Amorphous silica-like carbon dioxide

Among the group IV elements, only carbon forms stable double bonds with oxygen at ambient conditions. At variance with silica and germania, the non-molecular single-bonded crystalline form of carbon dioxide, phase V, only exists at high pressure. The amorphous forms of silica (a-SiO2) and germania (a-GeO2) are well known at ambient conditions; however, the amorphous, non-molecular form of CO2 has so far been described only as a result of first-principles simulations. Here we report the synthesis of an amorphous, silica-like form of carbon dioxide, a-CO2, which we call 'a-carbonia'. The compression of the molecular phase III of CO2 between 40 and 48 GPa at room temperature initiated the transformation to the non-molecular amorphous phase. Infrared spectra measured at temperatures up to 680 K show the progressive formation of C-O single bonds and the simultaneous disappearance of all molecular signatures. Furthermore, state-of-the-art Raman and synchrotron X-ray diffraction measurements on temperature-quenched samples confirm the amorphous character of the material. Comparison with vibrational and diffraction data for a-SiO2 and a-GeO2, as well as with the structure factor calculated for the a-CO2 sample obtained by first-principles molecular dynamics, shows that a-CO2 is structurally homologous to the other group IV dioxide glasses. We therefore conclude that the class of archetypal network-forming disordered systems, including a-SiO2, a-GeO2 and water, must be extended to include a-CO2.     

Crystal structure of the non-haem iron halogenase SyrB2 in syringomycin biosynthesis

Non-haem Fe(II)/alpha-ketoglutarate (alphaKG)-dependent enzymes harness the reducing power of alphaKG to catalyse oxidative reactions, usually the hydroxylation of unactivated carbons, and are involved in processes such as natural product biosynthesis, the mammalian hypoxic response, and DNA repair. These enzymes couple the decarboxylation of alphaKG with the formation of a high-energy ferryl-oxo intermediate that acts as a hydrogen-abstracting species. All previously structurally characterized mononuclear iron enzymes contain a 2-His, 1-carboxylate motif that coordinates the iron. The two histidines and one carboxylate, known as the 'facial triad', form one triangular side of an octahedral iron coordination geometry. A subclass of mononuclear iron enzymes has been shown to catalyse halogenation reactions, rather than the more typical hydroxylation reaction. SyrB2, a member of this subclass, is a non-haem Fe(II)/alphaKG-dependent halogenase that catalyses the chlorination of threonine in syringomycin E biosynthesis. Here we report the structure of SyrB2 with both a chloride ion and alphaKG coordinated to the iron ion at 1.6 A resolution. This structure reveals a previously unknown coordination of iron, in which the carboxylate ligand of the facial triad is replaced by a chloride ion.     

Predator learning favours mimicry of a less-toxic model in poison frogs

Batesian mimicry--resemblance of a toxic model by an edible mimic--depends on deceiving predators. Mimetic advantage is considered to be dependent on frequency because an increase in mimic abundance leads to breakdown of the warning signal. Where multiple toxic species are available, batesian polymorphism is predicted--that is, mimics diversify to match sympatric models. Despite the prevalence of batesian mimicry in nature, batesian polymorphism is relatively rare. Here we explore a poison-frog mimicry complex comprising two parapatric models and a geographically dimorphic mimic that shows monomorphism where models co-occur. Contrary to classical predictions, our toxicity assays, field observations and spectral reflectances show that mimics resemble the less-toxic and less-abundant model. We examine "stimulus generalization" as a mechanism for this non-intuitive result with learning experiments using naive avian predators and live poison frogs. We find that predators differ in avoidance generalization depending on toxicity of the model, conferring greater protection to mimics resembling the less-toxic model owing to overlap of generalized avoidance curves. Our work supports a mechanism of toxicity-dependent stimulus generalization, revealing an additional solution for batesian mimicry where multiple models coexist.     

Reconstructing the early evolution of Fungi using a six-gene phylogeny

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.     

Mapping and sequencing of structural variation from eight human genomes

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.     

Climate change decreases aquatic ecosystem productivity of Lake Tanganyika,Africa

Although the effects of climate warming on the chemical and physical properties of lakes have been documented, biotic and ecosystem-scale responses to climate change have been only estimated or predicted by manipulations and models. Here we present evidence that climate warming is diminishing productivity in Lake Tanganyika, East Africa. This lake has historically supported a highly productive pelagic fishery that currently provides 25-40% of the animal protein supply for the populations of the surrounding countries. In parallel with regional warming patterns since the beginning of the twentieth century, a rise in surface-water temperature has increased the stability of the water column. A regional decrease in wind velocity has contributed to reduced mixing, decreasing deep-water nutrient upwelling and entrainment into surface waters. Carbon isotope records in sediment cores suggest that primary productivity may have decreased by about 20%, implying a roughly 30% decrease in fish yields. Our study provides evidence that the impact of regional effects of global climate change on aquatic ecosystem functions and services can be larger than that of local anthropogenic activity or overfishing.