Ceased grazing management changes the ecosystem services of semi-natural grasslands

Understanding how drivers of change affect ecosystem services (ES) is of great importance. Indicators of ES can be developed based on biophysical measures and be used to investigate the service flow from ecosystems to socio-ecological systems. However, the ES concept is multivariate and the use of normalized composite indicators reduces complexity and facilitates communication between science and policy. The aim of this study is to analyze how land use change affects ES and species richness and how the effects are modified by environmental factors by using composite indicators based on biophysical indicators. Using multivariate and regression analyses, we analyze the effect of grazing management abandonment in semi-natural grasslands in Norway on six ES: nutrient cycling, pollination, forage quality, aesthetics and global and regional climate regulation in addition to species richness along soil and climate gradients. Nutrient cycling, forage quality, regional climate regulation, aesthetics and species richness are larger in managed compared to abandoned grasslands. There are trade-offs among ES as different management strategies provide various ES and these trade-offs vary along environmental gradients. Management policies that aim to conserve ES need to have conservation goals that are context dependent, should recognize ES trade-offs and be adapted to local conditions

PROlocalizer: integrated web service for protein subcellular localization prediction

Subcellular localization is an important protein property, which is related to function, interactions and other features. As experimental determination of the localization can be tedious, especially for large numbers of proteins, a number of prediction tools have been developed. We developed the PROlocalizer service that integrates 11 individual methods to predict altogether 12 localizations for animal proteins. The method allows the submission of a number of proteins and mutations and generates a detailed informative document of the prediction and obtained results. PROlocalizer is available at http://bioinf.uta.fi/PROlocalizer/

An In-Depth Study of the Use of Eosin Y for the Solar Photocatalytic Oxidative Coupling of Benzylic Amines

The direct utilization of solar light for synthetic photochemistry is a sustainable and efficient technological goal. Herein we report the first in-depth study on the use of the inexpensive organic photocatalyst eosin Y for solar photocatalysis by demonstrating the oxidative coupling of benzylic amines to form imines, a class of valuable intermediates in chemical synthesis. By the use of a unique experimental setup with a custom-built variable-intensity solar light simulator, replication of a natural-sunlight environment was achieved. The relative significance of different variables on the reaction rate constant was quantitatively evaluated through comprehensive experimental design. Reaction kinetics and mechanistic information were obtained using both a batch reactor and a spinning-disc reactor. A maximum pseudo-first-order rate constant of 1.59 × 10^–3 s^–1 was obtained at a maximum turnover frequency of 192 h^–1 through optimization of the reaction conditions. Experiments carried out using a spinning-disc reactor confirmed that the reaction was not mass-transfer-limited but rather photon-transfer-limited

Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies

Decadal Scale Variability of Larsen Ice Shelf Melt Captured by Antarctic Peninsula Ice Core

In this study, we used the stable water isotope record (δ18O) from an ice core drilled in Palmer Land, southern Antarctic Peninsula (AP). Utilizing δ18O we identified two climate regimes during the satellite era. During the 1979–1998 positive interdecadal Pacific oscillation (IPO) phase, a low-pressure system north of the Weddell Sea drove southeasterly winds that are associated with an increase in warm air mass intrusion onto the Larsen shelves, which melted and a decreased sea ice concentration in the Weddell Sea/increase in the Bellingshausen Sea. This climate setting is associated with anomaly low δ18O values (compared with the latter IPO period). There is significantly more melt along the northern AP ice shelf margins and on the Larsen D and southern Larsen C during the 1979–1998 IPO positive phase. The IPO positive climatic setting was coincidental with the Larsen A ice shelf collapse. In contrast, during the IPO negative phase (1999–2011), northerly winds caused a reduction in sea ice in the Bellingshausen Sea/Drake Passage region. Moreover, a Southern Ocean north of the Weddell Sea high-pressure system caused low-latitude warm humid air over the tip and east of the AP, a setting that is associated with increased northern AP snowfall, a high δ18O anomaly, and less prone to Larsen ice shelf melt

Flood risk assessment for infrastructure networks

A practical framework for flood risk screening was developed to assess the flood risk to water utility assets within the infrastructure network. The tool is a combination of probability and consequence assessments. The first takes into account how probable it is for a particular asset to flood and cause significant damage. The second estimates the level of consequences a flood will have, considering, for example, the level of loss of service, environmental pollution and cost. The consequence assessment is based on a dependency assessment that identifies knock‐on effects on other assets within the asset network and assesses the level of consequence they will have. The probability and consequence assessments are combined to produce a risk score that can be used to rank assets in a screening process that aims to assist companies in prioritising the investments required for taking action to reduce flood risk to their assets

Ice Core Chronologies from the Antarctic Peninsula: The Palmer, Jurassic, and Rendezvous Age-Scales

In this study, we present the age scales for three Antarctic Peninsula (AP) ice cores: Palmer, Rendezvous, and Jurassic. The three cores are all intermediate-depth cores, in the 133–141 m depth range. Non-sea-salt sulfate ([nssSO42−]) and hydrogen peroxide (H2O2) display marked seasonal variability suitable for annual-layer counting. The Palmer ice core covers 390 years, 1621–2011 C.E., and is one of the oldest AP cores. Rendezvous and Jurassic are lower elevation high-snow accumulation sites and therefore cover shorter intervals, 1843–2011 C.E. and 1874–2011 C.E., respectively. The age scales show good agreement with known volcanic age horizons. The three chronologies’ start and end dates of volcanic events are compared to the volcanic events in the published WAIS Divide core. The age difference for the Palmer age scale is ±6 months, Rendezvous ±9 months, and Jurassic ±7 months. Our results demonstrate the advantage of dating several cores from the same region at the same time. Additional confidence can be gained in the age scales by evaluating and finding synchronicity of [nssSO42−] peaks amongst the sites.</jats:p

SIMAP—structuring the network of protein similarities

Protein sequences are the most important source of evolutionary and functional information for new proteins. In order to facilitate the computationally intensive tasks of sequence analysis, the Similarity Matrix of Proteins (SIMAP) database aims to provide a comprehensive and up-to-date dataset of the pre-calculated sequence similarity matrix and sequence-based features like InterPro domains for all proteins contained in the major public sequence databases. As of September 2007, SIMAP covers ∼17 million proteins and more than 6 million non-redundant sequences and provides a complete annotation based on InterPro 16. Novel features of SIMAP include a new, portlet-based web portal providing multiple, structured views on retrieved proteins and integration of protein clusters and a unique search method for similar domain architectures. Access to SIMAP is freely provided for academic use through the web portal for individuals at http://mips.gsf.de/simap/and through Web Services for programmatic access at http://mips.gsf.de/webservices/services/SimapService2.0?wsdl

ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins

<p>Abstract</p> <p>Background</p> <p>The expansion of raw protein sequence databases in the post genomic era and availability of fresh annotated sequences for major localizations particularly motivated us to introduce a new improved version of our previously forged eukaryotic subcellular localizations prediction method namely "ESLpred". Since, subcellular localization of a protein offers essential clues about its functioning, hence, availability of localization predictor would definitely aid and expedite the protein deciphering studies. However, robustness of a predictor is highly dependent on the superiority of dataset and extracted protein attributes; hence, it becomes imperative to improve the performance of presently available method using latest dataset and crucial input features.</p> <p>Results</p> <p>Here, we describe augmentation in the prediction performance obtained for our most popular ESLpred method using new crucial features as an input to Support Vector Machine (SVM). In addition, recently available, highly non-redundant dataset encompassing three kingdoms specific protein sequence sets; 1198 fungi sequences, 2597 from animal and 491 plant sequences were also included in the present study. First, using the evolutionary information in the form of profile composition along with whole and N-terminal sequence composition as an input feature vector of 440 dimensions, overall accuracies of 72.7, 75.8 and 74.5% were achieved respectively after five-fold cross-validation. Further, enhancement in performance was observed when similarity search based results were coupled with whole and N-terminal sequence composition along with profile composition by yielding overall accuracies of 75.9, 80.8, 76.6% respectively; best accuracies reported till date on the same datasets.</p> <p>Conclusion</p> <p>These results provide confidence about the reliability and accurate prediction of SVM modules generated in the present study using sequence and profile compositions along with similarity search based results. The presently developed modules are implemented as web server "ESLpred2" available at <url>http://www.imtech.res.in/raghava/eslpred2/</url>.</p