Simplex‐based optimization of numerical and categorical inputs in early bioprocess development: Case studies in HT chromatography

Bioprocess development studies often involve the investigation of numerical and categorical inputs via the adoption of Design of Experiments (DoE) techniques. An attractive alternative is the deployment of a grid compatible Simplex variant which has been shown to yield optima rapidly and consistently. In this work, the method is combined with dummy variables and it is deployed in three case studies wherein spaces are comprised of both categorical and numerical inputs, a situation intractable by traditional Simplex methods. The first study employs in silico data and lays out the dummy variable methodology. The latter two employ experimental data from chromatography based studies performed with the filter‐plate and miniature column High Throughput (HT) techniques. The solute of interest in the former case study was a monoclonal antibody whereas the latter dealt with the separation of a binary system of model proteins. The implemented approach prevented the stranding of the Simplex method at local optima, due to the arbitrary handling of the categorical inputs, and allowed for the concurrent optimization of numerical and categorical, multilevel and/or dichotomous, inputs. The deployment of the Simplex method, combined with dummy variables, was therefore entirely successful in identifying and characterizing global optima in all three case studies. The Simplex‐based method was further shown to be of equivalent efficiency to a DoE‐based approach, represented here by D‐Optimal designs. Such an approach failed, however, to both capture trends and identify optima, and led to poor operating conditions. It is suggested that the Simplex‐variant is suited to development activities involving numerical and categorical inputs in early bioprocess development.     

The simplex algorithm for the rapid identification of operating conditions during early bioprocess development: case studies in FAb' precipitation and multimodal chromatography

This study describes a data-driven algorithm as a rapid alternative to conventional Design of Experiments (DoE) approaches for identifying feasible operating conditions during early bioprocess development. In general, DoE methods involve fitting regression models to experimental data, but if model fitness is inadequate then further experimentation is required to gain more confidence in the location of an optimum. This can be undesirable during very early process development when feedstock is in limited supply and especially if a significant percentage of the tested conditions are ultimately found to be sub-optimal. An alternative approach involves focusing solely upon the feasible regions by using the knowledge gained from each condition to direct the choice of subsequent test locations that lead towards an optimum. To illustrate the principle, this study describes the application of the Simplex algorithm which uses accumulated knowledge from previous test points to direct the choice of successive conditions towards better regions. The method is illustrated by two case studies; a two variable precipitation example investigating how salt concentration and pH affect FAb' recovery from E. coli homogenate and a three-variable chromatography example identifying the optimal pH and concentrations of two salts in an elution buffer used to recover ovine antibody bound to a multimodal cation exchange matrix. Two-level and face-centered central composite regression models were constructed for each study and statistical analysis showed that they provided a poor fit to the data, necessitating additional experimentation to confirm the robust regions of the search space. By comparison, the Simplex algorithm identified a good operating point using 50% and 70% fewer conditions for the precipitation and chromatography studies, respectively. Hence, data-driven approaches have significant potential for early process development when material supply is at a premium.     

Genetic mutation analysis at early stages of cell line development using next generation sequencing

A central goal for most biopharmaceutical companies is to reduce the development timeline to reach clinical proof of concept. This objective requires the development of tools that ensure the quality of biotherapeutic material destined for the clinic. Recent advances in high throughput protein analytics provide confidence in our ability to assess productivity and product quality attributes at early stages of cell line development. However, one quality attribute has, until recently, been absent from the standard battery of analytical tests facilitating informed choices early in cell line selection: genetic sequence confirmation. Techniques historically used for mutation analysis, such as detailed mass spectrometry, have limitations on the sample number and turnaround times making it less attractive at early stages. Thus, we explored the utility of Next‐Generation Sequencing (NGS) as a solution to address these limitations. Amplicon sequencing is one such NGS technique that is robust, rapid, sensitive, and amenable to multiplexing, all of which are essential attributes for our purposes. Here we report a NGS method based upon amplicon sequencing that has been successfully incorporated into our cell line development workflow alongside other high‐throughput protein analytical assays. The NGS method has demonstrated its value by identifying at least one Chinese hamster ovary (CHO) clone expressing a variant form of the biotherapeutic in each of the four clinical programs in which it has been utilized. We believe this sequence confirmation method is essential to safely accelerating the time to clinical proof of concept of biotherapeutics, and guard against delays related to sequence mutations. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:813–817, 2016     

Influence of Phonon Scattering on Exciton and Charge Diffusion in Polymer‐Fullerene Solar Cells

Thermally activated transport and phonon scattering in P3HT:PCBM (poly(3‐hexylthiophene‐2,5‐diyl):[6,6]‐phenylC61‐butyric acid methyl ester) bulk heterojunction (BHJ) organic solar cells is studied via temperature‐dependent external‐quantum‐efficiency (EQE) spectroscopy. The hopping barriers for combined exciton and charge transport are balanced for the individual blended materials in a sample, which possesses a blending ratio and a morphology that give rise to a maximal power‐conversion efficiency. Increasing the PCBM weight fraction leads to a reduction of exciton hopping barriers in PCBM, while for P3HT exciton hopping barriers remain constant. This reduction of PCBM exciton hopping barriers is attributed to a higher PCBM crystallinity in the PCBM‐rich solar cell as compared to the BHJ with the optimized blending ratio. The morphology‐dependent difference in exciton hopping activation energies between P3HT and PCBM is attributed to a higher impact of phonon scattering in P3HT than in PCBM, as concluded from the much stronger decrease of P3HT‐related temperature‐dependent external quantum efficiencies above room temperature in the PCBM‐rich BHJ solar cell. All EQE data of P3HT:PCBM‐based BHJ solar cells is modeled consistently over a broad temperature range by a simple analytical expression involving temperature activation and phonon scattering, without the need to distinguish two separate hopping regimes.     

Protein social behavior makes a stronger signal for partner identification than surface geometry

Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico‐chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross‐docking study leads to a sharp identification of its cellular/true/native partner(s). We define a sociability index, or S‐index, reflecting whether a protein likes or not to pair with other proteins. Formally, we propose a suitable normalization function that accounts for protein sociability and we combine it with a simple interface‐based (ranking) score to discriminate partners from non‐interactors. We show that sociability is an important factor and that the normalization permits to reach a much higher discriminative power than shape complementarity docking scores. The social effect is also observed with more sophisticated docking algorithms. Docking conformations are evaluated using experimental binding sites. These latter approximate in the best possible way binding sites predictions, which have reached high accuracy in recent years. This makes our analysis helpful for a global understanding of partner identification and for suggesting discriminating strategies. These results contradict previous findings claiming the partner identification problem being solvable solely with geometrical docking. Proteins 2016; 85:137–154. © 2016 Wiley Periodicals, Inc.     

Development of a flow‐injection analysis system with fluorescence detection for gatifloxacin determination in organized medium

This work reports the development and optimization of a flow injection analysis system with fluorescence detection (FIA–FLUO) for gatifloxacin (GFX) determination in organized medium. The analytical system was based on the enhanced fluorescence of gatifloxacin in micellar medium containing sodium dodecyl sulfate (SDS) at pH 6.0. The influence of physical (carrier flow rate, sample volume and volume of reaction coil) and chemical (pH, concentration of buffer and concentration of SDS) parameters that could affect the performance of the FIA system was evaluated in order to reach optimum conditions in terms of sensitivity and analytical throughput. Under optimized conditions, the FIA–FLUO system allowed the injection of 40 samples per hour with a limit of quantification of 72 µg/L and a RSD of 3.5% at 0.20 mg/L. Real samples of commercial pharmaceutical formulations containing GFX were analyzed, and no statistical difference was observed between the results obtained using the developed system and those obtained using the reference method based on high‐performance liquid chromatography with UV detection. Copyright © 2014 John Wiley & Sons, Ltd.     

Calibration of parameters in Dynamic Energy Budget models using Direct-Search methods

Dynamic Energy Budget (DEB) theory aims to capture the quantitative aspects of metabolism at the individual level, for all species. The parametrization of a DEB model is based on information obtained through the observation of natural populations and experimental research. Currently the DEB toolbox estimates these parameters using the Nelder–Mead Simplex method, a derivative-free direct-search method. However, this procedure presents some limitations regarding convergence and how to address constraints. Framed in the calibration of parameters in DEB theory, this work presents a numerical comparison between the Nelder–Mead Simplex method and the SID-PSM algorithm, a Directional Direct-Search method for which convergence can be established both for unconstrained and constrained problems. A hybrid version of the two methods, named as Simplex Directional Direct-Search, provides a robust and efficient algorithm, able to solve the constrained optimization problems resulting from the parametrization of the biological models.

     

Design of affinity membrane chromatographic columns

A method for affinity membrane column design, based on the analytical solution of the Thomas model for frontal analysis in membrane column adsorption, was developed. The method permits to find the operating conditions to reach a 93.5% of the column capacity as operating capacity, using a sharpness restriction for the system breakthrough curve. The solution of the model is presented in a graphic form and can be used in a wide range of operational conditions, provided that four design restrictions are fulfilled. The application of the method was illustrated using experimental data and a simple procedure. The implications of the results on the design and optimiztion of affinity membrane chromatographic columns are discussed.     

Stochastic Approximation Boosting for Incomplete Data Problems

Summary Boosting is a powerful approach to fitting regression models. This article describes a boosting algorithm for likelihood‐based estimation with incomplete data. The algorithm combines boosting with a variant of stochastic approximation that uses Markov chain Monte Carlo to deal with the missing data. Applications to fitting generalized linear and additive models with missing covariates are given. The method is applied to the Pima Indians Diabetes Data where over half of the cases contain missing values.     

Wheat leaf lipids during heat stress: I. High day and night temperatures result in major lipid alterations

Understanding how wheat (Triticum aestivum L.) plants under high temperature (HT) regulate lipid composition is critical to developing climate‐resilient varieties. We measured 165 glycerolipids and sterol derivatives under optimum and high day and night temperatures in wheat leaves using electrospray ionization‐tandem mass spectrometry. Levels of polar lipid fatty acyl chain unsaturation were lower in both heat‐tolerant genotype Ventnor and susceptible genotype Karl 92 under HT, compared with optimum temperature. The lower unsaturation was predominantly because of lower levels of 18:3 acyl chains and higher levels of 18:1 and 16:0 acyl chains. Levels of 18:3‐containing triacylglycerols increased threefold/more under HT, consistent with their possible role in sequestering fatty acids during membrane lipid remodelling. Phospholipids containing odd‐numbered or oxidized acyl chains accumulated in leaves under HT. Sterol glycosides (SG) and 16:0‐acylated sterol glycosides (ASG) were higher under HT than optimum temperatures. Ventnor had lower amounts of phospholipids with oxidized acyl chains under HT and higher amounts of SG and 16:0‐ASG than Karl 92. Taken together, the data demonstrate that wheat leaf lipid composition is altered by HT, in which some lipids are particularly responsive to HT, and that two wheat genotypes, chosen for their differing physiological responses to HT, differ in lipid profile under HT.     

Non‐Fullerene Acceptor‐Based Bulk Heterojunction Polymer Solar Cells: Engineering the Nanomorphology via Processing Additives

The performance of bulk heterojunction solar cells made from blends of a non‐fullerene acceptor, N,N′‐bis(2‐ethylhexyl)‐2,6‐bis(5″‐hexyl‐[2,2′;5′,2″]terthiophen‐5yl)‐1,4,5,8‐naphthalene diimide (NDI‐3TH), and poly(3‐hexylthiophene) (P3HT) donor is enhanced 10‐fold by using a processing additive in conjunction with an electron‐blocking and a hole‐blocking buffer layers. The power conversion efficiency of P3HT:NDI‐3TH solar cells improves from 0.14% to 1.5% by using a processing additive (1,8‐diiodooctane) at an optimum concentration of 0.2 vol%, which is far below the 2‐3 vol% optimum concentrations found in polymer/fullerene systems. TEM and AFM imaging show that the size and connectivity of the NDI‐3TH domains in the phase‐separated P3HT:NDI‐3TH blends vary strongly with the concentration of the processing additive. These results demonstrate, for the first time, that processing additives can be effective in the optimization of the morphology and performance of bulk heterojunction polymer solar cells based on non‐fullerene acceptors.     

Charge Carrier Dynamics in a Ternary Bulk Heterojunction System Consisting of P3HT,Fullerene, and a Low Bandgap Polymer

The photoresponse of P3HT:PC₆₁BM based organic solar cells can be enhanced by blending the bulk heterojunction with the low band gap polymer Si‐ PCPDTBT. Organic solar cells containing the resulting ternary blend as the photoactive layer deliver short circuit currents of up to 15.5 mA cm^?2. Morphological studies show modest phase separation without the perturbation of the crystallinity of the P3HT:PC₆₁BM matrix, in accordance with the measured acceptable fill factors. Picosecond time‐resolved pump‐probe spectroscopy reveals that the sensitization of P3HT:PC₆₁BM with Si‐PCPDTBT involves the transfer of photogenerated positive polarons from the low band gap polymer to P3HT within few hundreds of picoseconds. Intensity dependent experiments in combination with global fitting show that the charge transfer from Si‐PCPDTBT to P3HT competes with non‐geminate charge carrier recombination of the holes in the Si‐PCPDTBT phase with electrons in the PC₆₁BM phase, both processes being of diffusive nature. At excitation densities corresponding to steady state conditions under one sun, modelling predicts hole transfer efficiencies exceeding 90%, in accordance with IQE measurements. At higher pump intensities, bimolecular recombination suppresses the hole transfer process effectively.     

Alterations in wheat pollen lipidome during high day and night temperature stress

Understanding the adaptive changes in wheat pollen lipidome under high temperature (HT) stress is critical to improving seed set and developing HT tolerant wheat varieties. We measured 89 pollen lipid species under optimum and high day and/or night temperatures using electrospray ionization‐tandem mass spectrometry in wheat plants. The pollen lipidome had a distinct composition compared with that of leaves. Unlike in leaves, 34:3 and 36:6 species dominated the composition of extraplastidic phospholipids in pollen under optimum and HT conditions. The most HT‐responsive lipids were extraplastidic phospholipids, phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol, phosphatidic acid, and phosphatidylserine. The unsaturation levels of the extraplastidic phospholipids decreased through the decreases in the levels of 18:3 and increases in the levels of 16:0, 18:0, 18:1, and 18:2 acyl chains. PC and PE were negatively correlated. Higher PC:PE at HT indicated possible PE‐to‐PC conversion, lower PE formation, or increased PE degradation, relative to PC. Correlation analysis revealed lipids experiencing coordinated metabolism under HT and confirmed the HT responsiveness of extraplastidic phospholipids. Comparison of the present results on wheat pollen with results of our previous research on wheat leaves suggests that similar lipid changes contribute to HT adaptation in both leaves and pollen, though the lipidomes have inherently distinct compositions.     

Sensitive detection of sodium cromoglycate with glutathione‐capped CdTe quantum dots as a novel fluorescence probe

A sensitive and simple analytical strategy for the detection of sodium cromoglycate (SCG) has been established based on a readily detectable fluorescence quenching effect of SCG for glutathione‐capped (GSH‐capped) CdTe quantum dots (QDs). The fluorescence of GSH‐capped CdTe QDs could be efficiently quenched by SCG through electron transfer from GSH‐capped CdTe QDs to SCG. Under optimum conditions, the response was linearly proportional to the concentration of SCG between 0.6419 and 100 µg/mL, with a correlation coefficient (R) of 0.9964; the detection limit (3δ/K) was 0.1926 µg/mL. The optimum conditions and the influence of coexisting foreign substances on the reaction were also investigated. The very effective and simple method reported here has been successfully applied to the determination of SCG in synthetic and real samples. It is believed that the established approach could have good prospects for application in the fields of clinical diseases diagnosis and treatment. Copyright © 2015 John Wiley & Sons, Ltd.     

PATTERNS OF INTERSPECIFIC INTERACTIONS IN THE ULVA‐DOMINATED INTERTIDAL COMMUNITY IN A SOUTHERN COAST OF KOREA

The reproductive success of marine species with external fertilization depends on environmental conditions during gamete release. There is special interest presently in whether water motion causes sperm limitation under natural conditions. We investigated gamete release of Fucus vesiculosus from an exposed shore to ascertain: 1) when gametes are released during the tidal cycle, 2) when fertilization occurs, and 3) what the natural sperm:egg ratios are. Water samples were collected and concentrated over five minutes every half hour off Pemaquid Point, ME from three replicate sites within each of two locations using a pump‐filter device. Immunofluorescence microscopy revealed that gamete release occurred only on the two calmest spring tides. Sperm became present in the water column at the same time as oogonia (30 min^?1 h prior to high tide [HT]) and reached peak concentration at exactly HT. The sperm:egg ratio was 76:1 on 8 Oct 1999 and 21:1 on 8 Nov 1999 at exactly 30 min prior to HT and dropped sharply after HT. Gametes continued to be collected for several hours after HT but analysis of pronuclear position in aceto‐iron‐hematoxylin stained eggs revealed that all fertilization occurred at approximately HT. We modelled the total number of days when reproduction was possible using these results and wind and wave data from the National Data Buoy Center. Our research provides evidence that gamete release by F. vesiculosus occurs at slack HT on calm days and that sperm are not a limiting factor in fertilization for this species.     

纤维素酶解-超声偶联法提取葛根中总异黄酮的工艺优化

采用酶解-超声偶联新工艺对葛根中总异黄酮提取进行优化,以提高其收率.在单因素试验的基础上,利用Box-Behnken响应面试验设计,以蒸馏水作为提取溶剂,对温度、酶浓度、时间进行三因素三水平的试验设计优化.结果表明最佳提取工艺条件为:温度34℃、酶浓度0.63 mg/mL、时间62 min.在此条件下,葛根总异黄酮提取率为7.10％,与预测值的相对误差为0.34％.酶解-超声偶联工艺是一种新型、快速、有效的总黄酮提取方法.     

A novel analytical ultracentrifugation based approach to the low resolution structure of gum arabic

Under investigation are the structural properties of gum arabic, an industrially important biopolymer for use as a stabilizer or in drug delivery, using Analytical Ultracentrifugation—a well‐established, matrix‐free probe for macromolecular size and shape. These results are combined with chromatographically‐coupled methods (multi‐angle light scattering, differential press imbalance viscometry) to provide a global analysis of its structure in varying ionic strength conditions. This analysis indicates that gum Arabic may have a compact, elliptical structure in solution, the significance of which for biotechnological use is indicated. This modelling method can be applied to other biopolymers and synthetic polymers. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 618–625, 2016.     

Reliable HPLC separation,vibrational circular dichroism spectra,and absolute configurations of isoborneol enantiomers

Resolution of chiral compounds has played an important role in the pharmaceutical field, involving detailed studies of pharmacokinetics, physiological, toxicological, and metabolic activities of enantiomers. Herein, a reliable method by high‐performance liquid chromatography (HPLC) coupled with an optical rotation detector was developed to separate isoborneol enantiomers. A cellulose tris(3, 5‐dimethylphenylcarbamate)‐coated chiral stationary phase showed the best separation performance for isoborneol enantiomers in the normal phase among four polysaccharide chiral packings. The effects of alcoholic modifiers and column temperature were studied in detail. Resolution of the isoborneol racemate displayed a downward trend along with an increase in the content of ethanol and column temperature, indicating that less ethanol in the mobile phase and lower temperature were favorable to this process. Moreover, two isoborneol enantiomers were obtained via a semipreparative chiral HPLC technique under optimum conditions, and further characterized by analytical HPLC, and experimental and calculated vibrational circular dichroism (VCD) spectroscopy, respectively. The solution VCD spectrum of the first‐eluted component was consistent with the Density Functional Theory (DFT) calculated pattern based on the SSS configuration, indicating that this enantiomer should be (1S , 2S , 4S )‐(+)‐isoborneol. Briefly, these results have provided reliable information to establish a method for analysis, preparative separation, and absolute configuration of chiral compounds without typical chromophoric groups.     

A linear programming approach for identifying a consensus sequence on DNA sequences

MOTIVATION: Maximum-likelihood methods for solving the consensus sequence identification (CSI) problem on DNA sequences may only find a local optimum rather than the global optimum. Additionally, such methods do not allow logical constraints to be imposed on their models. This study develops a linear programming technique to solve CSI problems by finding an optimum consensus sequence. This method is computationally more efficient and is guaranteed to reach the global optimum. The developed method can also be extended to treat more complicated CSI problems with ambiguous conserved patterns. RESULTS: A CSI problem is first formulated as a non-linear mixed 0-1 optimization program, which is then converted into a linear mixed 0-1 program. The proposed method provides the following advantages over maximum-likelihood methods: (1) It is guaranteed to find the global optimum. (2) It can embed various logical constraints into the corresponding model. (3) It is applicable to problems with many long sequences. (4) It can find the second and the third best solutions. An extension of the proposed linear mixed 0-1 program is also designed to solve CSI problems with an unknown spacer length between conserved regions. Two examples of searching for CRP-binding sites and for FNR-binding sites in the Escherichia coli genome are used to illustrate and test the proposed method. AVAILABILITY: A software package, Global Site Seer for the Microsoft Windows operating system is available by http://www.iim.nctu.edu.tw/~cjfu/gss.htm     

Development and evaluation of an electromagnetic hypersensitivity questionnaire for Japanese people

The purpose of the present study was to evaluate the validity and reliability of a Japanese version of an electromagnetic hypersensitivity (EHS) questionnaire, originally developed by Eltiti et al. in the United Kingdom. Using this Japanese EHS questionnaire, surveys were conducted on 1306 controls and 127 self‐selected EHS subjects in Japan. Principal component analysis of controls revealed eight principal symptom groups, namely, nervous, skin‐related, head‐related, auditory and vestibular, musculoskeletal, allergy‐related, sensory, and heart/chest‐related. The reliability of the Japanese EHS questionnaire was confirmed by high to moderate intraclass correlation coefficients in a test–retest analysis, and high Cronbach's α coefficients (0.853–0.953) from each subscale. A comparison of scores of each subscale between self‐selected EHS subjects and age‐ and sex‐matched controls using bivariate logistic regression analysis, Mann–Whitney U‐ and χ² tests, verified the validity of the questionnaire. This study demonstrated that the Japanese EHS questionnaire is reliable and valid, and can be used for surveillance of EHS individuals in Japan. Furthermore, based on multiple logistic regression and receiver operating characteristic analyses, we propose specific preliminary criteria for screening EHS individuals in Japan. Bioelectromagnetics. 37:353–372, 2016. © 2016 The Authors. Bioelectromagnetics Published by Wiley Periodicals, Inc.