Complete 1H, 13C and 15N NMR assignments and secondary structure of the 269-residue serine protease PB92 from Bacillus alcalophilus

Summary The ¹H, ¹³C and ¹⁵N NMR resonances of serine protease PB92 have been assigned using 3D tripleresonance NMR techniques. With a molecular weight of 27 kDa (269 residues) this protein is one of the largest monomeric proteins assigned so far. The side-chain assignments were based mainly on 3D H(C)CH and 3D (H)CCH COSY and TOCSY experiments. The set of assignments encompasses all backbone carbonyl and CH_n carbons, all amide (NH and NH₂) nitrogens and 99.2% of the amide and CH_n protons. The secondary structure and general topology appear to be identical to those found in the crystal structure of serine protease PB92 [Van der Laan et al. (1992) Protein Eng., 5, 405–411], as judged by chemical shift deviations from random coil values, NH exchange data and analysis of NOEs between backbone NH groups.Abbreviations 2D/3D/4D two-/three-/four-dimensional - HSQC heteronuclear single-quantum coherence - HMQC heteronuclear multiple-quantum coherence - COSY correlation spectroscopy - TOCSY total correlation spectroscopy - NOE nuclear Overhauser enhancement (connectivity) - NOESY 2D NOE spectroscopy Experiment nomenclature (H(C)CH, etc.) follows the conventions used elsewhere [e.g. Ikura et al. (1990) Biochemistry, 29, 4659–4667].     

How to measure,report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal

There is growing international interest in better managing soils to increase soil organic carbon (SOC) content to contribute to climate change mitigation, to enhance resilience to climate change and to underpin food security, through initiatives such as international ‘4p1000’ initiative and the FAO's Global assessment of SOC sequestration potential (GSOCseq) programme. Since SOC content of soils cannot be easily measured, a key barrier to implementing programmes to increase SOC at large scale, is the need for credible and reliable measurement/monitoring, reporting and verification (MRV) platforms, both for national reporting and for emissions trading. Without such platforms, investments could be considered risky. In this paper, we review methods and challenges of measuring SOC change directly in soils, before examining some recent novel developments that show promise for quantifying SOC. We describe how repeat soil surveys are used to estimate changes in SOC over time, and how long‐term experiments and space‐for‐time substitution sites can serve as sources of knowledge and can be used to test models, and as potential benchmark sites in global frameworks to estimate SOC change. We briefly consider models that can be used to simulate and project change in SOC and examine the MRV platforms for SOC change already in use in various countries/regions. In the final section, we bring together the various components described in this review, to describe a new vision for a global framework for MRV of SOC change, to support national and international initiatives seeking to effect change in the way we manage our soils.     

Evaluating 50 years of time-series soil radiocarbon data: towards routine calculation of robust C residence times

In 1959, Athol Rafter began a substantial programme of monitoring the flow of ¹⁴C produced by atmospheric thermonuclear tests through New Zealand’s atmosphere, biosphere and soil. By building on the original measurements through ongoing sampling, a database of over 500 soil radiocarbon measurements spanning 50 years has now been compiled. The datasets, including an 11-point time series, allow strong focus on the robust quantification of residence times ranging from years to decades. We describe key aspects of the dataset, including the ability to identify critical assumptions inherent in calculating soil C residence times. The 3 most critical assumptions relate to: (1) the proportion of old C (“fraction passive”), (2) the lag time between photosynthesis and C entering the modeled pool, and (3) changes in the rates of C input (i.e., steady state). We demonstrate the ability to compare residence times in contrasting sites, such Andisols and non-Andisols, and the ability to calculate residence times across a range of soil depths. We use ¹⁴C in a two-box model to quantify soil carbon turnover parameters in deforested dairy pastures under similar climate in the Tokomaru silt loam (non-Andisol) versus the Egmont black loam (Andisol), originally sampled in 1962, 1965 and 1969, and resampled again in 2008. The ¹⁴C-based residence times of the main soil C pool in surface soil (~8 cm) are ~9 years in the Tokomaru soils compared to ~17 years for the Egmont soils. This difference represents nearly a doubling of soil C residence time, and roughly explains the doubling of the soil C stock. Passive soil C comprises 15% of the soil C pool in Tokomaru soils versus 27% in Egmont soils. A similar difference in residence times is found in a second surface soil comparison between the Bruntwood soil (Andisol) and the Te Kowhai soil (non-Andisol) with residence times of 18 and 27 years, respectively. The comparisons support evidence that C dynamics do differ in Andisols versus non-Andisols, as a result of both the mineral allophane and Al complexation. Expanding our calculations beyond surface soil, we show that thickening the calculation depth by combining horizons allows robust residence times to be calculated at a range of depths. Overall, the large and systematically collected dataset demonstrate that soil C residence times of the main soil C pool can be routinely calculated using ¹⁴C wherever samples collected 10 or more years apart in New Zealand grassland soils are available, and presumably under similar circumstances in other soils worldwide.     

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

Although it is generally recognized that global biodiversity is declining, few studies have examined long‐term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5‐year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.     

Review on Challenges and Recent Advances in the Electrochemical Performance of High Capacity Li‐ and Mn‐Rich Cathode Materials for Li‐Ion Batteries

Li and Mn‐rich layered oxides, xLi₂MnO₃·(1–x)LiMO₂ (M=Ni, Mn, Co), are promising cathode materials for Li‐ion batteries because of their high specific capacity that can exceed 250 mA h g^?1. However, these materials suffer from high 1^st cycle irreversible capacity, gradual capacity fading, low rate capability, a substantial charge‐discharge voltage hysteresis, and a large average discharge voltage decay during cycling. The latter detrimental phenomenon is ascribed to irreversible structural transformations upon cycling of these cathodes related to potentials ≥4.5 V required for their charging. Transition metal inactivation along with impedance increase and partial layered‐to‐spinel transformation during cycling are possible reasons for the detrimental voltage fade. Doping of Li, Mn‐rich materials by Na, Mg, Al, Fe, Co, Ru, etc. is useful for stabilizing capacity and mitigating the discharge‐voltage decay of xLi₂MnO₃·(1–x)LiMO₂ electrodes. Surface modifications by thin coatings of Al₂O₃, V₂O₅, AlF₃, AlPO₄, etc. or by gas treatment (for instance, by NH₃) can also enhance voltage and capacity stability during cycling. This paper describes the recent literature results and ongoing efforts from our groups to improve the performance of Li, Mn‐rich materials. Focus is also on preparation of cobalt‐free cathodes, which are integrated layered‐spinel materials with high reversible capacity and stable performance.     

Global habitat suitability models of terrestrial mammals

Detailed large-scale information on mammal distribution has often been lacking, hindering conservation efforts. We used the information from the 2009 IUCN Red List of Threatened Species as a baseline for developing habitat suitability models for 5027 out of 5330 known terrestrial mammal species, based on their habitat relationships. We focused on the following environmental variables: land cover, elevation and hydrological features. Models were developed at 300 m resolution and limited to within species' known geographical ranges. A subset of the models was validated using points of known species occurrence. We conducted a global, fine-scale analysis of patterns of species richness. The richness of mammal species estimated by the overlap of their suitable habitat is on average one-third less than that estimated by the overlap of their geographical ranges. The highest absolute difference is found in tropical and subtropical regions in South America, Africa and Southeast Asia that are not covered by dense forest. The proportion of suitable habitat within mammal geographical ranges correlates with the IUCN Red List category to which they have been assigned, decreasing monotonically from Least Concern to Endangered. These results demonstrate the importance of fine-resolution distribution data for the development of global conservation strategies for mammals.     

Microtubule-dependent mRNA transport in the model microorganism Ustilago maydis

Microtubule-dependent trafficking is essential in moving mRNAs over long distances. This transport mechanism regulates important cellular events such as determining polarity and local protein secretion. Key examples are developmental and neuronal processes studied in Drosophila melanogaster, Xenopus laevis as well as in mammalian cells. A simple eukaryotic system to uncover basic mechanisms was missing. Fungal models are generally well suited for this purpose, since transgenic strains can be generated easily by homologous recombination allowing in vivo studies at native expression levels. Substantial advances in understanding Ustilago maydis showed that this fungus fulfils important criteria to serve as model for microtubule-dependent mRNA trafficking. Here, we summarize progress focusing on target mRNAs, RNA localization elements, RNA-binding proteins, mRNPs, molecular motors and microtubule organization. This serves as the basis to discuss the novel mechanism of mRNP hitchhiking on endosomes as well as an unexpected link to unconventional secretion with its implications for applied sciences.