Segmented linear modeling of CHO fed‐batch culture and its application to large scale production

We describe a systematic approach to model CHO metabolism during biopharmaceutical production across a wide range of cell culture conditions. To this end, we applied the metabolic steady state concept. We analyzed and modeled the production rates of metabolites as a function of the specific growth rate. First, the total number of metabolic steady state phases and the location of the breakpoints were determined by recursive partitioning. For this, the smoothed derivative of the metabolic rates with respect to the growth rate were used followed by hierarchical clustering of the obtained partition. We then applied a piecewise regression to the metabolic rates with the previously determined number of phases. This allowed identifying the growth rates at which the cells underwent a metabolic shift. The resulting model with piecewise linear relationships between metabolic rates and the growth rate did well describe cellular metabolism in the fed‐batch cultures. Using the model structure and parameter values from a small‐scale cell culture (2 L) training dataset, it was possible to predict metabolic rates of new fed‐batch cultures just using the experimental specific growth rates. Such prediction was successful both at the laboratory scale with 2 L bioreactors but also at the production scale of 2000 L. This type of modeling provides a flexible framework to set a solid foundation for metabolic flux analysis and mechanistic type of modeling. Biotechnol. Bioeng. 2017;114: 785–797. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.     

Biological Invasions Across Spatial Scales: Intercontinental, Regional, and Local Dispersal of Cladoceran Zooplankton

The frequency of dispersal of invertebrates among lakes depends upon perspective and spatial scale. Effective passive dispersal requires both the transport of propagules and the establishment of populations large enough to be detected. At a global scale, biogeographic patterns of cladoceran zooplankton species suggest that effective dispersal among continents was originally rare, but greatly increased in the past century with expanded commerce. Genetic analysis allows some reconstruction of past dispersal events. Allozyme and mitochondrial DNA comparisons among New World and Old-World populations of several exotic cladocerans have provided estimates for likely source populations of colonists, their dispersal corridors, and timing of earlier dispersal events. Detecting the Old-World tropical exotic Daphnia lumholtzi early in its invasion of North America has allowed detailed analysis of its spatial spread. Twelve years of collection records indicate a rapid invasion of reservoirs in the United States, by both regional spread and long-distance jumps to new regions. Combining landscape features with zooplankton surveys from south-central US reservoirs revealed higher colonization rates of D. lumholtzi at lower landscape positions, a result which can be explained by either greater propagule load or by higher susceptibility of these downstream reservoirs. Because invaded reservoirs provide a source of propagules for nearby floodplain ponds, the rarity of this species in ponds suggests limitation by local environments. Such analyses of invading species over multiple spatial scales allow a better understanding of ecological processes governing invasion dynamics.     

横斑锦蛇的形态学性状初探

横斑锦蛇Euprepiophis perlacea是中国西部特有种,《中国濒危动物红皮书》极危物种,研究成果相对匮乏。本研究采用样带法和样方法在横斑锦蛇分布区内采集到标本20号,测量其鳞片特征、体长、尾长等形态学性状,结合文献资料中已有的5号标本数据,进行统计分析。结果表明,鳞片特征是有效的分类依据,尤其背鳞(19-19-17行)、左上唇鳞数(7)和右上唇鳞数(7)在所有标本中无任何变化,是鉴定该物种的最重要特征。对尾下鳞、体长、尾长、头长、头宽、头高、眼间距共7个形态学性状数据进行方差分析,性别间的差异均无统计学意义,未发现蛇类中普遍存在的两性异形现象。横斑锦蛇体色靓丽、无毒、性情温和、行动迟缓、分布区狭窄、种群数量稀少,分布区内人口密度高,人为干扰严重,急需加强科学研究、法制宣传和科普教育,以保障该物种种群延续。     

Spatial pattern of parasitism in Diatraea saccharalis Fab. (Lep., Crambidae) populations at two different spatial scales in sugarcane fields in Brazil

Abstract:  The biological control of Diatraea saccharalis is regarded as one of the best examples of successful classical biological control in Brazil. Since the introduction of the exotic parasitoid, Cotesia flavipes , the decrease in D. saccharalis infestation in sugarcane fields has been attributed to the effectiveness of this agent. Native Tachinidae fly parasitoids ( Lydella minense and Paratheresia claripalpis ) have also been implicated in the success. Quantitative data confirming the actual contribution of these agents to the control of D. saccharalis are, however, rather scant. The purpose of this study was to investigate the spatial pattern of parasitism of these parasitoids in D. saccharalis populations at two large spatial scales (fields and zones). To investigate this subject, a large data set comprising information collected from a sugarcane mill located in the state of São Paulo, Brazil (São João sugarcane mill) was analysed. When regressions between the proportion parasitism against host density were computed, the percentage of significant regressions with either a positive or a negative slope was very small at both spatial scales for both parasitoid species. Regressing the densities of tachinid-parasitized hosts against host densities per field showed that these parasitoids presented a 'moderate aggregative' response to host densities, as 53.33% of the regressions were positively significant. Cotesia flavipes was 'weakly aggregated' on host densities at the field level, because only 33.33% of the regressions were positively significant. At the zone level, neither aggregative nor spatial proportion parasitism responses were evident for either parasitoid species due to the small percentage of significant regressions computed.     

Multi‐scale characterization of the energy landscape of proteins with application to the C3D/Efb‐C complex

We present a novel multi‐level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi‐scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low‐dimensional landscape to efficiently focus on important interactions and examine low energy regions. This methodology provides a more extensive sampling of the low energy landscape than an MD simulation starting from a single crystal structure as it explores multiple trajectories of the protein. This enables us to obtain a broader view of the dynamics of proteins and it can help in understanding complex binding, improving docking results and more. In this work, we apply the methodology to provide an extensive characterization of the bound complexes of the C3d fragment of human Complement component C3 and one of its powerful bacterial inhibitors, the inhibitory domain of Staphylococcus aureus extra‐cellular fibrinogen‐binding domain (Efb‐C) and two of its mutants. We characterize several important interactions along the binding interface and define low free energy regions in the three complexes. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Fine‐scale spatial and temporal population genetics of Aedes japonicus,a new US mosquito,reveal multiple introductions

The newly introduced mosquito Aedes japonicus has expanded from its original range in Northeastern Asia to 29 US states (including Hawaii) plus Canada and northern Europe. Our objectives were to test an earlier hypothesis of multiple introductions of this species to the Northeastern US and evaluate putative temporal changes in genetic makeup. Using a panel of seven microsatellite loci, we confirmed the existence of two abundant genetic forms in specimens originally collected in 1999–2000 (F_ST value based on microsatellite data = 0.26) that matches the disjunctive distribution of mitochondrial haplotypes. To examine the distribution of the two genetic ‘types’ across Pennsylvania we created a fine‐scale genetic map of Ae. japonicus using 439 specimens collected from 54 Pennsylvania counties in 2002–2003. We also made direct comparisons between collections in 1999–2000 and new collections made in 2004–2005 obtained from the same areas in the northeastern US. We observed that the strong association between mtDNA haplotype and microsatellite signature seen in 1999–2000 had weakened significantly by 2002 across Pennsylvania, a trend continued to some extent in 2004–2005 in PA, NJ, and NY, indicating that once easily distinguishable separate introductions are merging. The two expanding genetic forms create a complex correlation between spatial and genetic distances. The existence of multiple introductions would be obscured without sampling early and across time with highly polymorphic molecular markers. Our results provide a high‐resolution analysis of the spatial and temporal dynamics of a newly introduced disease vector and argue that successive introductions may be a common pattern for invasive mosquitoes.     

Bioaugmentation for enhancing biological wastewater treatment

The literature on bioaugmentation products has been reviewed. Their manufacture and method of use is explained. The various applications are listed and the independent investigations, as opposed to manufacturers accounts, at laboratory and full scale are reviewed. The economics and kinetic modelling are also discussed. In laboratory investigations bioaugmentation often failed, whereas at full scale it was often successful, probably due to the imposition of steady state at laboratory scale. Most products require a period of acclimatisation before working; this and other possible reasons for failure are discussed.     

The effects of forest conversion to oil palm on ground‐foraging ant communities depend on beta diversity and sampling grain

Beta diversity – the variation in species composition among spatially discrete communities – and sampling grain – the size of samples being compared – may alter our perspectives of diversity within and between landscapes before and after agricultural conversion. Such assumptions are usually based on point comparisons, which do not accurately capture actual differences in total diversity. Beta diversity is often not rigorously examined. We investigated the beta diversity of ground‐foraging ant communities in fragmented oil palm and forest landscapes in Sabah, Malaysia, using diversity metrics transformed from Hill number equivalents to remove dependences on alpha diversity. We compared the beta diversities of oil palm and forest, across three hierarchically nested sampling grains. We found that oil palm and forest communities had a greater percentage of total shared species when larger samples were compared. Across all grains and disregarding relative abundances, there was higher beta diversity of all species among forest communities. However, there were higher beta diversities of common and very abundant (dominant) species in oil palm as compared to forests. Differences in beta diversities between oil palm and forest were greatest at the largest sampling grain. Larger sampling grains in oil palm may generate bigger species pools, increasing the probability of shared species with forest samples. Greater beta diversity of all species in forest may be attributed to rare species. Oil palm communities may be more heterogeneous in common and dominant species because of variable community assembly events. Rare and also common species are better captured at larger grains, boosting differences in beta diversity between larger samples of forest and oil palm communities. Although agricultural landscapes support a lower total diversity than natural forests, diversity especially of abundant species is still important for maintaining ecosystem stability. Diversity in agricultural landscapes may be greater than expected when beta diversity is accounted for at large spatial scales.     

Emergence,dispersal, and mate finding via a substrate‐borne sex pheromone in the parasitoid Metaphycus luteolus

Metaphycus luteolus Timberlake (Hymenoptera: Encyrtidae) is a facultatively gregarious parasitoid of soft scale insects. We conducted behavioral experiments to better understand the mating structure of this species. Emergence of male and female offspring is synchronized, beginning at the onset of photoperiod. Both sexes are able to disperse, although dispersal of males from natal patches appears to take longer than dispersal of females. We demonstrated the presence of a female‐produced contact pheromone using open arena bioassays and motion tracking software, testing residues deposited by walking females, and extracts of females. Males responded to the females' ‘chemical footprints’ and to acetone and hexane extracts of females by searching and arrestment on the chemical residues. Responses of males were dose dependent and diminished with time since the stimulus was deposited. Our findings support the hypothesis that non‐local mating among wasps emerging from different hosts may be quite common in these parasitoids. The implications of our results for the mating structure and previously documented sex ratio patterns of these parasitoids are described.