Statistical analysis and optimization of nitrogen,phosphorus, and inoculum concentrations for the biodegradation of petroleum hydrocarbons by response surface methodology

In order to optimize and evaluate the influence of nitrogen, phosphorus, and inoculum concentrations on the biodegradation of hydrocarbon contaminated effluents, experiments based on central composite design (CCD) method were carried out for 3 days, employing C1 mixed culture and intermittent aeration. The independent variables were nitrogen concentration (X ₁), phosphorus concentration (X ₂), and inoculum concentration (X ₃) and the removal of total petroleum hydrocarbons (TPH) was the dependent variable. The optimized nutrients ratio (C:N:P = 100:20:2.7) and inoculum concentration (1.32 g/l) provided TPH removal of 71.8% after processing for three days. Analysis using gas chromatography identified five hydrocarbons classes: paraffins, isoparaffins, olefins, naphthenics, and aromatics. The naphthenic compounds did not degrade as readily as the other hydrocarbons that were identified. The following degradation percentages were obtained: 87.1% for the paraffins, 77.7% for the isoparaffins, 78.6% for the olefins, 38.4% for the naphthenics, and 71.7% for the aromatics.     

Enzyme synthesis of oligosaccharides using cashew apple juice as substrate

The use of agriculture substrates in industrial biotechnological processes has been increasing because of their low cost. In this work, the use of clarified cashew apple juice was investigated as substrate for enzyme synthesis of prebiotic oligosaccharide. The results showed that cashew apple juice is a good source of reducing sugars and can be used as substrate for the production of dextransucrase by Leuconostoc citreum B-742 for the synthesis of oligosaccharides using the crude enzyme. Optimal oligosaccharide yield (approximately 80%) was obtained for sucrose concentrations lower than 60 g/L and reducing sugar concentrations higher than 100 g/L.     

Isolation,identification and characterization of a novel Rhodococcus sp. strain in biodegradation of tetrahydrofuran and its medium optimization using sequential statistics-based experimental designs

Statistics-based experimental designs were applied to optimize the culture conditions for tetrahydrofuran (THF) degradation by a newly isolated Rhodococcus sp. YYL that tolerates high THF concentrations. Single factor experiments were undertaken for determining the optimum range of each of four factors (initial pH and concentrations of K₂HPO₄ · 3H₂O, NH₄Cl and yeast extract) and these factors were subsequently optimized using the response surface methodology. The Plackett–Burman design was used to identify three trace elements (Mg²⁺, Zn²⁺and Fe²⁺) that significantly increased the THF degradation rate. The optimum conditions were found to be: 1.80 g/L NH₄Cl, 0.81 g/L K₂HPO₄ · 3H₂O, 0.06 g/L yeast extract, 0.40 g/L MgSO₄ · 7H₂O, 0.006 g/L ZnSO₄ · 7H₂O, 0.024 g/L FeSO₄ · 7H₂O, and an initial pH of 8.26. Under these optimized conditions, the maximum THF degradation rate increased to 137.60 mg THF h⁻¹ g dry weight in Rhodococcus sp. YYL, which was nearly five times of that by the previously described THF degrading Rhodococcus strain.     

Medium optimization for the production of avermectin B1a by Streptomyces avermitilis 14-12A using response surface methodology

Response surface methodology was employed to optimize the composition of medium for the production of avermectin B1a by Streptomyces avermitilis 14-12A in shaker flask cultivation. Corn starch and yeast extract were found to have significant effects on avermectin B1a production by the Plackett–Burman design. The steepest ascent method was used to access the optimal region of the medium composition, followed by an application of response surface. The analysis revealed that the optimum values of the tested variables were 149.57 g/l corn starch and 8.92 g/l yeast extract. A production of 5128 mg/l, which was in agreement with the prediction, was observed in verification experiment. In comparison to the production of original level (3528 mg/l), 1.45-fold increase had been obtained.     

Redesign of a protein–peptide interaction: Characterization and applications

The design of protein–peptide interactions has a wide array of practical applications and also reveals insight into the basis for molecular recognition. Here, we present the redesign of a tetratricopeptide repeat (TPR) protein scaffold, along with its corresponding peptide ligand. We show that the binding properties of these protein–peptide pairs can be understood, quantitatively, using straightforward chemical considerations. The recognition pairs we have developed are also practically useful for the specific identification of tagged proteins. We demonstrate the facile replacement of these proteins, which we have termed T‐Mods (TPR‐based recognition module), for antibodies in both detection and purification applications. The new protein–peptide pair has a dissociation constant that is weaker than typical antibody–antigen interactions, yet the recognition pair is highly specific and we have shown that this affinity is sufficient for both Western blotting and affinity purification. Moreover, we demonstrate that this more moderate affinity is actually advantageous for purification applications, because extremely harsh conditions are not required to dissociate the T‐Mod‐peptide interaction. The results we present are important, not only because they represent a successful application of protein design but also because they help define the properties that should be sought in other scaffolds that are being developed as antibody replacements.     

Divergent trends in anadromous salmonid populations in Norwegian and Scottish rivers

The Atlantic salmon (Salmo salar) is a charismatic anadromous fish of high conservation and economic value. Concerns have been expressed regarding the long-term viability of fisheries throughout the species''s distributional range because of abundance variations that cannot currently be explained or predicted. Here, we analyse long-term catch data obtained over a wide geographical range and across a range of spatial subscales to understand more fully the factors that drive population abundance. We use rod catch data from 84 Norwegian rivers over 125 years (1876–2000) and 48 Scottish rivers over 51 years (1952–2002). The temporal correlation in catches is very long-term, with trends persisting over several decades. The spatial correlation is relatively short-range, indicating strong local-scale effects on catch. Furthermore, Scottish salmon populations exhibit recent negative trends in contrast to some more positive trends in Norway—especially in the north.     

Ultra scale‐down studies of the effect of shear on cell quality; Processing of a human cell line for cancer vaccine therapy

Whole cell therapy is showing potential in the clinic for the treatment of many chronic diseases. The translation of laboratory‐scale methods for cell harvesting and formulation to commercial‐scale manufacturing offers major bioprocessing challenges. This is especially the case when the cell properties determine the final product effectiveness. This study is focused on developing an ultra scale‐down method for assessing the impact of the hydrodynamic environment on human cells that constitute the therapeutic product. Small volumes of a prostate cancer cell line, currently being developed in late phase II clinical trials as an allogeneic whole cell vaccine therapy for prostate cancer, were exposed to hydrodynamic shear rates similar to those present in downstream process, formulation and vial filling operations. A small scale rotating disc shear device (20 mL) was used over a range of disc speeds to expose cells to maximum shear rates ranging from 90 × 10³ to 175 × 10³ s^‐1 (equivalent maximum power dissipation rates of 14 × 10³ to 52 × 10³ W kg^‐1). These cells were subsequently analyzed for critical cell quality attributes such as the retention of membrane integrity and cell surface marker profile and density. Three cell surface markers (CD9, CD147, and HLAA‐C) were studied. The cell markers exhibited different levels of susceptibility to hydrodynamic shear but in all cases this was less than or equal to the loss of membrane integrity. It is evident that the marker, or combination or markers, which might provide the required immunogenic response, will be affected by hydrodynamic shear environment during bioprocessing, if the engineering environment is not controlled to within the limits tolerated by the cell components. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Composite S-layer lipid structures

Designing and utilization of biomimetic membrane systems generated by bottom-up processes is a rapidly growing scientific and engineering field. Elucidation of the supramolecular construction principle of archaeal cell envelopes composed of S-layer stabilized lipid membranes led to new strategies for generating highly stable functional lipid membranes at meso- and macroscopic scale. In this review, we provide a state of the art survey how S-layer proteins, lipids, and polysaccharides may be used as basic building blocks for the assembly of S-layer supported lipid membranes. These biomimetic membrane systems are distinguished by a nanopatterned fluidity, enhanced stability and longevity and thus, provide a dedicated reconstitution matrix for membrane-active peptides and transmembrane proteins. Exciting areas for application of composite S-layer membrane systems concern sensor systems involving specific membrane functions.     

Interaction of α-conotoxin ImII and its analogs with nicotinic receptors and acetylcholine-binding proteins: additional binding sites on Torpedo receptor

α-Conotoxins interact with nicotinic acetylcholine receptors (nAChRs) and acetylcholine-binding proteins (AChBPs) at the sites for agonists/competitive antagonists. α-Conotoxins blocking muscle-type or α7 nAChRs compete with α-bungarotoxin. However, α-conotoxin ImII, a close homolog of the α7 nAChR-targeting α-conotoxin ImI, blocked α7 and muscle nAChRs without displacing α-bungarotoxin ( Ellison et al. 2003, 2004 ), suggesting binding at a different site. We synthesized α-conotoxin ImII, its ribbon isomer (ImII iso ), 'mutant' ImII(W10Y) and found similar potencies in blocking human α7 and muscle nAChRs in Xenopus oocytes. Both isomers displaced [¹²⁵I]-α-bungarotoxin from human α7 nAChRs in the cell line GH₄C₁ (IC₅₀ 17 and 23 μM, respectively) and from Lymnaea stagnalis and Aplysia californica AChBPs (IC₅₀ 2.0–9.0 μM). According to SPR measurements, both isomers bound to immobilized AChBPs and competed with AChBP for immobilized α-bungarotoxin ( K _d and IC₅₀ 2.5–8.2 μM). On Torpedo nAChR, α-conotoxin [¹²⁵I]-ImII(W10Y) revealed specific binding ( K _d 1.5–6.1 μM) and could be displaced by α-conotoxin ImII, ImII iso and ImII(W10Y) with IC₅₀ 2.7, 2.2 and 3.1 μM, respectively. As α-cobratoxin and α-conotoxin ImI displaced [¹²⁵I]-ImII(W10Y) only at higher concentrations (IC₅₀≥ 90 μM), our results indicate that α-conotoxin ImII and its congeners have an additional binding site on Torpedo nAChR distinct from the site for agonists/competitive antagonists.