A model ensemble approach to determine the humus building efficiency of organic amendments in incubation experiments

Organic amendments are important to sustain soil organic matter (SOM) and soil functions in agricultural soils. Information about the contribution of organic amendments to SOM can be derived from incubation experiments. In this study, data from 72 incubated organic amendments including plant residues, digestates and manure were analysed. The incubation data was compiled from three experimental setups with varying incubation times, soils and incubation temperatures, in which CO2 release was measured continuously. The analysis of the incubation data was performed with an approach relying on conceptual parts of C-TOOL, CCB, Century, ICBM, RothC and Yasso which are all well-approved first-order carbon models that differ in structure and abstraction level. All models are an approximation of reality, whereby each model differs in understanding of the processes involved in soil carbon dynamics. To accumulate the advantages from each model a model ensemble was performed for each substrate. With the ability of each carbon model to compute the distribution of carbon into specific SOM pools a new approach for evaluating organic amendments in terms of humus building efficiency is presented that, depends on the weighted model fit of each ensemble member. Depending on the organic substrate added to the soil, the time course of CO2 release in the incubation studies was predicted with different accuracy by the individual model concepts. Averaging the output of the individual models leads to more robust prediction of SOM dynamics. The EHUM value is easy to interpret and the results are in accordance with the literature.Peer Reviewe

Charge-transfer states in triazole linked donor-acceptor materials: Strong effects of chemical modification and solvation

© the Owner Societies 2017. A series of 1,2,3-triazole linked donor-acceptor chromophores are prepared by Click Chemistry from ene-yne starting materials. The effects of three distinct chemical variations are investigated: enhancing the acceptor strength through oxidation of the sulphur atom, alteration of the double bond configuration, and variation of the triazole substitution pattern. A detailed photophysical characterization shows that these alterations have a negligible effect on the absorption while dramatically altering the emission wavelengths. In addition, strong solvatochromism is found leading to significant red shifts in the case of polar solvents. The experimental findings are rationalized and related to the electronic structure properties of the chromophores by time-dependent density functional theory as well as the ab initio algebraic diagrammatic construction method for the polarization propagator in connection with a new formalism allowing to model the influence of solvation onto long-lived excited states and their emission energies. These calculations highlight the varying degree of intramolecular charge transfer character present for the different molecules and show that the amount of charge transfer is strongly modulated by the conducted chemical modifications, by the solvation of the chromophores, and by the structural relaxation in the excited state. It is, furthermore, shown that enhanced charge separation, as induced by chemical modification or solvation, reduces the singlet-triplet gaps and that two of the investigated molecules possess sufficiently low gaps to be considered as candidates for thermally activated delayed fluorescence

Stability of persistent currents in a Bose-Einstein condensate confined in a toroidal trap

Motivated by recent experiments in Bose-Einstein condensed atoms that have been confined in toroidal traps, we examine the stability of persistent currents in such systems. We investigate the extent that the stability of these currents may be tunable, and the possible difficulties in their creation and detection.Comment: 6 pages, 5 figure

Evolutionary Origins and Functions of the Carotenoid Biosynthetic Pathway in Marine Diatoms

Carotenoids are produced by all photosynthetic organisms, where they play essential roles in light harvesting and photoprotection. The carotenoid biosynthetic pathway of diatoms is largely unstudied, but is of particular interest because these organisms have a very different evolutionary history with respect to the Plantae and are thought to be derived from an ancient secondary endosymbiosis between heterotrophic and autotrophic eukaryotes. Furthermore, diatoms have an additional xanthophyll-based cycle for dissipating excess light energy with respect to green algae and higher plants. To explore the origins and functions of the carotenoid pathway in diatoms we searched for genes encoding pathway components in the recently completed genome sequences of two marine diatoms. Consistent with the supplemental xanthophyll cycle in diatoms, we found more copies of the genes encoding violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZEP) enzymes compared with other photosynthetic eukaryotes. However, the similarity of these enzymes with those of higher plants indicates that they had very probably diversified before the secondary endosymbiosis had occurred, implying that VDE and ZEP represent early eukaryotic innovations in the Plantae. Consequently, the diatom chromist lineage likely obtained all paralogues of ZEP and VDE genes during the process of secondary endosymbiosis by gene transfer from the nucleus of the algal endosymbiont to the host nucleus. Furthermore, the presence of a ZEP gene in Tetrahymena thermophila provides the first evidence for a secondary plastid gene encoded in a heterotrophic ciliate, providing support for the chromalveolate hypothesis. Protein domain structures and expression analyses in the pennate diatom Phaeodactylum tricornutum indicate diverse roles for the different ZEP and VDE isoforms and demonstrate that they are differentially regulated by light. These studies therefore reveal the ancient origins of several components of the carotenoid biosynthesis pathway in photosynthetic eukaryotes and provide information about how they have diversified and acquired new functions in the diatoms

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

The Protein Structure Initiative’s Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI’s high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology

Rock glaciers and mountain hydrology: A review

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.In mountainous regions, climate change threatens cryospheric water resources, and understanding all components of the hydrological cycle is necessary for effective water resource management. Rockglaciers are climatically more resilient than glaciers and contain potentially hydrologically valuable ice volumes, and yet havereceived lessattention, even though rock glacier hydrologicalimportance may increase under future climate warming. In synthesising data from a range of global studies, we provide the first compre-hensive evaluation of the hydrological role played by rock glaciers. Weevaluate hydrological significanceover a range of temporal and spatial scales, alongsidethe complex multiple hydrological processes with which rock glaciers can interact diurnally, seasonally, annually, decadally and both at local and regional extents.We report that although no global-extent, complete inventory for rock glaciers exists currently, recent research efforts have greatly elaborated spatialcoverage.Using these research papers,we synthe-sise information on rock glacier spatial distribution, morphometric characteristics, surface and subsurface features, ice-storage and hydrological flow dynamics, water chemistry, and future resilience, from which we provide the first comprehensive evaluation of their hydrological contribution. We identify and discuss long-, intermediate-and short-term timescales for rock glacier storage, allowing a more balanced assess-ment of the contrasting perspectives regarding the relative significance of rock glacier-derived hydrological contributions compared to other water sources.We show that further empirical observations are required to gain a deeper hydrological understanding of rock glaciers, in terms of(i) their genesis and geomorpho-logical dynamics (ii) total ice/water volume; (iii) water discharge; and (iv) water quality. Lastly, we hypothesisethat at decadal and longer timescales, under future climate warming, degradation of ice within rock glaciers may represent an increasing hydrological contribution to downstream regions, and thus in-creased hydrological significance while rock glacier water stores persist.Royal Geographical SocietyNatural Environment Research Council (NERC

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology