Experimental design principles for isotopically instationary 13C labeling experiments

13C metabolic flux analysis (MFA) is a well-established tool in Metabolic Engineering that found numerous applications in recent years. However, one strong limitation of the current method is the requirement of an-at least approximate-isotopic stationary state at sampling time. This requirement leads to a principle lower limit for the duration of a 13C labeling experiment. A new methodological development is based on repeated sampling during the instationary transient of the 13C labeling dynamics. The statistical and computational treatment of such instationary experiments is a completely new terrain. The computational effort is very high because large differential equations have to be solved and, moreover, the intracellular pool sizes play a significant role. For this reason, the present contribution works out principles and strategies for the experimental design of instationary experiments based on a simple example network. Hereby, the potential of isotopically instationary experiments is investigated in detail. Various statistical results on instationary flux identifiability are presented and possible pitfalls of experimental design are discussed. Finally, a framework for almost optimal experimental design of isotopically instationary experiments is proposed which provides a practical guideline for the analysis of large-scale networks.     

Regression as a method to predict copy numbers in comparative genomic hybridization studies on bacteria

Comparative genomic hybridizations (CGH) using microarrays are performed with bacteria in order to determine the level of genomic similarity between various strains. The microarrays applied in CGH experiments are constructed on the basis of the genome sequence of one strain, which is used as a control, or reference, in each experiment. A strain being compared with the known strain is called the unknown strain. The ratios of fluorescent intensities obtained from the spots on the microarrays can be used to determine which genes are divergent in the unknown strain, as well as to predict the copy number of actual genes in the unknown strain. In this paper, we focus on the prediction of gene copy number based on data from CGH experiments. We assumed a linear connection between the log2 of the copy number and the observed log2-ratios, then predictors based on the factor analysis model and the linear random model were proposed in an attempt to identify the copy numbers. These predictors were compared to using the ratio of the intensities directly. Simulations indicated that the proposed predictors improved the prediction of the copy number in most situations. The predictors were applied on CGH data obtained from experiments with Enterococcus faecalis strains in order to determine copy number of relevant genes in five different strains.     

探讨生物活性接骨板研制的动物实验模型

目的探索生物活性接骨板修复骨折和骨缺损的动物实验模型,为研制不同强度的生物活性接骨板、观察骨折和骨缺损修复的机制提供实验对象。方法通过观察2.0cm兔股骨骨折和去骨膜缺损动物模型、2.0cm兔胫骨骨折和去骨膜缺损动物模型以及2.0cm兔桡骨骨折和去骨膜缺损动物模型,比较三种不同动物实验模型在兔节段性骨折和缺损实验修复中的大体标本及其术后4周的X线图片,了解三种动物实验模型在生物活性接骨板研制中的优缺点。结果2.0cm兔股骨骨折和去骨膜缺损组及2.0cm兔胫骨骨折和去骨膜缺损组术后均出现固定石膏脱落,生物活性接骨板断裂,骨折和缺损部位移位等现象;而2.0cm兔桡骨骨折和去骨膜缺损组术后4周X片发现生物活性接骨板的固定和复位良好,并且有骨痂形成。结论2.0cm兔桡骨骨折和去骨膜缺损动物模型,较好地模拟人体骨折和骨缺损的愈合过程,可能是研制生物活性接骨板的最佳动物实验模型之一。     

Post-pollination reproductive isolation between diurnally and nocturnally flowering daylilies, Hemerocallis fulva and Hemerocallis citrina

To examine whether floral and post-pollination isolation develops independently or not, we conducted a crossing experiment between Hemerocallis fulva and Hemerocallis citrina that shows large floral divergence adapted for diurnal and nocturnal pollinators that have been believed to be fully cross-fertile. Flowers of the two species from sympatric populations were hand-pollinated with conspecific pollen from the same population (control), interspecific pollen from the same area (sympatric cross), and interspecific pollen from the different area (allopatric cross). After capsule dehiscence, the fruit set, seed set per fruit and seed set per flower were determined among three cross categories. The seed sets per flower were 32 and 77% lower in sympatric and allopatric crosses than in the control when H. fulva was the pollen recipient. There was no difference in three reproductive measures among the cross categories when H. citrina was the pollen recipient. This finding indicates that post-pollination isolation does exist between H. fulva and H. citrina, although it is partial, asymmetric, and weakened in sympatry. Our result suggests that floral and post-pollination isolation may develop independently, and reinforcement may not be a general phenomenon in plants.     

A nomenclature and data model to describe NMR experiments

Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason for the absence of a universal naming system is that the information content of the coherence pathways is difficult to describe in full detail. We propose a system that describes the common and generic elements of the coherence pathways produced by pulse sequences. The system itself is formalised by an ‘NMR experiment protocol’ model, which is described in the Universal Modelling Language (UML) as part of the CCPN data model. Furthermore, normalized experiment names can be derived from this proposed model. We hope this article will stimulate discussion to organise the wealth of NMR experiments, and that by bringing this discussion into the public domain we can improve and expand our proposed system to include as much information and as many NMR experiments as possible. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Joint first authors     

Local adaptation in the monocarpic perennial Carlina vulgaris at different spatial scales across Europe

Spatial variation in environmental conditions can lead to local adaptation of plant populations, particularly if gene flow among populations is low. Many studies have investigated adaptation to contrasting environmental conditions, but little is known about the spatial scale of adaptive evolution. We studied population differentiation and local adaptation at two spatial scales in the monocarpic grassland perennial Carlina vulgaris. We reciprocally transplanted seedlings among five European regions (northwestern Czech Republic, central Germany, Luxembourg, southern Sweden and northwestern Switzerland) and among populations of different sizes within three of the regions. We recorded survival, growth and reproduction over three growing periods. At the regional scale, several performance traits and the individual fitness of C. vulgaris were highest if the plants were grown in their home region and they decreased with increasing transplant distance. The effects are likely due to climatic differences that increased with the geographical distance between regions. At the local scale, there were significant interactions between the effects of the population of origin and the transplant site, but these were not due to an enhanced performance of plants at their home site and they were not related to the geographical or environmental distance between the site of origin and the transplant site. The size of the population of origin did not influence the strength of local adaptation. The results of our study suggest that C. vulgaris consists of regionally adapted genotypes, and that distance is a good predictor of the extent of adaptive differentiation at large scales ( > 200 km) but not at small scales. We conclude that patterns of local adaptation should be taken into account for the efficient preservation of genetic resources, when assessing the status of a plant species and during conservation planning.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Ectomycorrhizal networks and seedling establishment during early primary succession

Ectomycorrhizal (ECM) fungal mycelia are the main organs for nutrient uptake in many woody plants, and often connect seedlings to mature trees. While it is known that resources are shared among connected plants via common mycorrhizal networks (CMNs), the net effects of CMNs on seedling performance in the field are almost unknown. CMNs of individual ECM fungal species were produced in an early succession volcanic desert by transplanting current-year seedlings of Salix reinii with ECM mother trees that had been inoculated with one of 11 dominant ECM fungal species. Most seedlings were connected to individual CMNs without being infected by other ECM fungi. Although control seedlings showed poor growth under severe nutrient competition with larger nonmycorrhizal mother trees, nutrient acquisition and growth of seedlings connected to CMNs were improved with most fungal species. The positive effects of CMNs on seedling performance were significantly different among ECM fungal species; for example, the maximum difference in seedling nitrogen acquisition was 1 : 5.9. The net effects of individual CMNs in the field and interspecific variation among ECM fungal species are shown.     

Development of mammalian production cell lines expressing CNTO736, a glucagon like peptide‐1‐MIMETIBODYTM: Factors that influence productivity and product quality

In an attempt to develop a high producing mammalian cell line expressing CNTO736, a Glucagon like peptide‐1‐antibody fusion protein (also known as a Glucagon like peptide‐1 MIMETIBODY^TM), we have noted that the N‐terminal GLP‐1 portion of the MIMETIBODY^TM was susceptible to proteolytic degradation during cell culture, which resulted in an inactive product. Therefore, a number of parameters that had an effect on productivity as well as product quality were examined. Results suggest that the choice of the host cell line had a significant effect on the overall product quality. Product expressed in mouse myeloma host cell lines had a lesser degree of proteolytic degradation and variability in O‐linked glycosylation as compared to that expressed in CHO host cell lines. The choice of a specific CHOK1SV derived clone also had an effect on the product quality. In general, molecules that exhibited minimal N‐terminal clipping had increased level of O‐linked glycosylation in the linker region, giving credence to the hypothesis that O‐linked glycosylation acts to protect against proteolytic degradation. Moreover, products with reduced potential for N‐terminal clipping had longer in vivo serum half‐life. These findings suggest that early monitoring of product quality should be an essential part of production cell line development and therefore, has been incorporated in our process of cell line development for this class of molecules. Biotechnol. Bioeng. 2009;103: 162–176. © 2008 Wiley Periodicals, Inc.     

The influence of littoral zone coarse woody habitat on home range size, spatial distribution, and feeding ecology of largemouth bass (Micropterus?salmoides)

Coarse woody habitat (CWH) may be a critical feature of lakes that influences fish distributions, movement patterns, and feeding habits. We used radio telemetry to examine the role of CWH in determining the movements of largemouth bass (Micropterus salmoides Lacepede) in the context of two whole-lake experiments that provided a gradient of four lake basins varying in natural and manipulated CWH. We also conducted diet studies on largemouth bass in these lakes to test for correlates among consumption rate and prey selectivity with bass behavior. Our results indicated that largemouth bass in basins with lower CWH abundances had larger home ranges, spent more time in deep water, were more selective predators, and showed lower consumption rates. Largemouth bass in basins with higher CWH abundances showed the opposite patterns. Low CWH abundances were correlated with a shift in largemouth bass foraging behavior from sit-and-wait to actively searching. This increased activity, coupled with the potential decline of prey fish species in the absence of CWH, may decrease largemouth bass growth potential regardless of the prey type consumed. Our results suggest that lakeshore residential development and associated removals of CWH from lakes may influence fish behavior, while CWH augmentation may reverse some of those changes. Handling editor: Steven Declerck