A transcription frame-based analysis of the genomic DNA sequence of a hyper-thermophilic archaeon for the identification of genes, pseudo-genes and operon structures

AbstractAn algorithm for identifying transcription units, independently regulated genes and operons, and pseudo-genes that are not expected to be expressed, has been developed by combining a system for predicting transcription and translation signals, and a system for scoring the triplet periodicity in ORF candidates. By using the algorithm, the 1.09 Mb sequence that covers approximately 60% of the genome of Pyrococcus sp. OT3 has been analyzed. The identified ORFs show the expected biological and physical characteristics, while the rejected ORF candidates do not. Frequent use of operon structures for transcription, and gene duplication followed by mutation or termination of the duplicated genes, are discussed

Description and evaluation of the process-based forest model 4C v2.2 at four European forest sites

The process-based model 4C (FORESEE) has been developed over the past 20 years to study climate impacts on forests and is now freely available as an open-source tool. The objective of this paper is to provide a comprehensive description of this 4C version (v2.2) for scientific users of the model and to present an evaluation of 4C at four different forest sites across Europe. The evaluation focuses on forest growth as well as carbon (net ecosystem exchange, gross primary production), water (actual evapotranspiration, soil water content), and heat fluxes (soil temperature) using data from the PROFOUND database. We applied different evaluation metrics and compared the daily, monthly, and annual variability of observed and simulated values. The ability to reproduce forest growth (stem diameter and biomass) differs from site to site and is best for a pine stand in Germany (Peitz, model efficiency ME=0.98). 4C is able to reproduce soil temperature at different depths in Sorø and Hyytiälä with good accuracy (for all soil depths ME > 0.8). The dynamics in simulating carbon and water fluxes are well captured on daily and monthly timescales (0.51 < ME < 0.983) but less so on an annual timescale (ME < 0). This model–data mismatch is possibly due to the accumulation of errors because of processes that are missing or represented in a very general way in 4C but not with enough specific detail to cover strong, site-specific dependencies such as ground vegetation growth. These processes need to be further elaborated to improve the projections of climate change on forests. We conclude that, despite shortcomings, 4C is widely applicable, reliable, and therefore ready to be released to the scientific community to use and further develop the model

Description and evaluation of the process-based forest model 4C v2.2 at four European forest sites

The process-based model 4C (FORESEE) has been developed over the past 20 years to study climate impacts on forests and is now freely available as an open-source tool. The objective of this paper is to provide a comprehensive description of this 4C version (v2.2) for scientific users of the model and to present an evaluation of 4C at four different forest sites across Europe. The evaluation focuses on forest growth as well as carbon (net ecosystem exchange, gross primary production), water (actual evapotranspiration, soil water content), and heat fluxes (soil temperature) using data from the PROFOUND database. We applied different evaluation metrics and compared the daily, monthly, and annual variability of observed and simulated values. The ability to reproduce forest growth (stem diameter and biomass) differs from site to site and is best for a pine stand in Germany (Peitz, model efficiency ME=0.98). 4C is able to reproduce soil temperature at different depths in Sorø and Hyytiälä with good accuracy (for all soil depths ME > 0.8). The dynamics in simulating carbon and water fluxes are well captured on daily and monthly timescales (0.51 < ME < 0.983) but less so on an annual timescale (ME < 0). This model–data mismatch is possibly due to the accumulation of errors because of processes that are missing or represented in a very general way in 4C but not with enough specific detail to cover strong, site-specific dependencies such as ground vegetation growth. These processes need to be further elaborated to improve the projections of climate change on forests. We conclude that, despite shortcomings, 4C is widely applicable, reliable, and therefore ready to be released to the scientific community to use and further develop the model.ISSN:1991-9603ISSN:1991-959

The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests

Process-based vegetation models are widely used to predict local and global ecosystem dynamics and climate change impacts. Due to their complexity, they require careful parameterization and evaluation to ensure that projections are accurate and reliable. The PROFOUND Database (PROFOUND DB) provides a wide range of empirical data to calibrate and evaluate vegetation models that simulate climate impacts at the forest stand scale. A particular advantage of this database is its wide coverage of multiple data sources at different hierarchical and temporal scales, together with environmental driving data as well as the latest climate scenarios. Specifically, the PROFOUND DB provides general site descriptions, soil, climate, CO2, nitrogen deposition, tree and forest stand-level, as well as remote sensing data for nine contrasting forest stands distributed across Europe. Moreover, for a subset of five sites, time series of carbon fluxes, atmospheric heat conduction, and soil water are also available. The climate and nitrogen deposition data contain several datasets for the historic period and a wide range of future climate change scenarios following the Representative Concentration Pathways (RCP2.6, RCP4.5, RCP6.0, RCP8.5). We also provide pre-industrial climate simulations that allow for model runs aimed at disentangling the contribution of climate change to observed forest productivity changes. The PROFOUND DB is available freely as a SQLite relational database or ASCII flat file version (at https://doi.org/10.5880/PIK.2019.008). The data policies of the individual, contributing datasets are provided in the metadata of each data file. The PROFOUND DB can also be accessed via the ProfoundData R-package (https://github.com/COST-FP1304-PROFOUND/ProfoundData), which provides basic functions to explore, plot, and extract the data for model set-up, calibration and evaluation