Calculation of relative binding affinities of fructose 1,6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method

The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between inhibitors and protein variants. In this article, the importance of hydrophobic and hydrophilic residues to the binding of adenosine monophosphate (AMP) to the fructose 1,6-bisphosphatase (FBPase), a target enzyme for type-II diabetes, was examined by FEP method. Five mutations were made to the FBPase enzyme with AMP inhibitor bound: 113Tyr --> 113Phe, 31Thr --> 31Ala, 31Thr --> 31Ser, 177Met --> 177Ala, and 30Leu --> 30Phe. These mutations test the strength of hydrogen bonds and van der Waals interactions between the ligand and enzyme. The calculated relative free energies indicated that: 113Tyr and 31Thr play an important role, each via two hydrogen bonds affecting the binding affinity of inhibitor AMP to FBPase, and any changes in these hydrogen bonds due to mutations on the protein will have significant effect on the binding affinity of AMP to FBPase, consistent to experimental results. Also, the free energy calculations clearly show that the hydrophilic interactions are more important than the hydrophobic interactions of the binding pocket of FBPase.     

Optimization of critical medium components for the maximal production of gentamicin by Micromonospora echinospora ATCC 15838 using response surface methodology

Optimization of the fermentation medium components for maximum gentamicin production by Micromonospora echinospora ATCC 15838 was carried out. Response surface methodology was applied to optimize the medium constituents. A 2⁴full-factorial central composite design was chosen to explain the combined effects of the four medium constituents, viz. starch, soyabean meal, K₂HPO₄, and CoCl₂ and to design a minimum number of experiments. A second order model was developed and fitted using least square method. The R ² value of the model was 0.9723, which shows that model is best fit for the present studies. The results of analysis of variance and regression of a second order model showed that the linear effects of starch (p<0.001697) and CoCl₂(p<7.99E-13), and cross product effects of starch and soyabean meal (p<0.029876) and soyabean meal and CoCl₂ (p<0.008909) were more significant, suggesting that these were critical variables having the greatest effect on the production of gentamicin in the production medium. The optimized medium consisting of 9 g/L starch, 3 g/L soyabean meal, 0.9 g/L K₂HPO₄, and 0.01 g/L CoCL₂ predicted 850 mg/L of gentamicin which was almost 110% higher than that of the unoptimized medium. The amounts of starch, soyabean meal, and K₂HPO₄ required were also reduced with RSM.     

Reducing Sugars Production from Corncobs: A Comparative Study of Chemical and Biotechnological Methods

Two commonly used chemical pretreatment processes, sulphuric acid, and sodium hydroxide, were tested to provide comparative performance data. A connection between solid to liquid ratio (S/L) and sugars released was observed with an increase in S/L ratio between 0.02 and 0.2. Enzymatic digestibility of 1 M of NaOH-pretreated corncobs were released 210.7 mg ml^?1 of sugars. Further, compared with different concentrations of acid pretreatments at 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, and 0.5 M concentrations, sodium hydroxide pretreatment of corncob substantially increased accessibility and digestibility of cellulose. Another additional observation made was whole-cell and crude enzymatic hydrolysis of different concentrations of acid and NaOH (0.05, 0.1, 0.25 M)-treated materials released lower amount of sugars compared with the sugars released (310.9 mg ml^?1) with whole-cell hydrolysis of 1 M of NaOH-treated corncobs. NaOH-pretreated corncobs contained higher content of sugars and which is more suitable for production of reducing sugars.     

Multiple Responses Optimization and Modeling of Lipase Production by <Emphasis Type="Italic">Rhodotorula mucilaginosa</Emphasis> MTCC-8737 Using Response Surface Methodology

Response surface methodology was employed to optimize culture medium for production of lipase with Rhodotorula sp. MTCC 8737. In the first step, a Plackett–Burman design was used to evaluate the effects of different inducers qualitatively. Of all the seven inducers tested, soybean oil showed significant influence on the lipase production. Further, response surface studies were conducted to quantitatively optimize by considering linear, interactive, and quadratic effects of test variables. A novel approach was proposed to optimize the lipase production system by optimizing the responses in terms of yield kinetics rather than optimizing the direct responses like lipase titer and biomass growth. The coefficient of determination (R ²) calculated for Y _P/S (0.769), Y _P/X (0.799), and Y _X/S (0.847) indicated that the statistical model could explain 76.9%, 79.99%, and 84.7% of variability in the response.     

Constitutive Expression and Optimization of Nutrients for Streptokinase Production by <Emphasis Type="Italic">Pichia pastoris</Emphasis> Using Statistical Methods

The Pichia pastoris clone producing streptokinase (SK) was optimized for its nutritional requirements to improve intracellular expression using statistical experimental designs and response surface methodology. The skc gene was ligated downstream of the native glyceraldehyde 3-phosphate dehydrogenase promoter and cloned in P. pastoris. Toxicity to the host was not observed by SK expression using YPD medium. The transformant producing SK at level of 1,120 IU/ml was selected, and the medium composition was investigated with the aim of achieving high expression levels. The effect of various carbon and nitrogen sources on SK production was tested by using Plackett–Burman statistical design and it was found that dextrose and peptone are the effective carbon and nitrogen sources among all the tested. The optimum conditions of selected production medium parameters were predicted using response surface methodology and the maximum predicted SK production of 2,136.23 IU/ml could be achieved with the production medium conditions of dextrose (x1), 2.90%; peptone (x2), 2.49%; pH, 7.2 (x3), and temperature, 30.4 (x4). Validation studies showed a 95% increase in SK production as compared to that before optimization at 2,089 IU/ml. SK produced by constitutive expression was found to be functionally active by plasminogen activation assay and fibrin clot lysis assay. The current recombinant expression system and medium composition may enable maximum production of recombinant streptokinase at bioreactor level.     

Effect of sodium substitution on superconductivity in Bi-based (2212) system

Samples with the nominal composition Bi₂Sr₂Ca_1−xNa_xCu₂O_y (if with X = 0.05, 0.2, 0.4 and 0.5) were prepared by the solid state reaction method. The role of Na and the effect of various heat treatments in the 2212 composition were studied. From the X-ray diffraction data it is found that the samples annealed for longer duration have shown a single phase 2212. From the DC four-probe resistivity data, it was found that the T_c (zero) varies from 79 to 89 K. It is believed that doping with an alkali element would reduce the oxygen content due to monovalency and gives an effect similar to that during heat treatment under low oxygen pressure or quenching. The presence of sodium in the samples was confirmed by electron probe microanalysis.     

Continuous Production of Oxytetracycline in Fluidized Bed Bioreactor by Immobilized Cells of Streptomyces varsoviensis MTCC-1537: Effect of Dilution and Glucose Loading Rates

Oxytetracycline (OT) production using glutaraldehyde cross-linked calcium alginate immobilized cells of Streptomyces varsoviensis in continuous fluidized bed reactor (FBR) was investigated. Initially, batch experiments were carried in stirred tank reactor (STR) and FBR using calcium alginate immobilized cells. Higher OT production of 0.45 gm/L was achieved by FBR when compared with 0.33 g/L of OT in STR. All subsequent studies were carried out in continuous mode of operation in FBR. During 21 days of operation, effect of glucose concentration and different dilution rates were studied. A maximum of 0.75 g/L OT was achieved in the medium having 10 g/L of glucose concentration. The highest OT concentration of 0.92 g/L and the highest yield of OT with respect to biomass at 0.1713 g/g were obtained at the dilution rate of 0.25 day⁻¹.     

Benzylation of aromatic compounds with different crystallites of MgO

Magnesium oxide nanocrystals are shown to be selective catalysts for the benzylation of aromatics with benzyl chloride, in the order xylene > toluene > benzene. Normal polycrystalline MgO is not as effective as the nanomaterials. However, at the highest surface area, normally most reactive MgO samples (aerogel prepared AP-MgO) were poorer catalysts than a hexagonal platelet form (CP-MgO) of lower surface area. During the catalysis, the MgO is partially converted to MgCl(2), but crystal shape differences are not washed out. Rate data, differential thermal analysis, and consideration of crystal shapes and faces suggest that the CP-MgO form is most catalytically active because of optimal adsorption, molecular trafficking, and desorption energies. The AP-MgO apparently adsorbs the reactants too strongly, and thereby this hinders the catalytic process. These results serve as another example of where nanocrystalline shape plays an important role.     

Biological Treatment of Toxic Petroleum Spent Caustic in Fluidized Bed Bioreactor Using Immobilized Cells of <Emphasis Type="Italic">Thiobacillus</Emphasis> RAI01

In the present studies, newly isolated Thiobacillus sp was used for the treatment of synthetic spent sulfide caustic in a laboratory-scale fluidized bed bioreactor. The sulfide oxidation was tested using Ca-alginate immobilized Thiobacillus sp. Initially, response surface methodology was applied for the optimization of four parameters to check the sulfide oxidation efficiency in batch mode. Further, reactor was operated in continuous mode for 51 days at different sulfide loading rates and retention times to test the sulfide oxidation and sulfate and thiosulfate formation. Sulfide conversions in the range of 90-98% were obtained at almost all sulfide loading rates and hydraulic retention times. However, increased loading rates resulted in lower sulfide oxidation capacity. All the experiments were conducted at constant pH of around 6 and temperature of 30 +/- 5 degrees C.     

Effect of Aeration and Agitation Regimes on Lipase Production by Newly Isolated Rhodotorula mucilaginosa–MTCC 8737 in Stirred Tank Reactor Using Molasses as Sole Production Medium

The influence of media and process parameters (aeration and agitation) on fermentation broth rheology and biomass formation has been studied in 1.5-l stirred tank reactor for lipase production using Rhodotorula mucilaginosa MTCC 8737. Molasses, as sole production medium, is used for lipase production by varying aeration (1, 2, and 3 vvm) and agitation speeds (100, 200, and 300 rpm). Maximum lipase activity of 72 U/ml was obtained during 96 h of fermentation at 2 vvm, 200 rpm, pH 7, and 25 +/- 2 degrees C temperature. Lipase production kinetics with respect to dry cell weight of biomass showed Y (P/S) of 25.71 U/mg, specific product formation of 10.9 U/mg DC, and Y (X/S) 2.35 mg/mg. Maximum lipase activity (MC 2) of 56 U/ml was observed at 1% molasses, and a further increase in the molasses concentration of (%) 1.5 and 2 inhibited the product formation of lipase with 15 and 8.5 U/ml, respectively. The production kinetics of molasses media showed Y (P/X) was 14 U/mg DC, Y (P/S) 16 U/mg, and Y (X/S) 1.14 mg/mg during 96 h of bioreactor operation. The k(L)a values for all batches (MC 1-MC 4) at 96 h of fermentation were 32, 28, 21, and 19/h, and the |oxygen transfer rate were 54.4, 56, 35.7, and 17.29 mg/l h, respectively. Increase in molasses concentration resulted in decreased lipase activity by increase in viscosity of the fermentation broth.