Atomistic mechanisms of huntingtin N‐terminal fragment insertion on a phospholipid bilayer revealed by molecular dynamics simulations

The huntingtin protein is characterized by a segment of consecutive glutamines (Q_N) that is responsible for its fibrillation. As with other amyloid proteins, misfolding of huntingtin is related to Huntington's disease through pathways that can involve interactions with phospholipid membranes. Experimental results suggest that the N‐terminal 17‐amino‐acid sequence (htt^NT) positioned just before the Q_N region is important for the binding of huntingtin to membranes. Through all‐atom explicit solvent molecular dynamics simulations, we unveil the structure and dynamics of the htt^NTQ_N fragment on a phospholipid membrane at the atomic level. We observe that the insertion dynamics of this peptide can be described by four main steps—approach, reorganization, anchoring, and insertion—that are very diverse at the atomic level. On the membrane, the htt^NT peptide forms a stable α‐helix essentially parallel to the membrane with its nonpolar side‐chains—mainly Leu‐4, Leu‐7, Phe‐11 and Leu‐14—positioned in the hydrophobic core of the membrane. Salt‐bridges involving Glu‐5, Glu‐12, Lys‐6, and Lys‐15, as well as hydrogen bonds involving Thr‐3 and Ser‐13 with the phospholipids also stabilize the structure and orientation of the htt^NT peptide. These observations do not significantly change upon adding the Q_N region whose role is rather to provide, through its hydrogen bonds with the phospholipids' head group, a stable scaffold facilitating the partitioning of the htt^NT region in the membrane. Moreover, by staying accessible to the solvent, the amyloidogenic Q_N region could also play a key role for the oligomerization of htt^NTQ_N on phospholipid membranes. Proteins 2014; 82:1409–1427. © 2014 Wiley Periodicals, Inc.     

Mutation and sexual selection: a test using barn swallows from Chernobyl

Abstract Secondary sexual characters have been hypothesized to be particularly susceptible to the deleterious effects of mutation because the expression of such characters is usually influenced by many more metabolic pathways than are ordinary morphological characters. We tested this hypothesis using the elevated mutation rates in the barn swallow ( Hirundo rustica ) of the Chernobyl region of Ukraine as a model system. A great deal is known about the relative importance of different characters for male mating success in this species. The importance of phenotypic characters for male mating success was quantified based on a long-term study of a Danish breeding population, by expressing phenotypic differences between mated and unmated males as the difference between log-transformed mean values. For field samples from Ukraine we likewise expressed the difference in male phenotype between individuals living in a relatively uncontaminated area and individuals from the Chernobyl region as the difference between log-transformed mean values. The standardized difference in male phenotype between the two regions in Ukraine for the 41 different characters was strongly positively correlated with the standardized difference in male phenotype between mated and unmated males from Denmark. The standardized difference in male phenotype between the two regions in Ukraine was significantly positively associated with sexual size dimorphism. However, the standardized difference in male phenotype between mated and unmated males was a much better predictor of standardized difference in male phenotype between the two regions in Ukraine than was the standardized difference in sexual size dimorphism, expressed as the difference between log-transformed mean values for males and females. These findings are consistent with the hypothesis that traits most important for sexual selection are particularly susceptible to the effects of deleterious mutations.     

Larval host plant affects fitness consequences of egg size variation in the seed beetle Stator limbatus

Egg size variation often has large effects on the fitness of progeny in insects. However, many studies have been unable to detect an advantage of developing from large eggs, suggesting that egg size variation has implications for offspring performance only under adverse conditions, such as during larval competition, periods of starvation, desiccation, or when larvae feed on low-quality resources. We test this hypothesis by examining the consequences of egg size variation for survivorship and development of a seed-feeding insect, Stator limbatus, on both a low-quality (Cercidium floridum) and a high-quality (Acacia greggii) host plant. Our results are consistent with the hypothesis. S. limbatus larval performance was affected by egg size only when developing on the poor-quality host (C. floridum); larvae from large eggs survived better on C. floridum than those from small eggs, while there was no evidence of an effect of egg size on progeny development time, body weight, or survivorship when larvae developed on A. greggii. These results indicate intense selection for large eggs within C. floridum-associated populations, but not in A. greggii-associated populations, so that egg size is predicted to vary among populations associated with different hosts. Our results also support this hypothesis; females from a C. floridum-associated population (Scottsdale) laid larger eggs than females from an A. greggii-associated population (Black Canyon City).     

Material and genetic benefits of female multiple mating and polyandry

The maintenance of female polyandry has traditionally been attributed to the material (direct) benefits derived from male mating resources (e.g. nuptial gifts) accrued by multiple mating. However, genetic (indirect) benefits offer a more robust explanation since only polyandrous, not monandrous, females may gain both material benefits from multiple mating and genetic benefits from multiple sires. Discriminating between material and genetic benefits is essential when addressing the mechanism by which polyandry is adaptively maintained, but are difficult to disentangle because they affect fitness in similar ways. To test the hypothesis that genetic benefits maintain polyandry, we compared four components of fitness (longevity, fecundity, hatching success and survivorship) between monandrous and polyandrous females in the ground cricket, Allonemobius socius. We discovered that females derived nongenetic benefits from mating multiply, in that the magnitude of the nuptial gift was positively associated with the number of eggs produced. However, polyandrous females had over a two-fold greater hatching success and a 43% greater offspring survivorship, leading to a significantly higher relative fitness than the monandrous strategy. These results were independent of the confounding effects of material benefits, implying that genetic contributions play a large role in the maintenance of polyandry and potentially in the antagonistic coevolutionary relationship between polyandry and male nuptial gifts. Copyright 2002 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour     

Mutation processes in natural populations of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> and <Emphasis Type="Italic">Hirundo rustica</Emphasis> from radiation-contaminated regions of Ukraine

Natural populations of Drosophila melanogaster and Hirundo rustica from regions of Ukraine exhibiting different levels of radiation contamination are investigated. Genetic monitoring was performed with respect to such parameters as the frequency of visible sex-linked mutations, frequency of gonad reduction in Drosophila, and rate of interphase manifestations of chromosomal instability in the erythrocytes of the birds. The results attest to a possible opposite dependence of the level of chromosomal instability among swallows and that of the rate of lethal mutations in the sex chromosome of Drosophila on the density of radiation contamination.     

Navigation and analysis of the energy landscape of small proteins using the activation-relaxation technique

The resolution of the protein folding problem has been tied to the development of a detailed understanding of the configurational energy or of the free energy landscape associated with these molecules. Using the activation-relaxation technique and a simplified energy model, we present here a detailed analysis of the energy landscape of 16-residue peptide that folds into a beta-hairpin. Our results support the concept of an energy landscape with an effective topology consistent with a scale-free network.     

Elevated Frequency of Cataracts in Birds from Chernobyl

Background

Radiation cataracts develop as a consequence of the effects of ionizing radiation on the development of the lens of the eye with an opaque lens reducing or eliminating the ability to see. Therefore, we would expect cataracts to be associated with reduced fitness in free-living animals.

Methodology/Principal Findings

We investigated the incidence of lens opacities typical of cataracts in more than 1100 free-living birds in the Chernobyl region in relation to background radiation. The incidence of cataracts increased with level of background radiation both in analyses based on a dichotomous score and in analyses of continuous scores of intensity of cataracts. The odds ratio per unit change in the regressor was 0.722 (95% CI 0.648, 0.804), which was less than odds ratios from investigations of radiation cataracts in humans. The relatively small odds ratio may be due to increased mortality in birds with cataracts. We found a stronger negative relationship between bird abundance and background radiation when the frequency of cataracts was higher, but also a direct effect of radiation on abundance, suggesting that radiation indirectly affects abundance negatively through an increase in the frequency of cataracts in bird populations, but also through direct effects of radiation on other diseases, food abundance and interactions with other species. There was no increase in incidence of cataracts with increasing age, suggesting that yearlings and older individuals were similarly affected as is typical of radiation cataract.

Conclusions/Significance

These findings suggest that cataracts are an under-estimated cause of morbidity in free-living birds and, by inference, other vertebrates in areas contaminated with radioactive materials.     

The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens

Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.     

Highly reduced mass loss rates and increased litter layer in radioactively contaminated areas

The effects of radioactive contamination from Chernobyl on decomposition of plant material still remain unknown. We predicted that decomposition rate would be reduced in the most contaminated sites due to an absence or reduced densities of soil invertebrates. If microorganisms were the main agents responsible for decomposition, exclusion of large soil invertebrates should not affect decomposition. In September 2007 we deposited 572 bags with uncontaminated dry leaf litter from four species of trees in the leaf litter layer at 20 forest sites around Chernobyl that varied in background radiation by more than a factor 2,600. Approximately one quarter of these bags were made of a fine mesh that prevented access to litter by soil invertebrates. These bags were retrieved in June 2008, dried and weighed to estimate litter mass loss. Litter mass loss was 40 % lower in the most contaminated sites relative to sites with a normal background radiation level for Ukraine. Similar reductions in litter mass loss were estimated for individual litter bags, litter bags at different sites, and differences between litter bags at pairs of neighboring sites differing in level of radioactive contamination. Litter mass loss was slightly greater in the presence of large soil invertebrates than in their absence. The thickness of the forest floor increased with the level of radiation and decreased with proportional loss of mass from all litter bags. These findings suggest that radioactive contamination has reduced the rate of litter mass loss, increased accumulation of litter, and affected growth conditions for plants.