Introgressive hybridization between two species of waterstriders (Hemiptera: Gerridae: Limnoporus): geographical structure and temporal change of a hybrid zone

Where the distribution ranges of the waterstriders Limnoporus notabilis and L. dissortis meet in western Canada, extensive hybridization and introgression occurs. Multivariate ordination analyses of genetic and morphometric data by principal component analysis revealed that a single axis separating the two parent species could account for nearly all the variation in both data sets. Maps of principal component scores for both data sets revealed geographical patterns of variation reflecting specific topographic features in the region. Comparisons of morphometric data from some of the samples collected in the 1980s and from the same sites revisited in the 1990s revealed substantial changes. An ‘island’ of dissortis‐like populations inside the range of L. notabilis in interior British Columbia expanded, and a marked local protrusion of notabilis‐like phenotypes into the range of L. dissortis on the east slope of the Rocky Mountains diminished during the decade between collections. We conclude that introgressive hybridization between these two species of waterstriders is a spatially complex and highly dynamic process.     

An assessment of seed quality and its influence on productivity estimation in an industrial antibiotic fermentation

This study investigates the benefits of including seed quality information into data-based models for final productivity estimation in an industrial antibiotic fermentation process. Multiway principal component analysis is applied to assess the seed quality using routinely gathered plant data. Multiway partial least-squares regression is then used to estimate the final productivity using data from the main fermentation only. The issue of selecting appropriate process variables as inputs is investigated. Subsequently, seed characteristics are included into the estimation models to assess the benefits of including information from this stage for productivity estimation. It is shown that it is possible to extract seed fermentation features related to the final productivity both at pilot and production scales. It is postulated that significant influential variations are mirrored in monitored variables during the main fermentation, and therefore seed quality is implicitly accounted for.     

Discrimination of Polygonati Rhizoma Species: An Investigation Utilizing High-Performance Liquid Chromatography Fingerprints and Chemometrics

Polygonati Rhizoma has been a famous traditional Chinese medicine (TCM) for two thousand years. It is increasingly being used not just as a traditional herbal medicine but also as a popular functional food. In this study, qualitative and quantitative analysis of PR from three different origins were initially performed using chemical fingerprint and chemometrics methods. Hierarchical cluster analysis (HCA) and Principal component analysis (PCA) were used to classify 60 PR samples from three different origins. The results revealed that the PR samples fell into three clusters related to the origins. In addition, pairwise comparison of varying PR and obtaining chemical markers between different species through the establishment of partial least squares discriminant analysis. Finally, chemical markers 9,13 and 17 were identified by LC/MS as disporopsin, 5,7-dihydroxy-3-(4′-hydroxybenzyl)-6,8-dimethylchroman-4-one and (3R)-5,7-dihydroxy-3-(4′-hydroxybenzyl)-6-methylchroman-4-one or isomer, respectively. In conclusion, these methods can be applied to identify and distinguish the quality of PR with other original plants and provide novel ideas for evaluating herbal products used in TCM.     

Papain in organic solvents: determination of conditions suitable for biocatalysis and the effect on substrate specificity and inhibition

Synthesis of N-CBZ-(N-Carbobenzoxy)-1-amino-acid methyl esters from N-CBZ-amino acids and methanol has been used as an assay to examine the properties of papain in organic solvents containing small amounts of water. Papain is active in solvents ranging in polarity from acetonitrile to tetrachloromethane. The optimal activity in each solvent varied only about three to four fold, but the amount of added water required to achieve it varied from 4% (v/v) in acetonitrile to 0.05% (v/v) in tetrachloromethane. The enzyme was generally more stable in hydrophobic solvents and at lower water contents. The apparent K(m) value of CBZ-glycine was 26 times higher in acetonitrile than in toluene due to differential partitioning of the substrate between aqueous and organic phases. The substrate specificity of the enzyme was qualitatively little different from that in aqueous solution, with amino acid derivatives still the best substrates. Nitrile analogs of substrates inhibited the enzyme, as they do in aqueous solution, and inhibition by a variety of substituted aromatic hydrocarbons showed that the main specificity of papain for hydrophobic side chains at its S(2) subsite, was little affected. The results show that papain can catalyze reactions under a variety of conditions in organic solvents but its substrate specificity is little changed from that in aqueous media.     

Rapid and quantitative detection of the microbial spoilage in chicken meat by diffuse reflectance spectroscopy (600-1100 nm)

AIMS: To evaluate the feasibility of visible and short-wavelength near-infrared (SW-NIR) diffuse reflectance spectroscopy (600-1100 nm) to quantify the microbial loads in chicken meat and to develop a rapid methodology for monitoring the onset of spoilage. METHODS AND RESULTS: Twenty-four prepackaged fresh chicken breast muscle samples were prepared and stored at 21 degrees C for 24 h. Visible and SW-NIR was used to detect and quantify the microbial loads in chicken breast muscle at time intervals of 0, 2, 4, 6, 8, 10, 12 and 24 h. Spectra were collected in the diffuse reflectance mode (600-1100 nm). Total aerobic plate count (APC) of each sample was determined by the spread plate method at 32 degrees C for 48 h. Principal component analysis (PCA) and partial least squares (PLS) based prediction models were developed. PCA analysis showed clear segregation of samples held 8 h or longer compared with 0-h control. An optimum PLS model required eight latent variables for chicken muscle (R = 0.91, SEP = 0.48 log CFU g(-1)). CONCLUSIONS: Visible and SW-NIR combined with PCA is capable of perceiving the change of the microbial loads in chicken muscle once the APC increases slightly above 1 log cycle. Accurate quantification of the bacterial loads in chicken muscle can be calculated from the PLS-based prediction method. SIGNIFICANCE AND THE IMPACT OF THE STUDY: Visible and SW-NIR spectroscopy is a technique with a considerable potential for monitoring food safety and food spoilage. Visible and SW-NIR can acquire a metabolic snapshot and quantify the microbial loads of food samples rapidly, accurately, and noninvasively. This method would allow for more expeditious applications of quality control in food industries.     

Navigating within thiamine diphosphate-dependent decarboxylases: Sequences,structures, functional positions,and binding sites

Thiamine diphosphate-dependent decarboxylases catalyze both cleavage and formation of C C bonds in various reactions, which have been assigned to different homologous sequence families. This work compares 53 ThDP-dependent decarboxylases with known crystal structures. Both sequence and structural information were analyzed synergistically and data were analyzed for global and local properties by means of statistical approaches (principle component analysis and principal coordinate analysis) enabling complexity reduction. The different results obtained both locally and globally, that is, individual positions compared with the overall protein sequence or structure, revealed challenges in the assignment of separated homologous families. The methods applied herein support the comparison of enzyme families and the identification of functionally relevant positions. The findings for the family of ThDP-dependent decarboxylases underline that global sequence identity alone is not sufficient to distinguish enzyme function. Instead, local sequence similarity, defined by comparisons of structurally equivalent positions, allows for a better navigation within several groups of homologous enzymes. The differentiation between homologous sequences is further enhanced by taking structural information into account, such as BioGPS analysis of the active site properties or pairwise structural superimpositions. The methods applied herein are expected to be transferrable to other enzyme families, to facilitate family assignments for homologous protein sequences.     

Fingerprint detection and process prediction by multivariate analysis of fed‐batch monoclonal antibody cell culture data

This work presents a sequential data analysis path, which was successfully applied to identify important patterns (fingerprints) in mammalian cell culture process data regarding process variables, time evolution and process response. The data set incorporates 116 fed‐batch cultivation experiments for the production of a Fc‐Fusion protein. Having precharacterized the evolutions of the investigated variables and manipulated parameters with univariate analysis, principal component analysis (PCA) and partial least squares regression (PLSR) are used for further investigation. The first major objective is to capture and understand the interaction structure and dynamic behavior of the process variables and the titer (process response) using different models. The second major objective is to evaluate those models regarding their capability to characterize and predict the titer production. Moreover, the effects of data unfolding, imputation of missing data, phase separation, and variable transformation on the performance of the models are evaluated. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1633–1644, 2015     

Multi-body simulation of a canine hind limb: model development, experimental validation and calculation of ground reaction forces

Background  

Among other causes the long-term result of hip prostheses in dogs is determined by aseptic loosening. A prevention of prosthesis complications can be achieved by an optimization of the tribological system which finally results in improved implant duration. In this context a computerized model for the calculation of hip joint loadings during different motions would be of benefit. In a first step in the development of such an inverse dynamic multi-body simulation (MBS-) model we here present the setup of a canine hind limb model applicable for the calculation of ground reaction forces.     

Substrate uptake,phosphorus repression,and effect of seed culture on glycopeptide antibiotic production: Process model development and experimental validation

Actinomycetes, the soil borne bacteria which exhibit filamentous growth, are known for their ability to produce a variety of secondary metabolites including antibiotics. Industrial scale production of such antibiotics is typically carried out in a multi‐substrate medium where the product formation may experience catabolite repression by one or more of the substrates. Availability of reliable process models is a key bottleneck in optimization of such processes. Here we present a structured kinetic model to describe the growth, substrate uptake and product formation for the glycopeptide antibiotic producer strain Amycolatopsis balhimycina DSM5908. The model is based on the premise that the organism is an optimal strategist and that the various metabolic pathways are regulated via key rate limiting enzymes. Further, the model accounts for substrate inhibition and catabolite repression. The model is also able to predict key phenomena such as simultaneous uptake of glucose and glycerol but with different specific uptake rates, and inhibition of glycopeptide production by high intracellular phosphate levels. The model is successfully applied to both production and seed medium with varying compositions and hence has good predictive ability over a variety of operating conditions. The model parameters are estimated via a well‐designed experimental plan. Adequacy of the proposed model was established via checking the model sensitivity to its parameters and confidence interval calculations. The model may have applications in optimizing seed transfer, medium composition, and feeding strategy for maximizing production. Biotechnol. Bioeng. 2010;105: 109–120. © 2009 Wiley Periodicals, Inc.     

基于CLUE-S模型验证的海岸围垦区景观驱动因子贡献率

基于1990、2000、2009年TM影像、社会统计数据、野外调查数据,采用冗余分析和主成分分析方法对长江口奉贤段围垦区海岸带景观动态变化驱动力因子的贡献度进行分析,并利用Kappa指数对CLUE-S模型所选驱动力模拟效力进行验证.结果表明:海岸带围垦区景观动态变化的人为驱动因子贡献度(57.1％)大于自然驱动因子贡献度(42.9％).CLUE-S模型模拟的正确率达82％,研究区主要景观类型(耕地、未利用地和养殖塘)的Kappa指数均大于0.75,CLUE-S模型的模拟效果较理想,所选驱动力因子很好地模拟了规则景观突变的空间分布特征.     

Near‐infrared spectroscopic evaluation of lyophilized viral vaccine formulations

This article examines the applicability of near‐infrared spectroscopy (NIRS) to evaluate the virus state in a freeze‐dried live, attenuated vaccine formulation. Therefore, this formulation was freeze‐dried using different virus volumes and after applying different pre‐freeze‐drying virus treatments (resulting in different virus states): (i) as used in the commercial formulation; (ii) without antigen (placebo); (iii) concentrated via a centrifugal filter device; and (iv) stressed by 96 h exposure to room temperature. Each freeze‐dried product was measured directly after freeze‐drying with NIR spectroscopy and the spectra were analyzed using principal component analysis (PCA). Herewith, two NIR spectral regions were evaluated: (i) the 7300–4000 cm^?1 region containing the amide A/II band which might reflect information on the coated proteins of freeze‐dried live, attenuated viruses; and (ii) the C–H vibration overtone regions (10,000–7500 and 6340–5500 cm^?1) which might supply information on the lipid layer surrounding the freeze‐dried live, attenuated viruses. The different pre‐freeze‐drying treated live, attenuated virus formulations (different virus states and virus volumes) resulted in different clusters in the scores plots resulting from the PCA of the collected NIR spectra. Secondly, partial least squares discriminant analysis models (PLS‐DA) were developed and evaluated, allowing classification of the freeze‐dried formulations according to virus pretreatment. The results of this study suggest the applicability of NIR spectroscopy for evaluating live, attenuated vaccine formulations with respect to their virus pretreatment and virus volume. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:1573–1586, 2013     

Raman spectroscopy and chemometrics for on‐line control of glucose fermentation by Saccharomyces cerevisiae

This work presents the use of Raman spectroscopy and chemometrics for on‐line control of the fermentation process of glucose by Saccharomyces cerevisiae. In a first approach, an on‐line determination of glucose, ethanol, glycerol, and cells was accomplished using multivariate calibration based on partial least squares (PLS). The PLS models presented values of root mean square error of prediction (RMSEP) of 0.53, 0.25, and 0.02% for glucose, ethanol and glycerol, respectively, and RMSEP of 1.02 g L^?1 for cells. In a second approach, multivariate control charts based on multiway principal component analysis (MPCA) were developed for detection of fermentation fault‐batch. Two multivariate control charts were developed, based on the squared prediction error (Q) and Hotelling's T². The use of the Q control chart in on‐line monitoring was efficient for detection of the faults caused by temperature, type of substrate and contamination, but the T² control chart was not able to monitor these faults. On‐line monitoring by Raman spectroscopy in conjunction with chemometric procedures allows control of the fermentative process with advantages in relation to reference methods, which require pretreatment, manipulation of samples and are time consuming. Also, the use of multivariate control charts made possible the detection of faults in a simple way, based only on the spectra of the system. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Natural hybridization between Vanilla claviculata (W.Wright) Sw. and V. barbellata Rchb.f. (Orchidaceae): genetic, morphological, and pollination experimental data

Vanilla claviculata (W.Wright) Sw. and K barbellata Rchb.f. grow sympatrically in the southwestern part of herto Rico. At three localities in the range of the two species, individuals with flowers that appeared Merent from previously known species were found. To test whether these were hybrids between V. claviculata and V. barbellata , 11 morphological floral characters were recorded at seven populations and allozyme profiles of the three taxa compared. Principal component analysis on the morphological characters gave three distinct groups with minor overlaps. The first component axis reflects variation in overall size of the flowers, while the second component reflects variation in the size of the distal aperture of the labellum. Allozyme data revealed that the putative hybrids have a significant surplus of heterozygotes ( F _IS = - 0.65) as expected in a F ₁ generation. Both data sets support the hypothesis that the individuals are hybrids, which is further augmented by interspecific pollination experiments between the putative parental species. This is the first case of natural hybridization reported in the genus Vanilla .     

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes

Alongside the well-studied membrane spanning helices, alpha-helical transmembrane (TM) proteins contain several functionally and structurally important types of substructures. Here, existing 3D structures of transmembrane proteins have been used to define and study the concept of reentrant regions, i.e. membrane penetrating regions that enter and exit the membrane on the same side. We find that these regions can be divided into three distinct categories based on secondary structure motifs, namely long regions with a helix-coil-helix motif, regions of medium length with the structure helix-coil or coil-helix and regions of short to medium length consisting entirely of irregular secondary structure. The residues situated in reentrant regions are significantly smaller on average compared to other regions and reentrant regions can be detected in the inter-transmembrane loops with an accuracy of approximately 70% based on their amino acid composition. Using TOP-MOD, a novel method for predicting reentrant regions, we have scanned the genomes of Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The results suggest that more than 10% of transmembrane proteins contain reentrant regions and that the occurrence of reentrant regions increases linearly with the number of transmembrane regions. Reentrant regions seem to be most commonly found in channel proteins and least commonly in signal receptors.     

近红外光谱分析法测定东北黑土有机碳和全氮含量

以我国东北黑土为研究对象,分析了2004-2005年采集的136个土壤样品在3699～12000 cm^-1范围的近红外光谱,利用偏最小二乘法建立了原始光谱吸光度与土壤有机碳、全氮和碳氮比之间的定量分析模型.结果表明：土壤有机碳和全氮的模型拟合效果良好,决定系数R²分别为0.92和0.91（P<0.001）,相对分析误差RPD分别为3.45和3.36,利用该模型对验证样本土壤有机碳和全氮的预测值与实测值之间的相关系数分别为0.94和0.93（P<0.001）,表明可以用近红外光谱分析法对黑土有机碳和全氮含量进行测定.但是利用近红外光谱分析法对土壤碳氮比的预测并不理想,虽然验证样本集黑土碳氮比模型预测值与实测值呈显著相关（r＝0.74,P<0.001）,但是校正模型的R²为0.61,RPD仅为1.61,建立的模型不能对黑土碳氮比做出合理的估测.     

Assessment of NIR spectroscopy for nondestructive analysis of physical and chemical attributes of sulfamethazine bolus dosage forms

The goal of this study was to assess the utility of near infrared (NIR) spectroscopy for the determination of content uniformity, tablet crushing strength (tablet hardness), and dissolution rate in sulfamethazine veterinary bolus dosage forms. A formulation containing sulfamethazine, corn starch, and magnesium stearate was employed. The formulations were wet granulated with a 10% (wt/vol) starch paste in a high shear granulator and dried at 60°C in a convection tray dryer. The tablets were compressed on a Stokes B2 rotary tablet press running at 30 rpm. Each sample was scanned in reflectance mode in the wavelengths of the NIR region. Principal component analysis (PCA) of the NIR tablet spectra and the neat raw materials indicated that the scores of the first 2 principal components were highly correlated with the chemical and physical attributes. Based on the PCA model, the significant wavelengths for sulfamethazine are 1514, (1660–1694), 2000, 2050, 2150, 2175, 2225, and 2275 nm; for corn starch are 1974, 2100, and 2325 nm; and for magnesium stearate are 2325 and 2375 nm. In addition, the loadings show large negative peaks around the water band regions (≈1420 and 1940 nm), indicating that the partial least squares (PLS) models could be affected by product water content. A simple linear regression model was able to predict content uniformity with a correlation coefficient of 0.986 at 1656 nm; the use of a PLS regression model, with 3 factors, had anr ² of 0.9496 and a sandard error of calibration of 0.0316. The PLS validation set had anr ² of 0.9662 and a standard error of 0.0354. PLS calibration models, based on tablet absorbance data, could successfully predict tablet crushing strength and dissolution in spite of varying active pharmaceutical ingredient (API) levels. Prediction plots based on these PLS models yielded correlation coefficients of 0.84 and 0.92 on independent validation sets for crushing strength and Q₁₂₀ (percentage dissolved in 120 minutes), respectively. Published: September 20, 2005 The opinions expressed in this paper are of the authors' personal views. They do not necessarily reflect the views or policies of the FDA.