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PubMed2005

Medium optimization by response surface methodology for poly-gamma-glutamic acid production using dairy manure as the basis of a solid substrate.

Dairy manure, supplemented with agro-industrial materials, was used as the solid substrate for high yield of poly-gamma-glutamic acid (gamma-PGA) by Bacillus subtilis CCTCC202048. The solid-state fermentation medium was optimized by response surface methodology. In the first optimization step, a Plackett-Burman design was used to evaluate the influence of related factors. Wheat bran, soybean cake and glutamic acid were found to be more compatible supplement with dairy manure and positively influenced on gamma-PGA production. In the second step, the concentrations of the three supplemental nutrients above were further optimized using a Box-Behnken design. The average gamma-PGA yield (4.70%) in triplicate under optimal conditions was obtained on the laboratory scale, whereas it was 3.58% at compost experiment. These would lay a foundation for lessening the pollution of dairy manure, increasing fertilizer efficiency and exploring a late-model organic fertilizer that retains water and nutrients.

Animals↗

PubMed2007

Codon optimization of Bacillus licheniformis beta-1,3-1,4-glucanase gene and its expression in Pichia pastoris.

Beta-1,3-1,4-glucanase (EC3.2.1.73) as an important industrial enzyme has been widely used in the brewing and animal feed additive industry. To improve expression efficiency of recombinant beta-1,3-1,4-glucanase from Bacillus licheniformis EGW039(CGMCC 0635) in methylotrophic yeast Pichia pastoris GS115, the DNA sequence encoding beta-1,3-1,4-glucanase was designed and synthesized based on the codon bias of P. pastoris, the codons encoding 96 amino acids were optimized, in which a total of 102 nucleotides were changed, the G+C ratio was simultaneously increased from 43.6 to 45.5%. At shaking flask level, beta-1,3-1,4-glucanase activity is 67.9 and 52.3 U ml(-1) with barley beta-glucan and lichenan as substrate, respectively. At laboratory fermentor level, the secreted protein concentration is approximately 250 mg l(-1). The beta-1,3-1,4-glucanase activity is 333.7 and 256.7 U ml(-1) with barley beta-glucan and lichenan as substrate, respectively; however, no activity of this enzyme on cellulose is observed. Compared to the nonoptimized control, expression level of the optimized beta-1,3-1,4-glucanase based on preferred codons in P. pastoris shown a 10-fold higher level. The codon-optimized enzyme was approximately 53.8% of the total secreted protein. The optimal acidity and temperature of this recombinant enzyme were pH 6.0 and 45 degrees C, respectively.

Bacillus↗

PubMed2025

Heterologous expression and optimization of the antimicrobial peptide acidocin 4356 in Komagataella phaffii to target Pseudomonas aeruginosa.

Multidrug-resistant (MDR) pathogens, particularly Pseudomonas aeruginosa, pose a serious global health threat due to their increasing prevalence and limited therapeutic options. Antimicrobial peptides (AMPs) offer promising alternatives to traditional antibiotics, yet their large-scale application remains constrained by high production costs and technical challenges. This research sought to develop a yeast-based system for the cost-efficient synthesis of acidocin 4356 (ACD), an antimicrobial peptide proven effective against P. aeruginosa. A codon-optimized ACD gene was cloned into the pPICZα-A expression vector and integrated into the Komagataella phaffii (formerly Pichia pastoris) GS115 genome. Colony PCR confirmed successful integration, and specific transformants demonstrated expression of the 6 × His-ECS-rACD fusion protein, as verified by SDS-PAGE and dot blot analysis. After Ni-NTA chromatography and enterokinase digestion, rACD was found at ~ 20 kDa instead of 8.3 kDa, suggesting oligomerization or post-translational modifications. Response surface methodology determined the optimal temperature, pH, and methanol concentration for peptide synthesis. Under optimal circumstances (21 °C, pH 6.24, and 1.089% methanol), rACD synthesis increased by 34.12% over baseline conditions (30 °C, pH 6, 1% methanol). AlphaFold structural modeling identified three α-helices in high-confidence regions, implicated in bacterial membrane disruption. Antimicrobial assays demonstrated potent rACD activity against P. aeruginosa, yielding a 58.29% reduction in growth at 150 µg/mL and MIC50 and MIC90 values of 143.04 and 320.64 µg/mL, respectively. These findings underscore K. phaffii as a robust platform for AMP production and highlight rACD's therapeutic potential as an effective agent against MDR P. aeruginosa, warranting further investigation into its clinical and industrial applications. KEY POINTS: • Developing a novel K. phaffii strain for heterologous expression supports efficient rACD peptide production. • Optimized conditions boosted expression yield by 34.12% above the reference fermentation settings. • Recombinant acidocin suppressed Pseudomonas aeruginosa growth by 58%, indicating anti-MDR activity.

Pseudomonas aeruginosa↗

PubMed1998

Recombinant bioprocess optimization for heterologous protein production using two-stage, cyclic fed-batch culture.

A two-stage, cyclic fed-batch bioprocess was designed, and its performance evaluated to improve rice alpha-amylase productivity by the yeast Yarrowia lipolytica SMY2 (MatA, ade1, ura3, xpr2), ATCC 201847, containing a replicative plasmid coding for a rice alpha-amlyase. Transcription of the recombinant gene is controlled by the XPR2 promoter. The first stage (or growth stage) was operated in the fed-batch mode, and the growth medium, designed to maintain a constant high cell density (i.e., 60 g/l), was fed according to a predetermined and preprogrammed optimal feed rate which, in turn, maintained the specific cell growth rate at an optimal value (i.e., 0.1 h-1). Typically, when the volume in the first stage reached a preset value, a portion of culture broth (i.e., 55%) was transferred to the second stage (or production stage). The remaining cells in the growth stage were then fed with fresh growth medium according to the bioprocess control strategy developed, while induction of alpha-amylase expression and its production was taking place in the second stage. The second stage was also operated in the fed-batch mode, and the production medium designed to maintain a constant high cell density and high productivity of heterologous protein was fed at a predetermined and preprogrammed rate, which maintained the specific cell growth rate at an optimal level. The volumetric alpha-amylase productivity achieved (1835 units l-1 h-1) from the two-stage, cyclic fed-batch culture process was twofold higher than that of the fed-batch culture process. The genetic stability of the recombinant strain and the design of optimal media for growth and production stages are also critically important to a successful implementation of the two-stage, cyclic fed-batch process for production of heterologous protein.

Recombinant Proteins↗

PubMed2000

Optimization of culture medium for the continuous cultivation of the microalga Haematococcus pluvialis.

The freshwater microalga Haematococcus pluvialis is one of the best microbial sources of the carotenoid astaxanthin, but this microalga shows low growth rates and low final cell densities when cultured with traditional media. A single-variable optimization strategy was applied to 18 components of the culture media in order to maximize the productivity of vegetative cells of H. pluvialis in semicontinuous culture. The steady-state cell density obtained with the optimized culture medium at a daily volume exchange of 20% was 3.77 x 10(5) cells ml(-1), three times higher than the cell density obtained with Bold basal medium and with the initial formulation. The formulation of the optimal Haematococcus medium (OHM) is (in g l(-1)) KNO3 0.41, Na2HPO4 0.03, MgSO4 x 7H2O 0.246, CaCl2 x 2H2O 0.11, (in mg l(-1)) Fe(III)citrate x H2O 2.62, CoCl2 x 6H2O 0.011, CuSO4 x 5H2O 0.012, Cr2O3 0.075, MnCl2 x 4H2O 0.98, Na2MoO4 x 2H2O 0.12, SeO2 0.005 and (in microg l(-1)]) biotin 25, thiamine 17.5 and B12 15. Vanadium, iodine, boron and zinc were demonstrated to be non-essential for the growth of H. pluvialis. Higher steady-state cell densities were obtained by a three-fold increase of all nutrient concentrations but a high nitrate concentration remained in the culture medium under such conditions. The high cell productivities obtained with the new optimized medium can serve as a basis for the development of a two-stage technology for the production of astaxanthin from H. pluvialis.

Chlorophyta↗

PubMed2003

Optimal HIV treatment by maximising immune response.

We present an optimal control model of drug treatment of the human immunodeficiency virus (HIV). Our model is based upon ordinary differential equations that describe the interaction between HIV and the specific immune response as measured by levels of natural killer cells. We establish stability results for the model. We approach the treatment problem by posing it as an optimal control problem in which we maximise the benefit based on levels of healthy CD4+ T cells and immune response cells, less the systemic cost of chemotherapy. We completely characterise the optimal control and compute a numerical solution of the optimality system via analytic continuation.

Algorithms↗

PubMed1997

On the non-existence of an optimal migration rate.

We show that an optimal migration rate may not exist in a population distributed over an infinite number of individual living sites if empty sites occur. This is the case when the mean number of offspring per individual mu is finite. We make the assumption of uniform migration to other sites whose rate is determined by the parent's genotype or the offspring's genotype at a single locus in a diploid hermaphrodite population undergoing random mating. In both cases, for mu small enough, any population at fixation would go to extinction. Moreover, in the latter case, for intermediate values of mu, the only fixation state that could resist the invasion of any mutant would lead the population to extinction. These are the two conditions for the non-existence of an optimal migration rate. They become less stringent as the cost for migration expressed by a coefficient of selection 1-beta becomes larger, that is closer to 1. The results are obtained assuming that the allele at fixation is either nondominant or dominant. Although the optimal migration rate is the same in both cases when it exists, the optimality properties may differ.

Alleles↗

PubMed2002

Radiation dose optimization in coronary angiography and percutaneous coronary intervention (PCI). I. Experimental studies.

The objectives of this study were to evaluate the influence on image quality and dose to the patient and operator of various equipment settings for percutaneous coronary intervention (PCI), and to optimize the set-up. With an Alderson phantom, different settings, such as projection, protective screens, filtration, image intensifier size and collimation, were evaluated. Kerma-area product (KAP) was recorded as a measure of patient dose and scattered radiation was measured with an ionization chamber. Effective dose for a standardized PCI procedure was measured with thermoluminescent dosimeters inside the phantom. Image quality was evaluated with a contrast-detail phantom. Based on these findings, the equipment set-up was optimized to a low fluoroscopy dose rate with a sufficient image quality. Several operating parameters affected dose, particularly scattered radiation. The optimization reduced the fluoroscopy KAP rate from 44 to 16 mGy cm(2)/s using 15 cm of acrylic. The effective dose was reduced from 13 to 4.6 mSv for a standardized PCI procedure. Radiation dose to patient and operator in PCI is heavily dependent on both equipment set-up and operating parameters which can be influenced by the operator. With a careful optimization, a large reduction of radiation dose is possible.

Angioplasty, Balloon, Coronary↗

PubMed2001

[Optimal thrombolysis].

Thrombolytic therapy is an established reperfusion strategy in acute myocardial infarction with proven long-term survival benefit. New thrombolytic agents including reteplase, lanoteplase, and tenecteplase have been developed to optimize thrombolytic therapy. With respect to efficacy the new thrombolytic agents show mortality equivalent to front-loaded alteplase, the present gold standard of thrombolytic therapy. With respect to ease of application there are advantages because third generation agents can be given as a single or double bolus instead of a bolus followed by an infusion. The most promising strategy to optimize coronary thrombolysis seems to be the combination of thrombolytic agents in reduced dose and GP IIb/IIIa blockers in full dose. The corresponding clinical trials (TIMI-14, SPEED, and INTRO-AMI) have also shown that there is an evolution in the surrogate end points for an optimal thrombolysis. In the past, optimal thrombolysis was associated with an open infarct-related coronary artery. A few years ago it was realized that TIMI-3 flow in the epicardial coronary artery was associated with the best results. Presently, normal myocardial microcirculation is regarded an additional prerequisite for further reduced mortality in acute myocardial infarction.

Abciximab↗

PubMed2004

Prehension synergies during nonvertical grasping, II: Modeling and optimization.

This study examines various optimization criteria as potential sources of constraints that eliminate (or at least reduce the degree of) mechanical redundancy in prehension. A model of nonvertical grasping mimicking the experimental conditions of Pataky et al. (current issue) was developed and numerically optimized. Several cost functions compared well with experimental data including energylike functions, entropylike functions, and a ''motor command'' function. A tissue deformation function failed to predict finger forces. In the prehension literature, the ''safety margin'' (SM) measure has been used to describe grasp quality. We demonstrate here that the SM is an inappropriate measure for nonvertical grasps. We introduce a new measure, the ''generalized safety margin'' (GSM), which reduces to the SM for vertical and two-digit grasps. It was found that a close-to-constant GSM accounts for many of the finger force patterns that are observed when grasping an object oriented arbitrarily with respect to the gravity field. It was hypothesized that, when determining finger forces, the CNS assumes that a grasped object is more slippery than it actually is. An ''operative friction coefficient'' of approximately 30% of the actual coefficient accounted for the offset between experimental and optimized data. The data suggest that the CNS utilizes an optimization strategy when coordinating finger forces during grasping.

Algorithms↗

PubMed2006

The main sequence of saccades optimizes speed-accuracy trade-off.

In primates, it is well known that there is a consistent relationship between the duration, peak velocity and amplitude of saccadic eye movements, known as the 'main sequence'. The reason why such a stereotyped relationship evolved is unknown. We propose that a fundamental constraint on the deployment of foveal vision lies in the motor system that is perturbed by signal-dependent noise (proportional noise) on the motor command. This noise imposes a compromise between the speed and accuracy of an eye movement. We propose that saccade trajectories have evolved to optimize a trade-off between the accuracy and duration of the movement. Taking a semi-analytical approach we use Pontryagin's minimum principle to show that there is an optimal trajectory for a given amplitude and duration; and that there is an optimal duration for a given amplitude. It follows that the peak velocity is also fixed for a given amplitude. These predictions are in good agreement with observed saccade trajectories and the main sequence. Moreover, this model predicts a small saccadic dead-zone in which it is better to stay eccentric of target than make a saccade onto target. We conclude that the main sequence has evolved as a strategy to optimize the trade-off between accuracy and speed.

Animals↗

PubMed2006

Simulating discrete and rhythmic multi-joint human arm movements by optimization of nonlinear performance indices.

An optimization approach applied to mechanical linkage models is used to simulate human arm movements. Predicted arm trajectories are the result of minimizing a nonlinear performance index that depends on kinematic or dynamic variables of the movement. A robust optimization algorithm is presented that computes trajectories which satisfy the necessary conditions with high accuracy. It is especially adapted to the analysis of discrete and rhythmic movements. The optimization problem is solved by parameterizing each generalized coordinate (e.g., joint angular displacement) in terms of Jacobi polynomials and Fourier series, depending on whether discrete or rhythmic movements are considered, combined with a multiple shooting algorithm. The parameterization of coordinates has two advantages. First, it provides an initial guess for the multiple shooting algorithm which solves the optimization problem with high accuracy. Second, it leads to a low dimensional representation of discrete and rhythmic movements in terms of expansion coefficients. The selection of a suitable feature space is an important prerequisite for comparison, recognition and classification of movements. In addition, the separate computational analysis of discrete and rhythmic movements is motivated by their distinct neurophysiological realizations in the cortex. By investigating different performance indices subject to different boundary conditions, the approach can be used to examine possible strategies that humans adopt in selecting specific arm motions for the performance of different tasks in a plane and in three-dimensional space.

Algorithms↗

PubMed2002

Model-based optimization of viral capsid protein production in fed-batch culture of recombinant Escherichia coli.

An optimized fed-batch cultivation process for the production of the polyoma virus capsid protein VP1 in recombinant Escherichia coli BL21 bacteria is presented. The optimization procedure maximizing the amount of desired protein is based on a mathematical model. The model distinguishes an initial cell growth phase from a protein production phase initiated by inducer injection. A new approach to model the target protein formation rate was elaborated, where product formation is primarily dependent on the specific biomass growth rate. Lower growth rates led to higher specific protein concentrations. The model was identified from a series of fed-batch experiments designed for parameter identification purposes and possesses good prediction quality. Then the model was used to determine optimal open-loop control profiles by manipulating the substrate feed rates in both phases as well as the induction time. Feed-rate optimization has been solved using Pontryagin's maximum principle. The solution was validated experimentally. A significant improvement of the process performance index was achieved.

Journal Article↗

PubMed2005

Application of a mathematical model and Differential Evolution algorithm approach to optimization of bacteriocin production by Lactococcus lactis C7.

The effect of pH and temperature on cell growth and bacteriocin production in Lactococcus lactis C7 was investigated in order to optimize the production of bacteriocin. The study showed that the bacteriocin production was growth-associated, but declined after reaching the maximum titer. The decrease of bacteriocin was caused by a cell-bound protease. Maximum bacteriocin titer was obtained at pH 5.5 and at 22 degrees C. In order to obtain a global optimized solution for production of bacteriocin, the optimal temperature for bacteriocin production was further studied. Mathematical models were developed for cell growth, substrate consumption, lactic acid production and bacteriocin production. A Differential Evolution algorithm was used both to estimate the model parameters from the experimental data and to compute a temperature profile for maximizing the final bacteriocin titer and bacteriocin productivity. This simulation showed that maximum bacteriocin production was obtained at the optimal temperature profile, starting at 30 degrees C and terminating at 22 degrees C, which was validated by experiment. This temperature profile yielded 20% higher maximum bacteriocin productivity than that obtained at a constant temperature of 22 degrees C, although the total amount of bacteriocin obtained was slightly decreased.

Algorithms↗

PubMed2005

QSPR modeling of the water solubility of diverse functional aliphatic compounds by optimization of correlation weights of local graph invariants.

The optimization of correlation weights scheme was used to model the water solubility (ln S) of diverse functional aliphatic compounds (n = 193). The optimized descriptor formulated based on the data of a training set (n = 96) generated statistically acceptable relations for the training set (r2 = 0.987), test set (n = 97; r2 = 0.986) and combined set (r2 = 0.987). When the relation of ln S values with the optimized molecular descriptor formulated based on the data of the training set was used for the calculation of ln S values of the training set, r(pred)2 value was found to be satisfactory (0.988), which is indicative of the predictive potential of the scheme. The results indicate the promising potential of the optimization of correlation weights scheme in modeling studies.

Alcohols↗

PubMed2003

Optimizing outcomes with antimicrobial therapy through pharmacodynamic profiling.

In patients with infection, improving the probability of positive treatment outcomes depends on optimizing the interactions between the host, pathogen, and drug. In this setting, optimal regimens must be utilized which not only maximize effectiveness in a specific patient, but also minimize the development of microbial resistance. The probability of achieving a specifically targeted antimicrobial exposure can be assessed using Monte Carlo simulation, a technique which integrates an agent's in vitro potency distribution (i.e., minimum inhibitory concentrations [MICs]) with the pharmacokinetic profile. The targeted pharmacodynamic parameters assessed by this technique include the ratio of peak concentration (C(max)) to MIC (C(max) : MIC); the ratio of the area under the plasma concentration-time curve (AUC) to MIC (AUC : MIC), and the time the drug concentration exceeds the MIC (T > MIC). Some antimicrobials, e.g., the aminoglycosides, are most effective/bactericidal when they have a high C(max) : MIC ratio; others, e.g., the fluoroquinolones, are more effective when the AUC : MIC ratio is high. In both of these scenarios, organism eradication is concentration-dependent, and the therapeutic goal is to maximize drug exposure. Like the fluoroquinolones, the efficacy of telithromycin, a newly developed ketolide, is most related to the AUC : MIC ratio. Outcome for other agents, such as the beta-lactams, is best predicted by the T > MIC; in this case, organism eradication is time-dependent, and the therapeutic goal is to optimize the duration of antimicrobial exposure. This article discusses how the use of currently available antimicrobials can be optimized through an appreciation of pharmacodynamic profiling.

Anti-Bacterial Agents↗

PubMed2003

Optimized polymerase chain reaction-based single-strand conformation polymorphism analysis of p53 gene applied to Bulgarian patients with invasive breast cancer.

During the last few decades a substantial amount of evidence has accumulated proving that the abrogation of the normal p53 pathway is a critical step in the initiation and progression of tumors. Decoding the genetic mechanisms involved in carcinogenesis requires screening for consistent genetic tumor alterations, including those concerning the p53 gene. Thus, practical, efficient, and inexpensive techniques for accurate determination of p53 mutational status are needed. Polymerase chain reaction/single-strand conformation polymorphism (PCR-SSCP) analysis is considered to be a useful tool to investigate the role of the p53 gene in the development and progression of human cancers. The sensitivity of the method can be increased considerably by varying the experimental conditions. Here we demonstrate a scheme of PCR-SSCP optimization for detection of p53 gene mutations of patients with various cancers. Optimal conditions for PCRSSCP of p53 exons 4-9 are reported. Such PCR-SSCP optimization could allow an increase in the sensitivity and reproducibility of the technique and facilitates screening of large series of patients to assess the clinical significance of p53 mutations in human cancers. Using the optimized PCR-SSCP analysis we screened Bulgarian patients with invasive breast cancer for p53 gene mutations and registered a 33.33% frequency of mutations. To date, there are no data concerning the p53 status of Bulgarian breast cancer patients. Screening for p53 gene mutations enables an accurate and routine determination of the p53 status of patients with cancer and may be applied in clinical oncology to cancer diagnosis, prediction of prognosis and response to treatment.

Base Sequence↗

PubMed2004

Optimization of cell density and dilution rate in Pichia pastoris continuous fermentations for production of recombinant proteins.

This paper provides an approach for optimizing the cell density (Xc) and dilution rate (D) in a chemostat for a Pichia pastoris continuous fermentation for the extracellular production of a recombinant protein, interferon tau (INF-tau). The objective was to maximize the volumetric productivity (Q, mg INF-tau l(-1) h(-1)), which was accomplished using response surface methodology (RSM) to model the response of Q as a function of Xc and D within the ranges 150< or = Xc < or =450 g cells (wet weight) l(-1) and 0.1 microm< or = D< or =0.9 microm (microm=0.0678 h(-1), the maximum specific growth rate obtained from a fed-batch phase controlled with a methanol sensor). The methanol and medium feed rates that resulted in the desired Xc and D were determined based on the mass balance. From the RSM model, the optimal Xc and D were 328.9 g l(-1) and 0.0333 h(-1) for a maximum Q of 2.73 mg l(-1) h(-1). The model of specific production rate (rho, mg INF-tau g(-1) cells h(-1)) was also established and showed the optimal Xc 287.7 g l(-1) and D=0.0361 h(-1) for the maximum rho (predicted to be 8.92 x 10(-3) mg(-1) g(-1) h(-1)). The methanol specific consumption rate (nu, g methanol g(-1) cells h(-1)) was calculated and shown to be independent of the cell density. The relationship between nu and mu (specific growth rate) was the same as that discovered from fed-batch fermentations of the same strain. The approach developed in this study is expected to be applicable to the optimization of continuous fermentations by other microorganisms.

Biomass↗