Amino acid sequence, crystallization and structure determination of reduced and oxidized cytochrome c6 from the green alga Scenedesmus obliquus.

Cytochrome c6from the unicellular green alga Scenedesmus obliquus was sequenced, crystallized in its reduced and oxidized state and the three-dimensional structure of the protein in both redox states was determined by X-ray crystallography. Reduced cytochrome c6crystallized as a monomer in the space group P 21212, whereas the oxidized protein crystallized as a dimer in the space group P 3121. The structures were solved by molecular replacement and refined to 1. 9 and 2.0 A, respectively.Comparison of the structures of both redox states revealed only slight differences on the protein surface, whereas a distortion along the axis between the heme iron and its coordinating Met61 residue was observed. No redox-dependent movement of internal water molecules could be detected. The high degree of similarity of the surfaces and charge distributions of both redox states, as well as the dimerization of cytochrome c6as observed in the oxidized crystal, is discussed with respect to its biological relevance and its implications for the reaction mechanisms between cytochrome c6and its redox partners. The dimer of oxidized cytochrome c6may represent a molecular structure occurring in a binary complex with cytochrome b6f. This assembly might be required for the correct orientation of cytochrome c6with respect to its redox partner cytochrome b6f, facilitating the electron transfer within the complex. If the dimerization is not redox-dependent in vivo, the almost identical surfaces of both redox states do not support a long range differentiation between reduced and oxidized cyt c6, i.e. a random collision model for the formation of an electron transfer complex must be assumed.     

Context‐dependent interactions between adult shrubs and seedlings in a semi‐arid shrubland

Abstract. Question: In semi‐arid systems, rainfall gradients can cause plant‐plant interactions to shift from negative to positive or vice versa. However, the importance of a second major abiotic factor, soil nutrients, has rarely been considered. We consider different combinations of both factors and ask: do net adult‐seedling interactions become less competitive and more facilitative with increasing overall abiotic harshness? Location: Succulent Karoo, Western Cape, South Africa. Methods: We examined the interactions between seedlings and adult shrubs at two sites. Sites differ in rainfall, and each contain two habitats: Nutrient‐rich mounds associated with underground termitaria and a relatively nutrient‐poor matrix. We carried out a spatial pattern analysis of community‐wide seedling‐adult associations. We then conducted field and greenhouse experiments to test the effects of soil and the presence of neighbouring shrubs on the growth and survival of six seedling species. Results: At the higher rainfall site, both competitive and facilitative effects of adults on seedlings were found but did not differ by habitat, despite the more benign conditions in the mound habitat. At the lower rainfall site, adult shrubs generally had neutral effects on seedlings in the matrix habitat. In the nutrient‐rich mound habitat, however, adult shrubs had strong and consistently competitive effects on seedlings. Conclusion: Seedling‐adult interactions could not be predicted by a simple overall gradient of abiotic harshness, demonstrating the need for more complex, mechanistic models to predict plant‐plant interactions. We suggest that rainfall and soil nutrients affect seedling‐adult relations through their interactive effects on the life‐history attributes of the species involved.     

Understanding the long‐term spatial dynamics of a semiarid grass‐shrub steppe through inverse parameterization for simulation models

Desertification threatens 70% of all dry lands worldwide by diminishing the provision of economic and ecosystem services. However, since long‐term vegetation dynamics of semiarid ecosystems are difficult to study, the opportunities to evaluate desertification and degradation properly are limited. In this study, we tailored, calibrated and tested a spatially‐explicit simulation model (DINVEG) to describe the long‐term dynamics of dominant grass and shrub species in the semiarid Patagonian steppe. We used inverse techniques to identify parameterizations that yield model outputs in agreement with detailed field data, and we performed sensitivity analyses to reveal the main drivers of long‐term vegetation dynamics. Whereas many parameterizations (10–45%) matched single field observations (e.g. grass and shrub cover, species‐specific density, aboveground net primary production [ANPP]), only a few parameterizations (0.05%) yielded simultaneous match of all field observations. Sensitivity analysis pointed to demographic constraints for shrubs and grasses in the emergence and recruitment phase, respectively, which contributed to balanced shrub‐grass abundances in the long run. Vegetation dynamics of simulations that matched all field observations were characterized by a stochastic equilibrium. The soil water content in the top layer (0–10 cm) during the emergence period was the strongest predictor of shrub densities and population growth rates and of growth rates of grasses. Grasses controlled the shrub demography because of the resource overlap of grasses with juvenile shrubs (i.e. water content in the top layer). In agreement with field observations, ecosystem function buffered the strong variability in precipitation (a simulated CV in ANPP of 16% vs CV in precipitation of 33%). Our results show that seedling emergence and recruitment are critical processes for long‐term vegetation dynamics in this steppe. The methods presented here could be widely applied when data for direct parameterization of individual‐based models are lacking, but data corresponding to model outputs are available. Our modeling methodology can reduce the need for long‐term data sets when answering questions regarding community dynamics.     

Crystallographic refinement and atomic models of two different forms of citrate synthase at 2·7 and 1·7 Å resolution

The structures of pig heart and chicken heart citrate synthase have been determined by multiple isomorphous replacement and restrained crystallographic refinement for two crystal forms, a tetragonal form at 2·7 Å and a monoclinic form at 1·7 Å resolution, with crystallographic R-values of 0·199 and 0·192, respectively. The structure determination involved a novel application of restrained crystallographic refinement, in that the refinement of incomplete models was necessary in order to completely determine the course of the polypeptide chain. The recently determined amino acid sequence (Bloxham et al., 1981) has been fitted to the models. The molecule has substantially different conformations in the two crystal forms, and there is evidence that a conformational change is required for enzymatic activity.The molecule is a dimer of identical subunits with 437 amino acid residues each. The conformation is all α-helix, with 40 helices per dimer packing tightly to form a globular molecule. Many of the helices are kinked in various ways or bent smoothly over a large angle. Several of the helices show an unusual antiparallel packing.Each subunit is clearly divided into a large and a small domain. The two crystal forms differ by the relative arrangement of the two domains. The tetragonal form represents an open configuration with a deep cleft between the two domains, the monoclinic form is closed. The structural change from the open to the closed form can be described by an 18 ° rotation of the small domain relative to the large domain.Crystallographic analyses were performed with the product citrate bound in both crystal forms, with coenzyme A (CoA) and a citryl-CoA analogue bound to the monoclinic form. These studies establish the CoA and the citrate binding sites, and the conformations of the two product molecules in atomic detail. The subunits are extensively interdigitated, with one subunit making significant contributions to both the citrate and the CoA binding sites of the other subunit. The adenine moiety of CoA is bound to the small domain, and the pantothenic arm is bound to the large domain. The citrate molecule is bound in a cleft between the large domain. The citrate molecule is bound in a cleft between the large and small domain, with the si carboxymethylene group facing the SH arm of coenzyme A. In the monoclinic form, the cysteamine part of CoA shields the bound citrate completely from the solution. Partial reaction of CoA-SH and aspartate 375 to form aspartyl-CoA, and citrate to form citryl-CoA may occur in the crystals. The conformation of CoA is compact, characterized by an internal hydrogen bond O-52 … N-7 and a tightlybound water molecule O-51 … HOH … O-20.     

Individual species–area relationships and spatial patterns of species diversity in a Great Basin,semi‐arid shrubland

Traditional biodiversity metrics operate at the level of a plant community but do not capture spatial variation in diversity from a ‘plant's‐eye view’ of a community. Recently‐developed statistics consider the spatial patterns of plants as well as the number and distribution of species in local plant neighborhoods to quantitatively assess multispecies spatial patterns from a ‘plant's‐eye view’. We used one such statistic, the individual species area relationship (ISAR), to assess spatial patterns of species diversity in a Great Basin (USA) semi‐arid shrubland through an analysis of a spatial dataset on shrub species and locations. In conjunction with appropriate null models, the ISAR blends species area relationships with second‐order spatial statistics to measure the expected species richness in local neighborhoods of variable size around the individuals of a focal species within a community. We found that, contrary to a previous analysis using more traditional methods, the community was well‐mixed with a typical shrub surrounded on average by 4.9 shrub neighbors of 2.1 species at a neighborhood scale of 1.0 m. We also found statistically significant fine‐scale variation in diversity patterns, such that neighborhoods of two species were more diverse than expected by a heterogeneous Poisson null model that accounted for larger‐scale habitat heterogeneity. However, this effect was caused by intraspecific aggregation of these species and was not due to positive interspecific association. Contrary to previous findings in other semi‐arid shrublands, our analysis suggests that the spatial pattern of the shrub community was not significantly structured by interspecific facilitation. This result supports growing evidence for balanced species patterns of adult plants in multispecies communities. Our approach may be used in other communities to describe complex multispecies spatial patterns, quantify species‐specific associations with diversity patterns, and to generate hypotheses regarding relationships between patterns and community‐structuring processes.     

Cellular Localisation of Adenylyl Cyclase: A Post-genome Perspective

The intracellular messenger cAMP is essential for vital processes ranging from ovulation to cognition. There are 10 genes for adenylyl cyclase (AC), the biosynthetic enzyme of cAMP. Nine of these encode membrane-bound proteins and one gives rise to soluble AC. The understanding of the biological significance of this molecular diversity is incomplete. Membrane-bound ACs conform to the same structural blueprint but have markedly different regulatory characteristics. AC mRNAs are differentially distributed in the body suggesting non-redundant physiological functions. The subcellular localisation of AC isoforms has not been examined in detail. Here we discuss the current knowledge on the intracellular targeting of AC isoforms, and highlight the technical problems of AC detection, some of which appear to be caused by the poor quality-control of commercially supplied antibodies. The principal message is that intracellular targeting of ACs may be isoform-specific and also dependent on the cellular context of expression.Invocation: This paper was written to honour one of the founders of chemical neuroanatomy—Professor Miklós Palkovits on his 70th birthday.     

Patch dynamics integrate mechanisms for savanna tree–grass coexistence

Many mechanisms have been suggested to explain the coexistence of woody species and grasses in savannas. However, evidence from field studies and simulation models has been mixed. Patch dynamics is a potentially unifying mechanism explaining tree–grass coexistence and the natural occurrence of shrub encroachment in arid and semi-arid savannas. A patch-dynamic savanna consists of a spatial mosaic of patches. Each patch maintains a cyclical succession between dominance of woody species and grasses, and the succession of neighbouring patches is temporally asynchronous. Evidence from empirical field studies supports the patch dynamics view of savannas. As a basis for future tests of patch dynamics in savannas, several hypotheses are presented and one is exemplarily examined: at the patch scale, realistically parameterized simulation models have generated cyclical succession between woody and grass dominance. In semi-arid savannas, cyclical successions are driven by precipitation conditions that lead to mass recruitment of shrubs in favourable years and to simultaneous collapse of shrub cohorts in drought years. The spatiotemporal pattern of precipitation events determines the scale of the savanna vegetation mosaic in space and time. In a patch-dynamic savanna, shrub encroachment is a natural, transient phase corresponding to the shrub-dominated phase during the successional cycle. Hence, the most promising management strategy for encroached areas is a large-scale rotation system of rangelands. In conclusion, patch dynamics is a possible scale-explicit mechanism for the explanation of tree–grass coexistence in savannas that integrates most of the coexistence mechanisms proposed thus far for savannas.     

HIV-1 continues to replicate and evolve in patients with natural control of HIV infection

Elucidating mechanisms leading to the natural control of HIV-1 infection is of great importance for vaccine design and for understanding viral pathogenesis. Rare HIV-1-infected individuals, termed HIV-1 controllers, have plasma HIV-1 RNA levels below the limit of detection by standard clinical assays (<50 to 75 copies/ml) without antiretroviral therapy. Although several recent studies have documented persistent low-grade viremia in HIV-1 controllers at a level not significantly different from that in HIV-1-infected individuals undergoing treatment with combination antiretroviral therapy (cART), it is unclear if plasma viruses are undergoing full cycles of replication in vivo or if the infection of new cells is completely blocked by host immune mechanisms. We studied a cohort of 21 HIV-1 controllers with a median level of viremia below 1 copy/ml, followed for a median of 11 years. Less than half of the cohort carried known protective HLA types (B*57/27). By isolating HIV-1 RNA from large volumes of plasma, we amplified single genome sequences of both pro-rt and env longitudinally. This study is the first to document that HIV-1 pro-rt and env evolve in this patient group, albeit at rates somewhat lower than in HIV-1 noncontrollers, in HLA B*57/27-positive, as well as HLA B*57/27-negative, individuals. Viral diversity and adaptive events associated with immune escape were found to be restricted in HIV-1 controllers, suggesting that replication occurs in the face of less overall immune selection.