Long-range organization of bacteriochlorophyll in chlorosomes of Chlorobium tepidum investigated by cryo-electron microscopy

Intact chlorosomes of Chlorobium tepidum were embedded in amorphous ice layers and examined by cryo-electron microscopy to study the long-range organization of bacteriochlorophyll (BChl) layers. End-on views reveal that chlorosomes are composed of several multi-layer tubules of variable diameter (20-30 nm) with some locally undulating non-tubular lamellae in between. The multi-layered tubular structures are more regular and larger in a C. tepidum mutant that only synthesizes [8-ethyl, 12-methyl]-BChl d. Our data show that wild-type C. tepidum chlorosomes do not have a highly regular, long-range BChl c layer organization and that they contain several multi-layered tubules rather than single-layer tubules or exclusively undulating lamellae as previously proposed.     

Molecular diagnostics of Meckel–Gruber syndrome highlights phenotypic differences between MKS1 and MKS3

Meckel–Gruber syndrome (MKS) is a recessively inherited, lethal disorder characterized by renal cystic dysplasia, occipital encephalocele, polydactyly and biliary dysgenesis. MKS is genetically heterogeneous with three loci mapped and two identified; MKS1 (17q23) and MKS3 (8q22.1). MKS1 is part of the Finnish disease heritage, while MKS3 has been described exclusively in consanguineous Asian families. Here we aimed to establish molecular diagnostics for MKS, determine the importance of MKS1 and MKS3 in non-consanguineous populations, and study genotype/phenotype correlations. The coding regions of MKS1 and MKS3 were screened for mutations by direct sequencing in 17 families clinically diagnosed with MKS in the US or The Netherlands. The clinical phenotype was compared to genic and allelic effects. Both mutations were identified in ten families; five MKS1 and five MKS3. All but two were compound heterozygotes, consistent with their non-consanguineous nature. The MKS1-Fin_major mutation accounted for 7/10 MKS1 mutations; two novel changes were additionally detected. Seven novel mutations were found in MKS3, including three missense changes. We concluded that MKS1 and MKS3 account for the majority of MKS in non-consanguineous populations of European origin. Polydactyly is usually found in MKS1 but rare in MKS3. Cases with no, or milder, CNS phenotypes were only found in MKS3; hypomorphic missense mutations may be associated with less severe CNS outcomes. This study is consistent with further genetic heterogeneity of MKS, but underlines the value of molecular diagnostics of the known genes to aid family planning decisions. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Uncoupling protein 2 modulates cell viability in adult rat cardiomyocytes

Uncoupling protein 2 (UCP2) is an inner mitochondrial membrane proton carrier that uncouples ATP synthesis. The aim of this study was to determine whether UCP2 plays a role in survival of adult rat cardiac myocytes. We first studied the effects of UCP2 overexpression in vitro. Overexpression of UCP2 in primary cardiomyocytes led to a significant decline in ATP level and the development of acidosis but had no observable effect on cell survival. When cardiomyocytes were challenged with hypoxia-reoxygenation, cells overexpressing UCP2 survived significantly less compared with control. This finding was associated with upregulation of proapoptotic protein Bcl-2 and 19-kDa interacting protein 3 (BNIP3). Furthermore, UCP2 short interfering RNA prevented both the increase in cell death and BNIP3 expression. To examine the in vivo role of UCP2 in the heart, we used the Dahl salt-sensitive rat heart-failure model. Northern blot analysis revealed that UCP2 mRNA level was significantly upregulated in rat heart failure along with BNIP3 protein level. In conclusion, UCP2 increases sensitivity of adult rat cardiac myocytes to hypoxia-reoxygenation by way of ATP depletion and acidosis, which in turn causes accumulation of prodeath protein BNIP3.     

Slow recovery from perturbations as a generic indicator of a nearby catastrophic shift

The size of the basin of attraction in ecosystems with alternative stable states is often referred to as "ecological resilience." Ecosystems with a low ecological resilience may easily be tipped into an alternative basin of attraction by a stochastic event. Unfortunately, it is very difficult to measure ecological resilience in practice. Here we show that the rate of recovery from small perturbations (sometimes called "engineering resilience") is a remarkably good indicator of ecological resilience. Such recovery rates decrease as a catastrophic regime shift is approached, a phenomenon known in physics as "critical slowing down." We demonstrate the robust occurrence of critical slowing down in six ecological models and outline a possible experimental approach to quantify differences in recovery rates. In all the models we analyzed, critical slowing down becomes apparent quite far from a threshold point, suggesting that it may indeed be of practical use as an early warning signal. Despite the fact that critical slowing down could also indicate other critical transitions, such as a stable system becoming oscillatory, the robustness of the phenomenon makes it a promising indicator of loss of resilience and the risk of upcoming regime shifts in a system.     

Superorganisms or loose collections of species? A unifying theory of community patterns along environmental gradients

The question whether communities should be viewed as superorganisms or loose collections of individual species has been the subject of a long‐standing debate in ecology. Each view implies different spatiotemporal community patterns. Along spatial environmental gradients, the organismic view predicts that species turnover is discontinuous, with sharp boundaries between communities, while the individualistic view predicts gradual changes in species composition. Using a spatially explicit multispecies competition model, we show that organismic and individualistic forms of community organisation are two limiting cases along a continuum of outcomes. A high variance of competition strength leads to the emergence of organism‐like communities due to the presence of alternative stable states, while weak and uniform interactions induce gradual changes in species composition. Dispersal can play a confounding role in these patterns. Our work highlights the critical importance of considering species interactions to understand and predict the responses of species and communities to environmental changes.     

Historical biogeography of the Isthmus of Panama

About 3 million years ago (Ma), the Isthmus of Panama joined the Americas, forming a land bridge over which inhabitants of each America invaded the other—the Great American Biotic Interchange. These invasions transformed land ecosystems in South and Middle America. Humans invading from Asia over 12000 years ago killed most mammals over 44 kg, again transforming tropical American ecosystems. As a sea barrier, the isthmus induced divergent environmental change off its two coasts—creating contrasting ecosystems through differential extinction and diversification. Approximately 65 Ma invading marsupials and ungulates of North American ancestry, and xenarthrans of uncertain provenance replaced nearly all South America's non‐volant mammals. There is no geological evidence for a land bridge at that time. Together with rodents and primates crossing from Africa 42 to 30 Ma, South America's mammals evolved in isolation until the interchange's first heralds less than 10 Ma. Its carnivores were ineffective marsupials. Meanwhile, North America was invaded by more competitive Eurasian mammals. The Americas had comparable expanses of tropical forest 55 Ma; later, climate change confined North American tropical forest to a far smaller area. When the isthmus formed, North American carnivores replaced their marsupial counterparts. Although invaders crossed in both directions, North American mammals spread widely, diversified greatly, and steadily replaced South American open‐country counterparts, unused to effective predators. Invading South American mammals were less successful. South America's birds, bats, and smaller rainforest mammals, equally isolated, mostly survived invasion. Its vegetation, enriched by many overseas invaders, remained intact. This vegetation resists herbivory effectively. When climate permitted, South America's rainforest, with its bats, birds and mammals, spread to Mexico. Present‐day tropical American vegetation is largely zoned by trade‐offs between exploiting well‐watered settings versus surviving droughts, exploiting fertile versus coping with poor soil, and exploiting lowland warmth versus coping with cooler altitudes. At the start of the Miocene, a common marine biota extended from Trinidad to Ecuador and western Mexico, which evolved in isolation from the Indo‐Pacific until the Pleistocene. The seaway between the Americas began shoaling over 12 Ma. About 10 Ma the land bridge was briefly near‐complete, allowing some interchange of land mammals between the continents. By 7 Ma, the rising sill had split deeper‐water populations. Sea temperature, salinity and sedimentary carbon content had begun to increase in the Southern Caribbean, but not the Pacific. By 4 Ma, the seaway's narrowing began to extinguish Caribbean upwellings. By 2 Ma, upwellings remained only along Venezuela; Caribbean plankton, suspension‐feeding molluscs and their predators had declined sharply, largely replaced by bottom‐dwelling corals and calcareous algae and magnificent coral reefs. Closing the seaway extinguished the Eastern Pacific's reef corals (successors recolonized from the Indo‐Pacific 6000 years ago), whereas many molluscs of productive waters that once thrived in the Caribbean now survive only in the Eastern Pacific. The present‐day productive Eastern Pacific, with few, small coral reefs and a plankton‐based ecosystem contrasts with the Caribbean, whose clear water favours expansive coral reefs and bottom‐dwelling primary producers. These ecosystems reflect the trade‐off between fast growth and effective defence with attendant longevity. Overfishing with new technologies during the last few centuries, however, has caused population crashes of ever‐smaller marine animals, devastating Caribbean ecosystems.     

A Genome-Wide Association Study Reveals Dominance Effects on Number of Teats in Pigs

Dominance has been suggested as one of the genetic mechanisms explaining heterosis. However, using traditional quantitative genetic methods it is difficult to obtain accurate estimates of dominance effects. With the availability of dense SNP (Single Nucleotide Polymorphism) panels, we now have new opportunities for the detection and use of dominance at individual loci. Thus, the aim of this study was to detect additive and dominance effects on number of teats (NT), specifically to investigate the importance of dominance in a Landrace-based population of pigs. In total, 1,550 animals, genotyped for 32,911 SNPs, were used in single SNP analysis. SNPs with a significant genetic effect were tested for their mode of gene action being additive, dominant or a combination. In total, 21 SNPs were associated with NT, located in three regions with additive (SSC6, 7 and 12) and one region with dominant effects (SSC4). Estimates of additive effects ranged from 0.24 to 0.29 teats. The dominance effect of the QTL located on SSC4 was negative (−0.26 teats). The additive variance of the four QTLs together explained 7.37% of the total phenotypic variance. The dominance variance of the four QTLs together explained 1.82% of the total phenotypic variance, which corresponds to one-fourth of the variance explained by additive effects. The results suggest that dominance effects play a relevant role in the genetic architecture of NT. The QTL region on SSC7 contains the most promising candidate gene: VRTN. This gene has been suggested to be related to the number of vertebrae, a trait correlated with NT.     

Complex agro-ecosystems for food security in a changing climate

Attempts to increase food crop yields by intensifying agricultural systems using high inputs of nonrenewable resources and chemicals frequently lead to de-gradation of natural resources, whereas most technological innovations are not accessible for smallholders that represent the majority of farmers world wide. Alternatively, cocultures consisting of assemblages of plant and animal species can support ecological processes of nutrient cycling and pest control, which may lead to increasing yields and declining susceptibility to extreme weather conditions with increasing complexity of the systems. Here we show that enhancing the complexity of a rice production system by adding combinations of compost, azolla, ducks, and fish resulted in strongly increased grain yields and revenues in a season with extremely adverse weather conditions on East Java, Indonesia. We found that azolla, duck, and fish increased plant nutrient content, tillering and leaf area expansion, and strongly reduced the density of six different pests. In the most complex system comprising all components the highest grain yield was obtained. The net revenues of this system from sales of rice grain, fish, and ducks, after correction for extra costs, were 114% higher than rice cultivation with only compost as fertilizer. These results provide more insight in the agro-ecological processes and demonstrate how complex agricultural systems can contribute to food security in a changing climate. If smallholders can be trained to manage these systems and are supported for initial investments by credits, their livelihoods can be improved while producing in an ecologically benign way.     

Bill redness is positively associated with reproduction and survival in male and female zebra finches

Sexual traits can serve as honest indicators of phenotypic quality when they are costly. Brightly coloured yellow to red traits, which are pigmented by carotenoids, are relatively common in birds, and feature in sexual selection. Carotenoids have been linked to immune and antioxidant function, and the trade-off between ornamentation and these physiological functions provides a potential mechanism rendering carotenoid based signals costly. Mutual ornamentation is also common in birds and can be maintained by mutual mate choice for this ornament or by a correlated response in one sex to selection on the other sex. When selection pressures differ between the sexes this can cause intralocus sexual conflict. Sexually antagonistic selection pressures have been demonstrated for few sexual traits, and for carotenoid-dependent traits there is a single example: bill redness was found to be positively associated with survival and reproductive output in male zebra finches, but negatively so in females. We retested these associations in our captive zebra finch population without two possible limitations of this earlier study. Contrary to the earlier findings, we found no evidence for sexually antagonistic selection. In both sexes, individuals with redder bills showed higher survival. This association disappeared among the females with the reddest bills. Furthermore, females with redder bills achieved higher reproductive output. We conclude that bill redness of male and female zebra finches honestly signals phenotypic quality, and discuss the possible causes of the differences between our results and earlier findings.