Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR)

Three homology models of the human ghrelin receptor (GHS-R1a) have been generated from the available X-ray structures of rhodopsin (RHO model), opsin (OPS model) and beta-2 adrenergic receptor (B2 model). The latter was used as a starting point for combined molecular dynamics simulation (MDS) and full atom normal modes analysis (NMA). A low-frequency normal mode (mode 16) perfectly reproduced the intracellular motions observed between B2 and RHO models; in the opposite direction along the same mode, the generated structures are closer to the OPS model, suggesting a direct link with GHS-R1a activation. This was in agreement with motions of the seven transmembranous segments, increase of the solvent accessibility of the 140-ERY-142 sequence, and flip of the Trp276 (C WLP) residue, some features related to GPCRs activation. According to our model, His280 was proposed to stabilize Trp276 in the active state; this was verified by site-directed mutagenesis and biochemical characterization of the resulting H280A and H280S mutants, which were fully functional but sharing an important decrease of their basal activities. Docking performed with short ghrelin derivatives Gly-Ser-Ser _[octa]-Phe-NH ₂ and Gly-Ser-Ser _[octa]-Phe-Leu-NH ₂ allowed the identification of a robust position of these peptides in the active site of the receptor. This model was refined by MDS and validated by docking experiments performed on a set of 55 ghrelin receptor ligands based on the 1,2,4- triazole scaffold. Finally, NMA performed on the obtained peptide-receptor complex suggested stabilization of the Trp276 residue and of the whole receptor in the active state, preventing the motion observed along mode 16 computed for the unbound receptor. Our results show that NMA offers a powerful approach to study the conformational diversity and the activation mechanism of GPCRs.     

Reproductive modes of three Ligularia weeds (Asteraceae) in grasslands in Qinghai-Tibet Plateau and their implications for grassland management

Ligularia virgaurea, L. sagitta and L. przewalskii are noxious weeds that are widely distributed in psychro-grasslands in the east of Qinghai-Tibet Plateau of China. However, little is known about reproductive modes and genetic diversity in the populations of L. virgaurea and L. sagitta under different environmental conditions, although such information is available for L. przewalskii. In this study, two experiments were conducted to examine the ex situ clonal growth of these weeds, and to determine the effects of reproductive modes on the diversity of their populations, using random amplified polymorphic DNA (RAPD) analysis. Transplanted seedlings of L. sagitta and L. virgaurea showed considerable clonal growth by forming rhizomes and ramets. The RAPD analysis showed that all individuals collected from natural populations were genetically different, indicating that no individuals originated from clonal growth. It is concluded that L. virgaurea and L. sagitta have the capacity for clonal growth, but the expression of their clonality is constrained by their growing conditions in natural grasslands. Sexual reproduction plays the major role in their population diversity in natural habitats, which requires that the control measures for these weeds should be targeted at the sexually reproducing populations.     

Enhancing students’ experimental planning competences by introducing and evaluating the IS4O teaching approach

ABSTRACT

We herein report the introduction of the IS⁴O (Improving Students’ Scientific Skills by Using Scaffolding Outlines) teaching approach and its implementation to successfully empower students with initial minor planning competences in mastering complex scientific challenges in the course of Germany’s most-renowned scientific competitions. The IS⁴O teaching approach itself comprises the unique combination of the differentiating teaching methods Backward Planning and Project Mapping as core teaching elements. The beneficial effect of the IS⁴O teaching approach on the enhancement of the students planning competences is also discussed. Based on the given results, this teaching approach is mandatory to empower students with initial minor competences in completing a scientific competition successfully with very high assignment of tasks.     

The oviduct is a brood chamber for facultative egg retention in the parthenogenetic oribatid mite Archegozetes longisetosus AOKI (Acari, Oribatida)

Archegozetes longisetosus is a parthenogenetic oribatid mite and a chelicerate model organism. We examined the localisation of processes between vitellogenesis and embryogenesis as well as the anatomy and histology of involved structures by means of light- and electron microscopy. The proximal oviduct is differentiated into an oviductal bulb, exhibiting a strong secretory epithelium. Here, solidification of the egg shell instantaneously occurs upon passing of the egg from the perivitelline space into the oviductal lumen. This is interpreted as an internalised oviposition with the generation boundary being effectively located at the ovary-oviduct transition, rendering the oviducts into functional brood chambers. The parity mode combines elements of oviparity and ovolarviparity with facultative egg retention.     

The chestnut blight fungus world tour: successive introduction events from diverse origins in an invasive plant fungal pathogen

Clonal expansion has been observed in several invasive fungal plant pathogens colonizing new areas, raising the question of the origin of clonal lineages. Using microsatellite markers, we retraced the evolutionary history of introduction of the chestnut blight fungus, Cryphonectria parasitica, in North America and western Europe. Combining discriminant analysis of principal components and approximate Bayesian computation analysis, we showed that several introduction events from genetically differentiated source populations have occurred in both invaded areas. In addition, a low signal of genetic recombination among different source populations was suggested in North America. Finally, two genetic lineages were present in both invaded areas as well as in the native areas, suggesting the existence of genetic lineages with a high capacity to establish in diverse environments and host species. This study confirmed the importance of multiple introductions, but questioned the role of genetic admixture in the success of introduction of a fungal plant pathogen.     

Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ-orbitrap mass analyzer

The success of a shotgun proteomic experiment relies heavily on the performance and optimization of both the LC and the MS systems. Despite this, little consideration has, so far, been given to the importance of evaluating and optimizing the MS instrument settings during data‐dependent acquisition mode. Moreover, during data‐dependent acquisition, the users have to decide and choose among various MS parameters and settings, making a successful analysis even more challenging. We have systematically investigated and evaluated the effect of enabling and disabling the preview mode for FTMS scan, the number of microscans per MS/MS scan, the number of MS/MS events, the maximum ion injection time for MS/MS, and the automatic gain control target value for MS and MS/MS events on protein and peptide identification rates on an LTQ‐Orbitrap using the Saccharomyces cerevisiae proteome. Our investigations aimed to assess the significance of each MS parameter to improve proteome analysis and coverage. We observed that higher identification rates were obtained at lower ion injection times i.e. 50–150 ms, by performing one microscan and 12–15 MS/MS events. In terms of ion population, optimal automatic gain control target values were at 5×10⁵–1×10⁶ ions for MS and 3×10³–1×10⁴ ions for MS/MS. The preview mode scan had a minimal effect on identification rates. Using optimized MS settings, we identified 1038 (±2.3%) protein groups with a minimum of two peptide identifications and an estimated false discovery rate of ～1% at both peptide and protein level in a 160‐min LC‐MS/MS analysis.     

做好实验准备工作,提高微生物学实验教学质量

完善的微生物学实验准备工作是确保实验成功的开始,也是提高微生物学实验教学质量的重要环节。从加强实验室管理,制定详细的实验准备内容,严格进行实验预做等方面介绍做好微生物学实验准备工作的经验,为提高实验教学质量,培养具有创新能力的人才提供参考和借鉴。     

Diagnostic tools for atrial tachyarrhythmias in implantable pacemakers: a review of technical options and pitfalls

Background. Correct pacemaker (PM) diagnosis of paroxysmal atrial tachyarrhythmias is crucial for their prevention and intervention with specific atrial pacing programmes. The PM mode switch to only ventricular pacing after detection of atrial tachyarrhythmias is often used as the parameter to quantify the ‘burden’ of atrial tachyarrhythmias. Objectives. This review addresses potential errors in the detection and diagnosis of atrial tachyarrhythmias, sometimes resulting in incorrect mode switches. The interpretation of PM-stored data of patients with atrial tachyarrhythmias and the results of trials of pace prevention and intervention can be better appreciated with more insight into the technical options and pitfalls. Results. Literature and clinical experience demonstrate that the correctness of PM-derived diagnosis of atrial tachyarrhythmias depends on 1) the sensitivity setting to detect the onset and perpetuation of atrial tachyarrhythmias frequently characterised by variable and low-voltage signals, 2) the rejection of far-field R wave sensing by the atrial sense amplifier, 3) the facility for verification of mode switches by a high-quality intracardiac registration of the nonmodified atrial electrogram. The configuration of the atrial lead also contributes to the diagnostic performance of the PM. Conclusion. Not only pacing algorithms and diverse technical PM features but also the atrial lead configuration are currently the limiting factors to the fully reliable, automated detection and diagnosis of atrial tachyarrhythmias. If these technical shortcomings can be improved, better signal processing will result. Then atrial pacing to prevent or suppress atrial tachyarrhythmias will be more justified. (Neth Heart J 2008;16:201-10.)     

Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach

Understanding how and why certain clades diversify greatly in morphology whereas others do not remains a major theme in evolutionary biology. Projecting families of phylogenies into multivariate morphospaces can distinguish two scenarios potentially leading to unequal morphological diversification: unequal magnitude of change per phylogenetic branch, and unequal efficiency in morphological innovation. This approach is demonstrated using a case study of skulls in sister clades within the South American fish superfamily Anostomoidea. Unequal morphological diversification in this system resulted not from the morphologically diverse clade changing more on each phylogenetic branch, but from that clade distributing an equal amount of change more widely through morphospace and innovating continually. Although substantial morphological evolution occurred throughout the less diverse clade's history, most of that clade's expansion in morphospace occurred in the most basal branches, and more derived portions of that radiation oscillated within previously explored limits. Because simulations revealed that there is a maximum 2.7% probability of generating two clades that differ so greatly in the density of lineages within morphospace under a null Brownian model, the observed difference in pattern likely reflects a difference in the underlying evolutionary process. Clade-specific factors that may have promoted or arrested morphological diversification are discussed.