Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity

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GTPase activation of elongation factor EF‐Tu by the ribosome during decoding

We have used single‐particle reconstruction in cryo‐electron microscopy to determine a structure of the Thermus thermophilus ribosome in which the ternary complex of elongation factor Tu (EF‐Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF‐Tu, but before the release of EF‐Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 Å. Secondary structure elements in tRNA, EF‐Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF‐Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF‐Tu.     

BH3-mimetic drugs prevent tumour onset in an orthotopic mouse model of hepatoblastoma

Drug resistance and metastasis remain major challenges in the treatment of high-risk hepatoblastoma (HB) and require the development of alternative therapeutic strategies. Modulation of apoptosis in HB cells enhances the sensitivity of these cells towards various drugs and has been discussed to enforce treatment. We investigated the impact of apoptosis sensitisers, BH3-mimetics, on the interaction between the host and HB to reduce tumour growth and dissemination while enhancing immunity. BH3-mimetics, such as obatoclax and ABT-737, enhanced the apoptosis-inducing effect of TRAIL and TNF-α resistant HB cells (HepT1 and HUH6). Tumour cell migration was inhibited by ABT-737 and more markedly by obatoclax. In an orthotopic model of HB, tumour uptake was reduced when the cells were pretreated with low concentrations of obatoclax. Only 1 of 7 mice developed HB in the liver, compared with an incidence of 0.8 in the control group. In summary, our study showed that apoptosis sensitisers had broader effects on HB cells than expected including migration and susceptibility to cytokines in addition to the known effects on drug sensitization. Sensitising HB to apoptosis may also allow resistant HB to be targeted by immune cells and prevent tumour cell dissemination.     

Loop analysis and qualitative modeling: limitations and merits

Richard Levins has advocated the scientific merits of qualitative modeling throughout his career. He believed an excessive and uncritical focus on emulating the models used by physicists and maximizing quantitative precision was hindering biological theorizing in particular. Greater emphasis on qualitative properties of modeled systems would help counteract this tendency, and Levins subsequently developed one method of qualitative modeling, loop analysis, to study a wide variety of biological phenomena. Qualitative modeling has been criticized for being conceptually and methodologically problematic. As a clear example of a qualitative modeling method, loop analysis shows this criticism is indefensible. The method has, however, some serious limitations. This paper describes loop analysis, its limitations, and attempts to clarify the differences between quantitative and qualitative modeling, in content and objective. Loop analysis is but one of numerous types of qualitative analysis, so its limitations do not detract from the currently underappreciated and underdeveloped role qualitative modeling could have within science.

Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea

Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in a parallel study (D. de Beer, F. Wenzhöfer, T. Ferdelman, S.E. Boehme, M. Huettel, J.E.E. van Beusekom, M.E. Böttcher, N. Musat, N. Dubilier, Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Romo Basin, Wadden Sea, Limnol. Oceanogr. 50 (2005) 113–127). Comparative 16S rRNA sequence analysis revealed a high bacterial diversity. Most sequences retrieved by PCR with a general bacterial primer set were affiliated with Bacteroidetes, Gammaproteobacteria, Deltaproteobacteria and the Pirellula cluster of Planctomycetales. Fluorescence in situ hybridization (FISH) and slot-blot hybridization with group-specific rRNA-targeted oligonucleotide probes were used to characterize the microbial community structure over depth (0–12 cm) and seasons (March, July, October). We found high abundances of bacteria with total cell numbers up to 3×10⁹ cells ml⁻¹ and a clear seasonal variation, with higher values in July and October versus March. The microbial community was dominated by members of the Planctomycetes, the Cytophaga/Flavobacterium group, Gammaproteobacteria, and bacteria of the Desulfosarcina/Desulfococcus group. The high abundance (1.5×10⁷–1.8×10⁸ cells ml⁻¹ accounting for 3–19% of all cells) of presumably aerobic heterotrophic polymer-degrading planctomycetes is in line with the high permeability, deep oxygen penetration, and the high rates of aerobic mineralization of algal biomass measured in the sandy sediments by de Beer et al. (2005). The high and stable abundance of members of the Desulfosarcina/Desulfococcus group, both over depth and season, suggests that these bacteria may play a more important role than previously assumed based on low sulfate reduction rates in parallel cores (de Beer et al., 2005).     

Assembly of the Drosophila larval exoskeleton requires controlled secretion and shaping of the apical plasma membrane.

The apical plasma membrane of epithelial cells plays a central role in producing and shaping the apical extracellular matrix (aECM) that eventually adopts a stereotypic architecture required for the physical and physiological needs of the epithelium. To assess the implication of the apical plasma membrane on aECM differentiation, we have studied the function of the apical plasma membrane t-SNARE Syntaxin 1A in the embryo of the fruit fly Drosophila melanogaster during differentiation of the stratified exoskeleton, the cuticle, which is composed of proteins and the polysaccharide chitin. The cuticle layers of syntaxin1A deficient larvae are rudimentary. Consistently, Syntaxin 1A is required for the secretion of O-glycosylated proteins and components involved in pigmentation and protein cross-linking. By contrast, localization of chitin synthesis and organising proteins to the apical plasma membrane or to the extracellular space does not depend on Syntaxin 1A activity. However, chitin microfibrils have a random orientation instead of being arranged in parallel. This correlates with the lack of corrugations at the apical plasma membrane of epidermal cells, the apical undulae that have been proposed to be crucial for chitin microfibril orientation. Hence, Syntaxin 1A contributes to cuticle differentiation by controlling correct apical plasma membrane topology as well as mediating secretion of a subset of extracellular proteins required for layer organisation. Our data also indicate that yet another unidentified t-SNARE is needed in parallel to Syntaxin 1A to deliver extracellular material for complete cuticle assembly. Evidently, coordination of apical membrane modelling and two secretion routes are essential for stereotypic aECM organisation.     

Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG

Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.