Combining electron crystallography and X-ray crystallography to study the MlotiK1 cyclic nucleotide-regulated potassium channel

We have recently reported the X-ray structure of the cyclic nucleotide-regulated potassium channel, MlotiK1. Here we describe the application of both electron and X-ray crystallography to obtain high quality crystals. We suggest that the combined application of these techniques provides a useful strategy for membrane protein structure determination. We also present negative stain projection and cryo-data projection maps. These maps provide new insights about the properties of the MlotiK1 channel. In particular, a comparison of a 9 Å cryo-data projection with calculated model maps strongly suggests that there is a very weak interaction between the pore and the S1–S4 domains of this 6 TM tetrameric cation channel and that the S1–S4 domains can adopt multiple orientations relative to the pore.     

Habitat selection by an Alpine ungulate: the significance of forage characteristics varies with scale and season

Habitat selection in ungulates should ensure access to abundant forage of sufficiently high quality. Species living in rugged mountain areas have to face nutritional bottlenecks regularly and should show particularly sophisticated habitat selection behaviour. However, patterns and mechanisms of such adaptations remain little studied. We analysed habitat selection and its seasonal variability of 10 GPS‐collared red deer Cervus elaphus living in a topographically challenging landscape of the Swiss Alps. We hypothesised that resource selection by red deer was scale‐dependent and predicted that scale‐dependence would vary among seasons in relation to seasonal changes of available forage biomass and quality, which we sampled across the entire study area of 250 km². The studied population of Alpine red deer undertook altitudinal migrations and showed scale‐dependent habitat selection that was strongest in winter and declined through spring and summer. Selection occurred mostly at the larger (landscape/home‐range location) scale and less so at the smaller (within home‐range) scale. Topographic parameters were selected mainly at the landscape scale and mostly in winter. About 70% of all instances of preference for habitat parameters were associated with above‐average forage characteristics, represented mostly by higher crude protein content, in a few cases also by higher biomass or both. The overall pattern of space use by red deer characterised by migration and seasonal habitat selection was therefore closely linked to the quality of food resources, although some trade‐offs with avoiding human disturbance may also have been involved.     

Diabetes and apoptosis: lipotoxicity

Obesity is an established risk factor in the pathogenesis of insulin resistance, type 2 diabetes mellitus and cardiovascular disease; all components that are part of the metabolic syndrome. Traditionally, insulin resistance has been defined in a glucocentric perspective. However, elevated systemic levels of fatty acids are now considered significant contributors towards the pathophysiological aspects associated with the syndrome. An overaccumulation of unoxidized long-chain fatty acids can saturate the storage capacity of adipose tissue, resulting in a lipid ‘spill over’ to non-adipose tissues, such as the liver, muscle, heart, and pancreatic-islets. Under these circumstances, such ectopic lipid deposition can have deleterious effects. The excess lipids are driven into alternative non-oxidative pathways, which result in the formation of reactive lipid moieties that promote metabolically relevant cellular dysfunction (lipotoxicity) and programmed cell-death (lipoapoptosis). Here, we focus on how both of these processes affect metabolically significant cell-types and highlight how lipotoxicity and sequential lipoapoptosis are as major mediators of insulin resistance, diabetes and cardiovascular disease.     

Induction of tetraploid poplar and black locust plants using colchicine: chloroplast number as an early marker for selecting polyploids in vitro

Tetraploid plants were produced by inducing chromosome doubling using colchicine in in vitro shoot tips of poplar and black locust clones. Many of the plants treated with colchicine showed modified morphological characteristics like stunted growth, thicker leaves and modified leaf morphology. The counting of chloroplast number in the epidermal guard cells of stomata was used for the rapid screening of tetraploids. The differences in mean chloroplast numbers between diploid and tetraploid plants were highly significant. For all plants tested, the tetraploid genotype had almost double the number of chloroplasts per guard cell compared to the diploid origin. Some plants were further analysed by flow cytometry to verify their ploidy status that was determined by chloroplast numbers. The results of this study demonstrated for the first time that chloroplast counting in poplar and black locust could be an effective and reliable method for pre-screening large numbers of plants for their ploidy level. The protocol might be applicable in a wide scope of breeding programs.     

Synergistic effect of immobilized laminin and nerve growth factor on PC12 neurite outgrowth

Immobilized extracellular matrix proteins and neurotrophins have been extensively studied to enhance neuronal adhesion and proliferation on surfaces for applications in nerve tissue engineering and neuroprosthetic devices. This article describes how the coimmobilization of laminin, an extracellular matrix protein and nerve growth factor (NGF), a neurotrophin can enhance neurite outgrowth observed separately with each type of molecule. In the absence of immobilized NGF, PC12 neurite outgrowth is influenced strongly by the presence of NGF in solution and unaffected by significant increases in laminin surface density (18.7–93.5 ng/mm²). However, when both laminin and NGF are immobilized together, the surface density of laminin is an important factor in determining whether or not the neurite outgrowth‐promoting effect of NGF can be obtained. PC12 neurite outgrowth on surfaces with coimmobilized laminin and NGF with surface densities of 27.6 ng/mm² and 1.4 ng/mm², respectively, are similar to that observed on surfaces with immobilized laminin and dissolved NGF. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Optimal data collection for correlated mutation analysis

The main objective of correlated mutation analysis (CMA) is to predict intraprotein residue-residue interactions from sequence alone. Despite considerable progress in algorithms and computer capabilities, the performance of CMA methods remains quite low. Here we examine whether, and to what extent, the quality of CMA methods depends on the sequences that are included in the multiple sequence alignment (MSA). The results revealed a strong correlation between the number of homologs in an MSA and CMA prediction strength. Furthermore, many of the current methods include only orthologs in the MSA, we found that it is beneficial to include both orthologs and paralogs in the MSA. Remarkably, even remote homologs contribute to the improved accuracy. Based on our findings we put forward an automated data collection procedure, with a minimal coverage of 50% between the query protein and its orthologs and paralogs. This procedure improves accuracy even in the absence of manual curation. In this era of massive sequencing and exploding sequence data, our results suggest that correlated mutation-based methods have not reached their inherent performance limitations and that the role of CMA in structural biology is far from being fulfilled.     

Factors important in evolutionary shaping of immunoglobulin gene loci

Background

The extraordinary diversity characterizing the antibody repertoire is generated by both evolution and lymphocyte development. Much of this diversity is due to the existence of immunoglobulin (Ig) variable region gene segment libraries, which were diversified during evolution and, in higher vertebrates, are used in generating the combinatorial diversity of antibody genes. The aim of the present study was to address the following questions: What evolutionary parameters affect the size and structure of gene libraries? Are the number of genes in libraries of contemporary species, and the corresponding gene locus structure, a random result of evolutionary history, or have these properties been optimized with respect to individual or population fitness? If a larger number of genes or different genome structures do not increase the fitness, then the current structure is probably optimized.

Results

We used a simulation of variable region gene library evolution. We measured the effect of different parameters on gene library size and diversity, and the corresponding fitness. We found compensating relationships between parameters, which optimized Ig library size and diversity.

Conclusions

We conclude that contemporary species' Ig libraries have been optimized by evolution in terms of Ig sequence lengths, the number and diversity of Ig genes, and antibody-antigen affinities.