NMR structural studies of the myristoylated N-terminus of ADP ribosylation factor 6 (Arf6)

Arf proteins are guanine nucleotide binding proteins that are implicated in endocytotic pathways and vesicle trafficking. The two widely studied isoforms of Arf proteins (Arf1 and Arf6) have different cellular functions and localizations but similar structures. Arf proteins have an N-terminal helix with a covalently bound myristoyl group. Except structural models, there are no three dimensional structures of the myristoylated N-terminal peptide or the intact myristoylated Arf proteins. However, understanding the role of both the myristoyl group and the N-terminal helix based on the details of their molecular structures is of great interest. In the solution structure of myristoylated N-terminal peptide of Arf6 described here, the myristoyl group folds toward the N-terminus to interact with the hydrophobic residues in particular, the phenyl ring. Also, the structure of the dodecylphosphocholine (DPC) micelle-bound of the peptide together with paramagnetic studies showed that the myristoyl group is inserted into the micelle while residues V4-G10 interact with the surface of the micelle. The structural differences between the unbound and micelle-bound myristoylated N-terminal peptide of Arf6 involves the myristoyl group and the side chains of the hydrophobic residues.     

Changes in zoeae of the snow crab, Chionoecetes opilio, with variation in incubation temperature

The purpose of this study was to evaluate the effect of embryonic incubation temperature on the morphology, energetic content, and individual weights of C. opilio zoeae. Ovigerous female C. opilio were collected by trawl from the eastern Bering Sea in the summer of 2002 and were held in the laboratory at five temperature treatments (− 1, 0, 1, 3, and 6 °C) from embryo stage five to hatching. The mean duration of incubation ranged from 240 d at 6 °C to 353 d at − 1 °C. No relationship between larval weight and caloric content with incubation temperature was detected, indicating that increased development time at cooler temperatures may not have an energetic cost. However, several morphological features varied with temperature. Most larval characters including rostro-dorsal length, rostral spine length, lateral spine length, and carapace width were smaller at the warmest incubation temperature. Protopodite length did not differ with temperature. The length of the 3rd abdominal somite consistently increased with increased temperature and may serve as a suitable indicator that could be used in field populations to infer temperature of incubation. Variation in morphology with temperature could confound identification of C. opilio zoeae from those of a congener, Chionoecetes bairdi because identification of C. bairdi is based on the length of the 3rd abdominal somite.     

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.     

孵化温度对乌龟胚胎能量利用及矿物质代谢的影响

在24℃、27℃、30℃和33℃条件下孵化乌龟(Chinemysreevesii)卵,检测温度对胚胎利用卵内能量和矿物质的影响。孵化温度显著影响乌龟胚胎的能量利用。卵在温和温度下(27℃和30℃)比在高温(33℃)和低温(24℃)孵化有较高的干物质、脂肪和能量转化率。因而,27℃和30℃新生幼体的总能量高于33℃和24℃下孵出的幼体。新生幼体内剩余卵黄随温度升高而增大。27℃下新生幼体的躯干能量显著高于其它温度。此外,孵化温度显著影响乌龟胚胎钙代谢,但对镁和钾代谢影响微弱。24℃下胚胎从卵黄和卵壳吸收的总钙量小于其它温度条件下胚胎,与之相对应,24℃下孵出卵卵壳内残留较多的钙。由此可见,温和温度(27-30℃)可提高胚胎能量转化效率,促进胚胎从卵黄和卵壳吸收较多的矿物质,有利于孵出发育良好的乌龟幼体     

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