Facile and statistical optimization of transfection conditions for secretion of foreign proteins from insect Drosophila S2 cells using green fluorescent protein reporter

Insect Drosophila melanogaster S2 cells were developed as a plasmid-based and therefore nonlytic expression system for functional foreign proteins. Transfection is an important step to introduce foreign target DNA into cells and should be properly optimized to obtain maximum production yield. Single factor search (SFS) methodology is still generally used to determine optimal condition in a biological system. Although this method is relatively simple to perform, it has many disadvantages such as not considering interactions between several factors and not covering the entire region of the solution pool. Therefore, we approached this optimization problem statistically with response surface (RSM) and evolutionary operation (EVOP) methodologies and compared the transfection efficiencies with the traditional SFS method. We employed secreted green fluorescent protein (GFP) as a reporter for determination of optimal transfection condition and secreted human erythropoietin (hEPO) as a confirming foreign model protein. Consequently, we arrived at the best optimal transient transfection condition (1 microg of plasmid DNA, 5 microg of lipofectin, 2 x 10(6) cells of initial cell number, and 18 h of transfection duration time) through a systematic access in a series of SFS, RSM, and EVOP. The secreted hEPO yield using optimal transient transfection condition by EVOP methodology was enhanced by about 1.8-fold compared to that of traditional SFS. This optimized transient transfection condition can be used as a basis for optimal stable transfections. A linear relationship between secreted GFP fluorescence intensity and secreted hEPO concentration indicated that facile and noninvasive determination of optimal transfection conditions for expression and secretion of foreign proteins in S2 cell cultures was made possible by simple measurement of GFP fluorescence.     

Experimental optimization of a step aeration waste treatment process

Evolutionary operation (EVOP) was used to experimentally investigate the optimum steady state operating conditions for a step aeration activated sludge waste treatment process. A laboratory scale two tank step aeration activated sludge unit with fixed total volume, total influent flow rate, recycle flow rate, and sludge wasting rate was employed. The volume ratio and flow rate ratio which minimized effluent chemical oxygen demand were determined. The results indicate that EVOP is a useful technique for improving the performance of biological processes.     

Optimization of physicochemical parameters for gallic acid production by evolutionary operation-factorial design technique

The interaction effects of five variable parameters on gallic acid yield by the application of Evolutionary Operation (EVOP)-factorial design technique is presented in this paper. The methodology combines the advantage of factorial techniques for designing experiments with five parameters and that of EVOP methodology for the systematic analysis of experimental results. It facilitates the selection of optimum conditions or directs the changes desired for individual parameters for the designing of subsequent experiments. Decision were taken according to the decision-making procedure available in the literature. Standard deviation and error limits based on 95% confidence were also calculated according to the relationship given in literature. The best combinations of the physicochemical parameters at optimal levels of 32 °C, 93% relative humidity, 4.5 pH, 72 h incubation period, 20 g substrate weight and 0.4:1 solid–liquid ratio resulted in gallic acid yield of 90.9% under modified solid-state fermentation (MSSF).     

Optimum DNA curvature using a hybrid approach involving an artificial neural network and genetic algorithm

In the present paper, a hybrid technique involving artificial neural network (ANN) and genetic algorithm (GA) has been proposed for performing modeling and optimization of complex biological systems. In this approach, first an ANN approximates (models) the nonlinear relationship(s) existing between its input and output example data sets. Next, the GA, which is a stochastic optimization technique, searches the input space of the ANN with a view to optimize the ANN output. The efficacy of this formalism has been tested by conducting a case study involving optimization of DNA curvature characterized in terms of the RL value. Using the ANN-GA methodology, a number of sequences possessing high RL values have been obtained and analyzed to verify the existence of features known to be responsible for the occurrence of curvature. A couple of sequences have also been tested experimentally. The experimental results validate qualitatively and also near-quantitatively, the solutions obtained using the hybrid formalism. The ANN-GA technique is a useful tool to obtain, ahead of experimentation, sequences that yield high RL values. The methodology is a general one and can be suitably employed for optimizing any other biological feature.     

Optimization of Nutrient Requirements and Culture Conditions for the Production of Rhamnolipid from Pseudomonas aeruginosa (MTCC 7815) using Mesua ferrea Seed Oil

Environmental awareness has led to a serious consideration for biological surfactants and hence non-edible vegetable oils may serve as a substitute carbon source for bio-surfactant production (rhamnolipid) which might be an alternative to complex synthetic surfactants. There are reports of rhamnolipid production from plant based oil giving higher production than that of glucose because of their hydrophobicity and high carbon content. Therefore the contribution of non-edible oil such as Mesua ferrea seed oil could serve as a good carbon source for rhamnolipid production. Moreover the use of rhamnolipid production from non-edible plant based seed oil has not been reported elsewhere. The present work focus on the optimal production of rhamnolipid by considering both micro and macro nutrients and culture conditions using response surface methodology. The study observes that micronutrients play a significant role in rhamnolipid production from Pseudomonas aeruginosa (MTCC 7815). The investigation results with the statistically optimize parameters able to produce a higher rhamnolipid production and this methodology could be used to optimize the nutrients requirements and culture conditions. The present findings would assist in bioremediation of crude oil contaminated ecosystems.     

Optimum DNA Curvature Using a Hybrid Approach Involving an Artificial Neural Network and Genetic Algorithm

Abstract

In the present paper, a hybrid technique involving artificial neural network (ANN) and genetic algorithm (GA) has been proposed for performing modeling and optimization of complex biological systems. In this approach, first an ANN approximates (models) the nonlinear relationship(s) existing between its input and output example data sets. Next, the GA, which is a stochastic optimization technique, searches the input space of the ANN with a view to optimize the ANN output. The efficacy of this formalism has been tested by conducting a case study involving optimization of DNA curvature characterized in terms of the R_L value. Using the ANN-GA methodology, a number of sequences possessing high R_L values have been obtained and analyzed to verify the existence of features known to be responsible for the occurrence of curvature. A couple of sequences have also been tested experimentally. The experimental results validate qualitatively and also near-quantitatively, the solutions obtained using the hybrid formalism. The ANN-GA technique is a useful tool to obtain, ahead of experimentation, sequences that yield high R_L values. The methodology is a general one and can be suitably employed for optimizing any other biological feature.     

Optimization of Process Variables for Lipase Biosynthesis from <Emphasis Type="Italic">Rhizopus oligosporus</Emphasis> NRRL 5905 Using Evolutionary Operation Factorial Design Technique

Extracellular lipase was produced from Rhizopus oligosporus NRRL 5905 through solid state fermentation (SSF). To provide an optimum fermentation conditions for maximum lipase yield, five process variables (temperature, liquid–solid ratio, pH, incubation period and spore concentration) were optimized using evolutionary operation (EVOP) factorial design technique taking into account the interaction between the process variables. Optimization through EVOP resulted in around 3 fold increase in lipase activity (77 U gds⁻¹) at a liquid–solid ratio of 1.5:1, fermentation temperature of 35°C, initial fermentation pH 6, incubation period 5 days and a spore concentration of 10⁸ spores ml⁻¹.     

Biological constraints in algal biotechnology

In the past decade, considerable progress has been made in developing the appropriate biotechnology for microalgal mass cultivation aimed at establishing a new agro-industry. This review points out the main biological constraints affecting algal biotechnology outdoors and the requirements for making this biotechnology economically viable. One of them is the availability of a wide variety of algal species and improved strains that favorably respond to varying environmental conditions existing outdoors. It is thus just a matter of time and effort before a new methodology like genetic engineering can and will be applied in this field as well. The study of stress physiology and adaptation of microalgae has also an important application in further development of the biotechnology for mass culturing of microalgae. In outdoor cultures, cells are exposed to severe changes in light and temperature much faster than the time scale required for the cells to acclimate. A better understanding of those parameters and the ability to rapidly monitor those conditions will provide the growers with a better knowledge on how to optimize growth and productivity. Induction of accumulation of high value products is associated with stress conditions. Understanding the physiological response may help in providing a better production system for the desired product and, at a later stage, give an insight of the potential for genetic modification of desired strains. The potential use of microalgae as part of a biological system for bioremediation/detoxification and wastewater treatment is also associated with growing the cells under stress conditions. Important developments in monitoring and feedback control of the culture behavior through application of on-line chlorophyll fluorescence technique are in progress. Understanding the process associated with those unique environmental conditions may help in choosing the right culture conditions as well as selecting strains in order to improve the efficiency of the biological process.     

Efficient optimization of time-varying inputs in a fed-batch cell culture process using design of dynamic experiments

In cell culture process development, we rely largely on an iterative, one-factor-at-a-time procedure based on experiments that explore a limited process space. Design of experiments (DoE) addresses this issue by allowing us to analyze the effects of process inputs on process responses systematically and efficiently. However, DoE cannot be applied directly to study time-varying process inputs unless an impractically large number of bioreactors is used. Here, we adopt the methodology of design of dynamic experiments (DoDE) and incorporate dynamic feeding profiles efficiently in late-stage process development of the manufacture of therapeutic monoclonal antibodies. We found that, for the specific cell line used in this article, (1) not only can we estimate the effect of nutrient feed amount on various product attributes, but we can also estimate the effect, develop a statistical model, and use the model to optimize the slope of time-trended feed rates; (2) in addition to the slope, higher-order dynamic characteristics of time-trended feed rates can be incorporated in the design but do not have any significant effect on the responses we measured. Based on the DoDE data, we developed a statistical model and used the model to optimize several process conditions. Our effort resulted in a tangible improvement in productivity—compared with the baseline process without dynamic feeding, this optimized process in a 200-L batch achieved a 27% increase in titer and > 92% viability. We anticipate our application of DoDE to be a starting point for more efficient workflows to optimize dynamic process conditions in process development.     

Application of reverse micelle extraction process for amylase recovery using response surface methodology

The effect of different process variables of reverse micelle extraction process like pH, addition of surfactant (AOT) concentration and potassium chloride (KCl) concentration on amylase recovery has been studied and analysed. Solid-state fermentation was used for the production of amylase enzyme. Response surface methodology (RSM) using central composite rotatable design (CCRD) was employed to analyse and optimize the enzyme extraction process. The regression analysis indicates that the effect of AOT concentration, and KCl concentration were significant, whereas the effect of pH was non-significant on enzyme recovery. For the maximum recovery of enzyme, the optimum operating condition for pH, AOT concentration (M) and KCl concentration were 10.43, 0.05 and 1.00, respectively. Under these optimal conditions, the enzyme recovery was 83.16%.     

A mechanism-based ICAT strategy for comparing relative expression and activity levels of glycosidases in biological systems

An activity-based isotope-coded affinity tagging (AB-ICAT) strategy for proteome-wide quantitation of active retaining endoglycosidases has been developed. Two pairs of biotinylated, cleavable, AB-ICAT reagents (light H(8) and heavy D(8)) have been synthesized, one incorporating a recognition element for cellulases and the other incorporating a recognition element for xylanases. The accuracy of the AB-ICAT methodology in quantifying relative glycosidase expression/activity levels in any two samples of interest has been verified using several pairs of model enzyme mixtures where one or more enzyme amounts and/or activities were varied. The methodology has been applied to the biomass-degrading secretomes of the soil bacterium, Cellulomonas fimi, under induction by different polyglycan growth substrates to obtain a quantitative profile of the relative expression/activity levels of individual active retaining endoglycanases per C. fimi cell. Such biological profiles are valuable in understanding the strategies employed by biomass-degrading organisms in exploiting environments containing different biomass polysaccharides. This is the first report on the application of an activity-based ICAT method to a biological system.     

The anaerobic utilisation of cyanide in the presence of sugars by microbial cultures can involve an abiotic process

The degradation of cyanide under anaerobic conditions in the presence of a growing culture of a strain of Klebsiella planticola has been shown to be due to a chemical process dependent upon the presence of a reducing sugar in the medium. The conversion of cyanide to ammonia was independent of any biological factors under these conditions.     

Metalloporphyrins as chemical mimics of cytochrome P-450 systems

Certain synthetic metalloporphyrins have been shown to mimic the in vivo metabolism of some pharmaceuticals. Oxidation, hydroxylation and N-demethylation yielded synthetic metabolites. If found to be general, this lays the foundation of a predictive basis to optimize analog desing of inhibitors with reduced oxidative reactivity, to determine the proclivity of drugs to form biological active metabolites, and provides a convenient methodology for their preparation.

Certain Synthetic metalloporphyrins have been shown to mimic the in vivo metabolism of some pharmaceuticals. Oxidation. hydroxylation and N-demethylation yielded synthetic metabolites. If found to be general, this lays the foundation of a predictive basis to optimize analog design of inhibitors with reduced oxidative reactivity, to determine the proclivity of drugs to form biologically active metabolites, and provides a convenient methodology for their preparation.     

碳纳米管固定化纤维素酶的最佳工艺研究

纤维素酶在环保、医药、食品等领域都具有广泛的应用前景,但由于纤维素酶的生产成本较高,生物活性较低,使得纤维素酶的应用受到了限制。为了寻找一种固定化纤维素酶的方法,使酶可以重复多次使用,首次以多壁碳纳米管为载体固定化纤维素酶,研究功能化的多壁碳纳米管固定化纤维素酶的固定化条件,采用正交试验对酶固定化中的主要条件进行优化,并通过傅里叶变换红外光谱仪对多壁碳纳米管（multiwalled carbon nanotube,MWCNTs）、纤维素酶及固定化纤维素酶的结构进行表征。结果表明,固定化纤维素酶的最佳工艺条件为：酶浓度5 mg·mL-1,温度40 ℃,pH 5.0,固定化时间3 h;通过傅里叶变换红外光谱证实纤维素酶成功固定到多壁碳纳米管上。     

响应面法优化粉被虫草中虫草素的提取工艺

【背景】粉被虫草是民间常用药用真菌,具有抗辐射等多种药理作用,虫草素是其重要的活性物质。【目的】探究粉被虫草中提取虫草素的影响因素,为制取虫草素提供参考。【方法】以虫草素得率为指标,用响应面法优化超声提取工艺。分别考察超声时间、液料比和超声功率对提取效率的影响,在单因素实验基础上进行3因素3水平的响应面分析实验。【结果】最优提取条件为超声时间606 s、液料比45.9:1、超声功率400 W,在此条件下虫草素得率为6.136 mg/g,与模型预测值接近,方程拟合良好。【结论】首次对粉被虫草中虫草素的提取条件进行了研究,将对制取虫草素提供参考,有利于粉被虫草的深度开发利用。     

Evolutionary operation (EVOP) to optimize three-dimensional biological experiments

Evolutionary operation (EVOP) is used as an efficient technique for optimization of three variable experimental parameters using two-level factorial designs with center points. For metabolic function like enzyme synthesis by microorganisms, small amounts of metal ions, surfactants, and vitamins act as inducers. The desired quantities of these chemicals are, however, species dependent and have to be found out or each microorganism. By employing the EVOP technique, the requirements of these chemicals have been optimized for the production of protease by Rhizopus oryzae (RO, IIT KGP). (c) 1993 John Wiley & Sons, Inc.     

Object-oriented biological system integration: a SARS coronavirus example

MOTIVATION: The importance of studying biology at the system level has been well recognized, yet there is no well-defined process or consistent methodology to integrate and represent biological information at this level. To overcome this hurdle, a blending of disciplines such as computer science and biology is necessary. RESULTS: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. The scalability of this object-oriented software engineering approach indicates that we can apply this technology for the integration of large complex biological systems. AVAILABILITY: A navigable web-based version of the system is freely available at http://people.musc.edu/~zhengw/SARS/Software-Process.htm     

Optimization of the Extraction Process and Antioxidant Activity of Polysaccharide Extracted from Centipeda minima

The purpose of this study is to optimize the extraction process and study antioxidant activity of Polysaccharide extracted from Centipeda minima. The Box-Behnken design-response surface methodology was adopted to optimize the extraction process of polysaccharides from Centipeda minima. We purified the crude polysaccharides from Centipeda minima, as well as determined the purity, monosaccharide composition, and molecular weight of the purified fraction. Fourier transform infrared spectrometer (FT-IR) and scanning electron microscopy (SEM) were used to analyze the structural features of the polysaccharides. Further, we investigated the antioxidant activities of different fractions of polysaccharides. Consequently, the results showed that the optimum extraction conditions for polysaccharides were: a liquid-solid ratio of 26 mL/g, extraction temperature of 85.5 °C, and extraction time of 2.4 h. Moreover, the yield of polysaccharides measured under these conditions was close to the predicted value. After purification, we obtained four components of Centipeda minima polysaccharides (CMP). The purity, monosaccharide composition, molecular weight, and structural characteristics of CMP were different, but with similar infrared absorption spectra. CMP exhibited a typical infrared absorption characteristic of a polysaccharide. Besides, CMP displayed good antioxidant activity, with potential to scavenge DPPH radical, hydroxyl radical, and superoxide radical. Therefore, this study provides a reference for future research on the structure and biological activity of CMP, and lays a theoretical foundation for food processing and medicinal development of CMP.     

Inverse drug screens: a rapid and inexpensive method for implicating molecular targets

Identification of gene products that function in some specific process of interest is a common goal in developmental biology. Although use of drug compounds to probe biological systems has a very long history in teratology and toxicology, systematic hierarchical drug screening has not been capitalized upon by the developmental biology community. This "chemical genetics" approach can greatly benefit the study of embryonic and regenerative systems, and we have formalized a strategy for using known pharmacological compounds to implicate specific molecular candidates in any chosen biological phenomenon. Taking advantage of a hierarchical structure that can be imposed on drug reagents in a number of fields such as ion transport, neurotransmitter function, metabolism, and cytoskeleton, any assay can be carried out as a binary search algorithm. This inverse drug screen methodology is much more efficient than exhaustive testing of large numbers of drugs, and reveals the identity of a manageable number of specific molecular candidates that can then be validated and targeted using more expensive and specific molecular reagents. Here, we describe the process of this loss-of-function screen and illustrate its use in uncovering novel bioelectrical and serotonergic mechanisms in embryonic patterning. This technique is an inexpensive and rapid complement to existing molecular screening strategies. Moreover, it is applicable to maternal proteins, and model species in which traditional genetic screens are not feasible, significantly extending the opportunities to identify key endogenous players in biological processes.     

Optimization of the anaerobic treatment of a waste stream from an enhanced oil recovery process

The aim of this work was to optimize the anaerobic treatment of a waste stream from an enhanced oil recovery (EOR) process. The treatment of a simulated waste water containing about 150 mg chemical oxygen demand (COD)/L of total petroleum hydrocarbons (TPH) and the saturation level of CO₂ was evaluated. A two-step anaerobic system was undertaken in the mesophilic temperature range (30-40 °C). The method of evolutionary operation EVOP factorial design was used to optimize pH, temperature and organic loading rate with the target parameters of CO₂ reduction and CH₄ production in the first reactor and TPH removal in the second reactor. The results showed 98% methanogenic removal of CO₂ and CH₄ yield of 0.38 L/gCOD in the first reactor and 83% TPH removal in the second reactor. In addition to enhancing CO₂ and TPH removal and CH₄ production, application of this method showed the degree of importance of the operational variables and their interactive effects for the two reactors in series.