecules, 2015
Production of xanthan gum using immobilized cells of Xanthomonas campestris and Xanthomonas pelar... more Production of xanthan gum using immobilized cells of Xanthomonas campestris and Xanthomonas pelargonii grown on glucose or hydrolyzed starch as carbon sources was investigated. Calcium alginate (CA) and calcium alginate-polyvinyl alcohol-boric acid (CA-PVA) beads were used for the immobilization of cells. Xanthan titers of 8.2 and 9.2g/L were obtained for X. campestris cells immobilized in CA-PVA beads using glucose and hydrolyzed starch, respectively, whereas those for X. pelargonii were 8 and 7.9 g/L, respectively. Immobilized cells in CA-PVA beads were successfully employed in three consecutive cycles for xanthan production without any noticeable degradation of the beads whereas the CA beads were broken after the first cycle. The results of this study suggested that immobilized cells are advantageous over the free cells for xanthan production. Also it was shown that the cells immobilized in CA-PVA beads are more efficient than cells immobilized in CA beads for xanthan production.
ABSTRACT Rock samples from the Asmary outcrop formation of the Ahwaz oil rich zone with a porosit... more ABSTRACT Rock samples from the Asmary outcrop formation of the Ahwaz oil rich zone with a porosity of 16% and permeability of 1 md and MIS crude oil with an API value of 42.5 and moderate asphaltene content of 3%, were used to study the effect of the incubation time and flow rate of the displacing fluid in MEOR operations. Five species of rod shaped, gram positive, thermophile and facultative bacteria were isolated and purified from the crude. Due to the high sweep efficiency prevailing in the core flooding system, the effect of the displacing brine flow rate on the oil recovery efficiency was found not to be significant. On the other hand, a 100% increase in incubation time from 7 to 14 days resulted in an increase from 3% to 4% in the total cumulative production. Application of a cyclic operation was not effective in promoting the efficiency of the MEOR operation, probably due to the stronger effect of flooding on the removal of valuable metabolites, as compared to undesired ones, before the stationary phase of the microbial kinetics. While qualitative measurements did not show a strong change in the water-rock contact angle, more than a 4-fold increase in capillary number occurred after microbial treatment, implying that reduction of interfacial tension was the stronger mechanism of oil recovery in this work.
To reclaim the surfactant molecules from oil in water emulsions, an electroflotation technique wa... more To reclaim the surfactant molecules from oil in water emulsions, an electroflotation technique was utilized. A two staged separation mechanism was suggested to describe the process and its theoretical aspects were explained in detail. The effects of operating parameters such as flotation time and current density on recovery efficiency of surfactants from emulsions stabilized by ionic (sodium dodecyl sulphate: SDS) and non ionic (Tween 80) surfactants were investigated using a simple electroflotation column. The results revealed that the surfactant recovery efficiencies for all of the experiments were higher than 70% after 30 minutes treatment. Consequently, the presented method could be considered as an effective process in recycling the valuable surfactants from the emulsions existing in industrial wastes.
AIM: The main goal of the present study was to examine the possibility of using starch as the mai... more AIM: The main goal of the present study was to examine the possibility of using starch as the main substrate for microbial production of xanthan gum by Xanthomonas campestris and Xanthomonas pelargonii. METHODS: The bacteria were cultivated on starch hydrolyzate and glucose (as a reference) at three different sugar concentrations of 20, 30, and 40 g/L. Samples were taken at different time intervals (24, 48, and 72 h) from cultivation broth and concentration of xanthan was determined. General linear regression method was employed to analyze the results. RESULTS: For starch hydrolyzate and glucose, the highest xanthan concentration of 8.7 and 7.8 g/L, respectively, was achieved at 40 g/l of substrate concentration after 48 h for Xanthomonas campestris. For all substrate concentrations, maximum xanthan production was obtained after 48 h while prolonged cultivation time (72 h) reduced the concentration significantly. Generally, differences between product yields obtained in cultures con...
Human growth hormone (hGH) is synthesized and stored by somatotroph cells of the anterior pituita... more Human growth hormone (hGH) is synthesized and stored by somatotroph cells of the anterior pituitary gland and can effect on body metabolism. This protein can be used to treat hGH deficiency, Prader-Willi syndrome and Turner syndrome. The limitations in current technology for soluble recombinant protein production, such as inclusion body formation, decrease its usage for therapeutic purposes. To achieve high levels of soluble form of recombinant human growth hormone (rhGH) we used suitable host strain, appropriate induction temperature, induction time and culture media composition. For this purpose, 32 experiments were designed using Taguchi method and the levels of produced proteins in all 32 experiments were evaluated primarily by ELISA and dot blotting and finally the purified rhGH protein products assessed by SDS-PAGE and Western blotting techniques. Our results indicate that media, bacterial strains, temperature and induction time have significant effects on the production of rhGH. The low cultivation temperature of 25°C, TB media (with 3% ethanol and 0.6M glycerol), Origami strain and a 10-h induction time increased the solubility of human growth hormone.
Physical chemistry chemical physics : PCCP, Jan 22, 2015
Bio-electrosynthesis is one of the significant developments in reverse microbial fuel cell techno... more Bio-electrosynthesis is one of the significant developments in reverse microbial fuel cell technology which is potentially capable of creating organic compounds by combining CO2 with H2O. Accordingly, the main objective in the current study was to present a model of microbial electrosynthesis for producing organic compounds (acetate) based on direct conduction of electrons in biofilms. The proposed model enjoys a high degree of rigor because it can predict variations in the substrate concentration, electrical potential, current density and the thickness of the biofilm. Additionally, coulombic efficiency was investigated as a function of substrate concentration and cathode potential. For a system containing CO2 as the substrate and Sporomusa ovata as the biofilm forming microorganism, an increase in the substrate concentration at a constant potential can lead to a decrease in coulombic efficiency as well as an increase in current density and biofilm thickness. On the other hand, an i...
Journal of peptide science : an official publication of the European Peptide Society, 2015
The world is entering the third decade of the acquired immunodeficiency syndrome (AIDS) pandemic.... more The world is entering the third decade of the acquired immunodeficiency syndrome (AIDS) pandemic. The primary cause of the disease has known to be human immunodeficiency virus type I (HIV-1). Recently, peptides are shown to have high potency as drugs in the treatment of AIDS. Therefore, in the present study, we have developed a method to predict anti-HIV-1 peptides using support vector machine (SVM) as a powerful machine learning algorithm. Peptide descriptors were represented based on the concept of Chou's pseudo-amino acid composition (PseAAC). HIV-1 P24-derived peptides were examined to predict anti-HIV-1 activity among them. The efficacy of the prediction was then validated in vitro. The mutagenic effect of validated anti-HIV-1 peptides was further investigated by the Ames test. Computational classification using SVM showed the accuracy and sensitivity of 96.76% and 98.1%, respectively. Based on SVM classification algorithm, 3 out of 22 P24-derived peptides were predicted to...
High-mobility group proteins are a superfamily of DNA-binding proteins that bind to the DNA minor... more High-mobility group proteins are a superfamily of DNA-binding proteins that bind to the DNA minor groove and bend it, whereas most of the transcription factors such as centromere protein B (CENP-B), octamer (Oct)-1, growth factor independence 1 (Gfi-1), and WRKY bind to the major groove of DNA. Classification of proteins using their DNA-binding features is the aim of this study. Nuclear localization signals play more important roles in entering DNA-binding proteins to nucleus and doing their functions; therefore, they have been considered as a feature which is important for DNA-binding manner in proteins. Nuclear localization signals (NLSs) were predicted by two prediction web servers, and then, their sequence ordered features were extracted by Chou's pseudo amino acid composition (PseAAC) and ProtParam. Multilayer perceptron was used as an artificial neural network for analyzing the features by calculating the correlation coefficient and 30-fold cross-validation. Another used d...
ABSTRACT Dibenzothiophene (DBT) is a recalcitrant organic sulfur compound which remains in the cr... more ABSTRACT Dibenzothiophene (DBT) is a recalcitrant organic sulfur compound which remains in the crude oil after hydrodesulfurization (HDS) process and can be removed by biodesulfurization (BDS). The objective of this study was the isolation of novel strain capable more BDS rate and optimization of DBT removal by both growing and resting cells. Response surface Methodology (RSM) was applied for evaluating the interactive effects of three independent factors including DBT concentration, temperature and pH. The three factors Box-Benken design with three center points was performed to generate the optimum condition for DBT removal by growing cells in aqueous medium and resting cells in biphasic medium. Among the isolated bacteria from oil-contaminated soil, a gram-positive, non-spore forming isolate designated PD1 showed the high BDS rate and capable to convert the DBT to 2-hydroxybiphenyl (2-HBP) as the final product. Analysis of variance (ANOVA) demonstrated that all of the studied parameters in the growing cells system showed significant effect on BDS rate, while in the resting cells effect of pH was not significant (P > 0.05). Maximum 2-HBP production (0.21 mM) by growing cells of PD1 strain was obtained at 0.38 mM initial DBT concentration, pH 6.88 and temperature of 27.57°C. For resting cells, maximum BDS activity of PD1 strain was determined as 0.46 μM 2-HBP/min g DCW at optimum pH 6.29, temperature of 26.13°C and DBT concentration of 7.73 mM. The BDS efficiency of Rhodococcus erythropolis PD1 (NCBI Gene Bank Accession no. JX625154) was increased by setting each factor at the optimum level.
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Papers by Davoud Biria