Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii

Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.     

Large herbivores limit CO2 uptake and suppress carbon cycle responses to warming in West Greenland

Changes in the terrestrial carbon cycle may ameliorate or exacerbate future climatic warming. Research on this topic has focused almost exclusively on abiotic drivers, whereas biotic factors, including trophic interactions, have received comparatively little attention. We quantified the singular and interactive effects of herbivore exclusion and simulated warming on ecosystem CO₂ exchange over two consecutive growing seasons in West Greenland. Exclusion of caribou and muskoxen over the past 8 years has led to dramatic increases in shrub cover, leaf area, ecosystem photosynthesis, and a nearly threefold increase in net C uptake. These responses were accentuated by warming, but only in the absence of herbivores. Carbon cycle responses to herbivore exclusion alone and combined with warming were driven by changes in gross ecosystem photosynthesis, as limited differences in ecosystem respiration were observed. Our results show that large herbivores can be of critical importance as mediators of arctic ecosystem responses to climate change.     

Studies on the paradox of seedling rarity in Vaccinium myrtillus L. in NE Scotland

Summary

On the moors studied Vaccinium myrtillus produced many berries containing highly viable seed, yet seedlings were rare. Offtake of berries by birds or mammalian herbivores was apparently minor, most berries simply falling from the bushes when ripe. Fallen berries quickly disappeared, probably being removed by small rodents. Berries were fed experimentally to captive field voles and capercaillies, and it was found that only c. 1% of the seeds survived. For the voles, most of these viable seeds probably resulted from contamination of the droppings with partially-eaten berries or discarded extracted seeds, processes which must contribute to dispersal in the wild. The soil seed-bank was shown to be small, and the viability of buried seed declined from c. 90% to c. 20% in 3 years, due to decay in the soil H horizon and premature germination in the litter layer. Fewer seedlings established from experimental sowings on grass and Vaccinium myrtillus turf than on bare peat. We conclude that Vaccinium myrtillus has a seed-dispersal strategy which secures some long-distance movement by frugivores at the expense of much lost seed, and that the small seed-bank and low numbers of seedlings result from poor defence of the seeds and weak competitive ability of the seedlings; other attributes of Vaccinium myrtillus, e.g. efficient vegetative reproduction, compensate for these losses and enable it to be a successful species.     

Geographic range determinants of two commercially important marine molluscs

Aim We modelled the spatial abundance patterns of two abalone species (Haliotis rubra Donovan 1808 and H. laevigata Leach 1814) inhabiting inshore rocky reefs to better understand the importance of current sea surface temperature (SST) (among other predictors) and, ultimately, the effect of future climate change, on marine molluscs. Location Southern Australia. Methods We used an ensemble species distribution modelling approach that combined likelihood‐based generalized linear models and boosted regression trees. For each modelling technique, a two‐step procedure was used to predict: (1) the current probability of presence, followed by (2) current abundance conditional on presence. The resulting models were validated using an independent, spatially explicit dataset of abalone abundance patterns in Victoria. Results For both species, the presence of reef was the main driver of abalone occurrence, while SST was the main driver of spatial abundance patterns. Predictive maps at c. 1‐km resolution showed maximal abundance on shallow coastal reefs characterized by mild winter SSTs for both species. Main conclusions Sea surface temperature was a major driver of abundance patterns for both abalone species, and the resulting ensemble models were used to build fine‐resolution predictive range maps (c. 1 km) that incorporate measures of habitat suitability and quality in support of resource management. By integrating this output with structured spatial population models, a more robust understanding of the potential impacts of threatening human processes such as climate change can be established.     

Comparative structural analyses of purified glycogen particles from rat liver,human skeletal muscle and commercial preparations

Glycogen is a cellular energy store that is crucial for whole body energy metabolism, metabolic regulation and exercise performance. To understand glycogen structure we have purified glycogen particles from rat liver and human skeletal muscle tissues and compared their biophysical properties with those found in commercial glycogen preparations. Ultrastructural analysis of commercial liver glycogens fails to reveal the classical α-rosette structure but small irregularly shaped particles. In contrast, commercial slipper limpet glycogen consists of β-particles with similar branching and chain lengths to purified rat liver glycogen together with a tendency to form small α-particles, and suggest it should be used as a source of glycogen for all future studies requiring a substitute for mammalian liver glycogen.     

Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.     

Improvement of a Potential Anthrax Therapeutic by Computational Protein Design

Past anthrax attacks in the United States have highlighted the need for improved measures against bioweapons. The virulence of anthrax stems from the shielding properties of the Bacillus anthracis poly-γ-d-glutamic acid capsule. In the presence of excess CapD, a B. anthracis γ-glutamyl transpeptidase, the protective capsule is degraded, and the immune system can successfully combat infection. Although CapD shows promise as a next generation protein therapeutic against anthrax, improvements in production, stability, and therapeutic formulation are needed. In this study, we addressed several of these problems through computational protein engineering techniques. We show that circular permutation of CapD improved production properties and dramatically increased kinetic thermostability. At 45 °C, CapD was completely inactive after 5 min, but circularly permuted CapD remained almost entirely active after 30 min. In addition, we identify an amino acid substitution that dramatically decreased transpeptidation activity but not hydrolysis. Subsequently, we show that this mutant had a diminished capsule degradation activity, suggesting that CapD catalyzes capsule degradation through a transpeptidation reaction with endogenous amino acids and peptides in serum rather than hydrolysis.     

Restricted Hematopoietic Progenitors and Erythropoiesis Require SCF from Leptin Receptor+ Niche Cells in the Bone Marrow

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