Isotope labeling to determine the dynamics of metabolic response in CHO cell perfusion bioreactors using MALDI‐TOF‐MS

The steady‐state operation of Chinese hamster ovary (CHO) cells in perfusion bioreactors requires the equilibration of reactor dynamics and cell metabolism. Accordingly, in this work we investigate the transient cellular response to changes in its environment and their interactions with the bioreactor hydrodynamics. This is done in a benchtop perfusion bioreactor using MALDI‐TOF MS through isotope labeling of complex intracellular nucleotides (ATP, UTP) and nucleotide sugars (UDP‐Hex, UDP‐HexNAc). By switching to a ¹³C₆ glucose containing feed media during constant operation at 20 × 10⁶ cells and a perfusion rate of 1 reactor volume per day, isotopic steady state was studied. A step change to the ¹³C₆ glucose medium in spin tubes allowed the determination of characteristic times for the intracellular turnover of unlabeled metabolites pools, (≤0.56 days), which were confirmed in the bioreactor. On the other hand, it is shown that the reactor residence time (1 day) and characteristic time for glucose uptake (0.33 days), representative of the bioreactor dynamics, delayed the consumption of ¹³C₆ glucose in the bioreactor and thus the intracellular ¹³C enrichment. The proposed experimental approach allowed the decoupling of bioreactor hydrodynamics and intrinsic dynamics of cell metabolism in response to a change in the cell culture environment. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1630–1639, 2017     

Genetic basis of sex-specific color pattern variation in Drosophila malerkotliana

Pigmentation is a rapidly evolving trait that can play important roles in mimicry, sexual selection, thermoregulation, and other adaptive processes in many groups of animals. In Drosophila, pigmentation can differ dramatically among closely related taxa, presenting a good opportunity to dissect the genetic changes underlying species divergence. In this report, we investigate the genetic basis of color pattern variation between two allopatric subspecies of Drosophila malerkotliana, a widespread member of the ananassae species subgroup. In D. malerkotliana malerkotliana, the last three abdominal segments are darkly pigmented in males but not in females, while in D. malerkotliana pallens both sexes lack dark pigmentation. Composite interval mapping in F(2) hybrid progeny shows that this difference is largely controlled by three quantitative trait loci (QTL) located on the 2L chromosome arm, which is homologous to the 3R of D. melanogaster (Muller element E). Using highly recombinant introgression strains produced by repeated backcrossing and phenotypic selection, we show that these QTL do not correspond to any of the candidate genes known to be involved in pigment patterning and synthesis in Drosophila. These results, in combination with similar analyses in other Drosophila species, indicate that different genetic and molecular changes are responsible for the evolution of similar phenotypic traits in different lineages. This feature makes Drosophila color patterns a powerful model for investigating how the genetic basis of trait evolution is influenced by the intrinsic organization of regulatory pathways controlling the development of these traits.     

METAMODELS AND PHYLOGENETIC REPLICATION: A SYSTEMATIC APPROACH TO THE EVOLUTION OF DEVELOPMENTAL PATHWAYS

Molecular genetic analysis of phenotypic variation has revealed many examples of evolutionary change in the developmental pathways that control plant and animal morphology. A major challenge is to integrate the information from diverse organisms and traits to understand the general patterns of developmental evolution. This integration can be facilitated by evolutionary metamodels—traits that have undergone multiple independent changes in different species and whose development is controlled by well-studied regulatory pathways. The metamodel approach provides the comparative equivalent of experimental replication, allowing us to test whether the evolution of each developmental pathway follows a consistent pattern, and whether different pathways are predisposed to different modes of evolution by their intrinsic organization. A review of several metamodels suggests that the structure of developmental pathways may bias the genetic basis of phenotypic evolution, and highlights phylogenetic replication as a value-added approach that produces deeper insights into the mechanisms of evolution than single-species analyses.     

Effects of epistasis and the evolution of genetic architecture: Exact results for a 2-locus model

We study a two-locus model of a quantitative trait with a continuum-of alleles and multilinear epistasis that evolves under mutation, selection, and genetic drift. We derive analytical results based on the so-called House of Gauss approximation for the genetic variance, the mean phenotype, and the mutational variance in the balance of the evolutionary forces. The analytical work is complemented by extensive individual-based computer simulations. We find that (1) analytical results are accurate in a large parameter space; (2) epistasis always reduces the equilibrium genetic variance, as predicted in earlier studies that exclude drift; (3) large-scale stochastic fluctuations and non-equilibrium phenomena like adaptive inertia can strongly influence the evolution of the genetic architecture of the trait.     

Effects of Simultaneous Deletion of pUL11 and Glycoprotein M on Virion Maturation of Herpes Simplex Virus Type 1

The conserved membrane-associated tegument protein pUL11 and envelope glycoprotein M (gM) are involved in secondary envelopment of herpesvirus nucleocapsids in the cytoplasm. Although deletion of either gene had only moderate effects on replication of the related alphaherpesviruses herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PrV) in cell culture, simultaneous deletion of both genes resulted in a severe impairment in virion morphogenesis of PrV coinciding with the formation of huge inclusions in the cytoplasm containing nucleocapsids embedded in tegument (M. Kopp, H. Granzow, W. Fuchs, B. G. Klupp, and T. C. Mettenleiter, J. Virol. 78:3024-3034, 2004). To test whether a similar phenotype occurs in HSV-1, a gM and pUL11 double deletion mutant was generated based on a newly established bacterial artificial chromosome clone of HSV-1 strain KOS. Since gM-negative HSV-1 has not been thoroughly investigated ultrastructurally and different phenotypes have been ascribed to pUL11-negative HSV-1, single gene deletion mutants were also constructed and analyzed. On monkey kidney (Vero) cells, deletion of either pUL11 or gM resulted in ca.-fivefold-reduced titers and 40- to 50%-reduced plaque diameters compared to those of wild-type HSV-1 KOS, while on rabbit kidney (RK13) cells the defects were more pronounced, resulting in ca.-50-fold titer and 70% plaque size reduction for either mutant. Electron microscopy revealed that in the absence of either pUL11 or gM virion formation in the cytoplasm was inhibited, whereas nuclear stages were not visibly affected, which is in line with the phenotypes of corresponding PrV mutants. Simultaneous deletion of pUL11 and gM led to additive growth defects and, in RK13 cells, to the formation of large intracytoplasmic inclusions of capsids and tegument material, comparable to those in PrV-ΔUL11/gM-infected RK13 cells. The defects of HSV-1ΔUL11 and HSV-1ΔUL11/gM could be partially corrected in trans by pUL11 of PrV. Thus, our data indicate that PrV and HSV-1 pUL11 and gM exhibit similar functions in cytoplasmic steps of virion assembly.     

The Genetic Basis of Phenotypic Adaptation II: The Distribution of Adaptive Substitutions in the Moving Optimum Model

We consider a population that adapts to a gradually changing environment. Our aim is to describe how ecological and genetic factors combine to determine the genetic basis of adaptation. Specifically, we consider the evolution of a polygenic trait that is under stabilizing selection with a moving optimum. The ecological dynamics are defined by the strength of selection, , and the speed of the optimum, ; the key genetic parameters are the mutation rate Θ and the variance of the effects of new mutations, ω. We develop analytical approximations within an “adaptive-walk” framework and describe how selection acts as a sieve that transforms a given distribution of new mutations into the distribution of adaptive substitutions. Our analytical results are complemented by individual-based simulations. We find that (i) the ecological dynamics have a strong effect on the distribution of adaptive substitutions and their impact depends largely on a single composite measure , which combines the ecological and genetic parameters; (ii) depending on γ, we can distinguish two distinct adaptive regimes: for large γ the adaptive process is mutation limited and dominated by genetic constraints, whereas for small γ it is environmentally limited and dominated by the external ecological dynamics; (iii) deviations from the adaptive-walk approximation occur for large mutation rates, when different mutant alleles interact via linkage or epistasis; and (iv) in contrast to predictions from previous models assuming constant selection, the distribution of adaptive substitutions is generally not exponential.AN important aim for both empirical and theoretical evolutionary biologists is to better understand the genetics of adaptation (e.g., Orr 2005a). For example, among the multitude of mutations that arise in a population, which ones are eventually fixed and contribute to evolutionary change? That is, given a distribution of new mutations, what is the distribution of adaptive substitutions (or fixed mutations)? Here, distribution means the probability distribution of the effects of mutations on either the phenotype or the fitness of their carriers. In principle, both the distribution of new mutations and the distribution of adaptive substitutions can be measured empirically, the former from mutation accumulation experiments (Eyre-Walker and Keightley 2007) and the latter from QTL (e.g., Bradshaw et al. 1998) or experimental evolution (Elena and Lenski 2003) studies. However, as only a small subset of all mutations is beneficial, such measurements are difficult. Therefore, a large role in studying the genetics of adaptation has to be played by theoretical modeling.In recent years, several different approaches have emerged for modeling the process of adaptation. Considerable work exists, in particular, in the context of Fisher''s geometric model (e.g., Fisher 1930; Kimura 1983; Orr 1998; Welch and Waxman 2005; Martin and Lenormand 2006), Gillespie''s mutational landscape model (e.g., Gillespie 1983, 1984; Orr 2002), various models of so-called “adaptive walks” on rugged fitness landscapes (e.g., Kauffman and Levin 1987; Kauffman 1993), and models of clonal interference in asexual populations (e.g., Gerrish and Lenski 1998; Park and Krug 2007). Together, these models have yielded several robust predictions. For example, both Fisher''s geometric model and the mutational landscape model predict that the distribution of adaptive substitutions should be approximately exponential (with respect to either phenotype or fitness) (Orr 1998, 2002, 2005a,b). This means that most substitutions have little effect, but that a significant fraction of the overall evolutionary change is due to a small number of substitutions with large effects. These results are in qualitative agreement with empirical data (Orr 2005a; Elena and Lenski 2003) and have shed new light on the classical debate about micro- vs. macromutationalism (Fisher 1930; Provine 2001).One way to look at adaptation is to view selection as a sieve that transforms the distribution of new mutations into the distribution of adaptive substitutions (Turner 1981; Orr and Betancourt 2001). This perspective emphasizes the role of environmental factors and directly leads to the question of how different selective regimes (sieves) affect the adaptive process. Yet, almost all studies to date have focused on the simplest possible ecological scenario: a population that, after a sudden change in the environment, is now under constant stabilizing selection.In reality, however, environmental change is often gradual rather than sudden (e.g., Hairston et al. 2005; Thompson 2005; Parmesan 2006; Perron et al. 2008). To account for this possibility, several authors (Bello and Waxman 2006; Collins et al. 2007; Kopp and Hermisson 2007; Sato and Waxman 2008; Kopp and Hermisson 2009) have recently turned to the so-called moving optimum model, which was originally devised in the field of quantitative genetics (e.g., Lynch et al. 1991; Lynch and Lande 1993; Bürger and Lynch 1995; Bürger 1999; Waxman and Peck 1999; Bürger and Gimelfarb 2002; Nunney 2003; Jones et al. 2004). In this model, the selectively favored value of a quantitative trait changes over time, such that the trait is under a mixture of stabilizing and directional selection. An important aspect of the moving optimum model is that it introduces an additional timescale (the timescale of environmental change), which is absent in the previous models.In a recent article (Kopp and Hermisson 2009) and a previous note (Kopp and Hermisson 2007), we have used the moving optimum model to investigate the time to fixation of a single mutation and the order in which mutations of different phenotypic effect go to fixation. However, the fastest mutations in the short term are not necessarily those that dominate evolution in the long term. The present article focuses on this long-term evolution, which can be characterized by the distribution of adaptive substitutions.     

Trophic ecology of the pikeperch (Sander lucioperca) in its introduced areas: a stable isotope approach in southwestern France

During the last decades, non-native predatory fish species have been largely introduced in European lakes and rivers, calling for detailed information on the trophic ecology of co-existing native and non-native predators. The present study describes the trophic ecology of the introduced pikeperch (Sander lucioperca) in two southwestern French rivers, using stable isotope analysis. Pikeperch could be categorized as a top-predator, and had a significantly higher trophic position (TP, mean±SE=4.2±0.1) compared to other predatory fish such as the native pike (Esox lucius, TP=3.7±0.1) and the introduced European catfish (Silurus glanis, TP=3.8±0.1). Most studies of resource use in freshwaters consider predatory fish as ecologically equivalent; however, this study showed that the pikeperch occupied a higher trophic niche compared to other predatory species in the Lot and Tarn rivers (Garonne River basin). This apparent specialization may thus have consequences upon interspecific relationships within the predatory guild and upon the functional organization of biological communities. To cite this article: D. Kopp et al., C. R. Biologies 332 (2009).