Evaluation of different sources of uncertainty in climate change impact research using a hydro-climatic model ensemble

The international research project QBic3 (Quebec-Bavarian Collaboration on Climate Change) aims at investigating the potential impacts of climate change on the hydrology of regional scale catchments in Southern Quebec (Canada) and Bavaria (Germany). Yet, the actual change in river runoff characteristics during the next 70 years is highly uncertain due to a multitude of uncertainty sources. The so-called hydro-climatic ensemble that is constructed to describe the uncertainties of this complex model chain consists of four different global climate models, downscaled by three different regional climate models, an exchangeable bias correction algorithm, a separate method to scale RCM outputs to the hydrological model scale and several hydrological models of differing complexity to assess the impact of different hydro model concepts. This choice of models and scenarios allows for the inter-comparison of the uncertainty ranges of climate and hydrological models, of the natural variability of the climate system as well as of the impact of scaling and correction of climate data on mean, high and low flow conditions. A methodology to display the relative importance of each source of uncertainty is proposed and results for past runoff and potential future changes are presented

Construction and Characterization of T7 Bacteriophages Harboring Apidaecin-Derived Sequences

The global spread of multi- and pan-resistant bacteria has triggered research to identify novel strategies to fight these pathogens, such as antimicrobial peptides and, more recently, bacteriophages. In a proof-of-concept study, we have genetically modified lytic T7Select phages targeting Escherichia coli Rosetta by integrating DNA sequences derived from the proline-rich antimicrobial peptide, apidaecin. This allowed testing of our hypothesis that apidaecins and bacteriophages can synergistically act on phage-sensitive and phage-resistant E. coli cells and overcome the excessive cost of peptide drugs by using infected cells to express apidaecins before cell lysis. Indeed, the addition of the highly active synthetic apidaecin analogs, Api802 and Api806, to T7Select phage-infected E. coli Rosetta cultures prevented or delayed the growth of potentially phage-resistant E. coli Rosetta strains. However, high concentrations of Api802 also reduced the T7Select phage fitness. Additionally, plasmids encoding Api802, Api806, and Api810 sequences transformed into E. coli Rosetta allowed the production of satisfactory peptide quantities. When these sequences were integrated into the T7Select phage genome carrying an N-terminal green fluorescent protein (GFP-) tag to monitor the expression in infected E. coli Rosetta cells, the GFP–apidaecin analogs were produced in reasonable quantities. However, when Api802, Api806 and Api810 sequences were integrated into the T7Select phage genome, expression was below detection limits and an effect on the growth of potentially phage-resistant E. coli Rosetta strains was not observed for Api802 and Api806. In conclusion, we were able to show that apidaecins can be integrated into the T7Select phage genome to induce their expression in host cells, but further research is required to optimize the engineered T7Select phages for higher expression levels of apidaecins to achieve the expected synergistic effects that were visible when the T7Select phages and synthetic Api802 and Api806 were added to E. coli Rosetta cultures

Hydrogen bonding in a mixture of protic ionic liquids: A molecular dynamics simulation study

We report results of molecular dynamics (MD) simulations characterising the hydrogen bonding in mixtures of two different protic ionic liquids sharing the same cation: triethylammonium-methylsulfonate (TEAMS) and triethylammonium-triflate (TEATF). The triethylammonium-cation acts as a hydrogen-bond donor, being able to donate a single hydrogen-bond. Both, the methylsulfonate- and the triflate-anions can act as hydrogen-bond acceptors, which can accept multiple hydrogen bonds via their respective SO3-groups. In addition, replacing a methyl-group in the methylsulfonate by a trifluoromethyl-group in the triflate significantly weakens the strength of a hydrogen bond from an adjacent triethylammonium cation to the oxygen-site in the SO3-group of the anion. Our MD simulations show that these subtle differences in hydrogen bond strength significantly affect the formation of differently-sized hydrogen-bonded aggregates in these mixtures as a function of the mixture-composition. Moreover, the reported hydrogen-bonded cluster sizes can be predicted and explained by a simple combinatorial lattice model, based on the approximate coordination number of the ions, and using statistical weights that mostly account for the fact that each anion can only accept three hydrogen bonds

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

Background: Enrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-based) or incorporate (network-based) known interactions between genes. However, the often subtle benefits and disadvantages of the individual methods are confusing for most biological end users and there is currently no convenient way to combine methods for an enhanced result interpretation. Results: We present the EnrichmentBrowser package as an easily applicable software that enables (1) the application of the most frequently used set-based and network-based enrichment methods, (2) their straightforward combination, and (3) a detailed and interactive visualization and exploration of the results. The package is available from the Bioconductor repository and implements additional support for standardized expression data preprocessing, differential expression analysis, and definition of suitable input gene sets and networks. Conclusion: The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. It combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways

Using a nested single-model large ensemble to assess the internal variability of the North Atlantic Oscillation and its climatic implications for central Europe

Central European weather and climate are closely related to atmospheric mass advection triggered by the North Atlantic Oscillation (NAO), which is a relevant index for quantifying internal climate variability on multi-annual timescales. It remains unclear, however, how large-scale circulation variability affects local climate characteristics when downscaled using a regional climate model. In this study, 50 members of a single-model initial-condition large ensemble (LE) of a nested regional climate model are analyzed for a NAO-climate relationship. The overall goal of the study is to assess whether the range of NAO internal variability is represented consistently between the driving global climate model (GCM;the Canadian Earth System Model version 2 - CanESM2) and the nested regional climate model (RCM;the Canadian Regional Climate Model version 5 - CRCM5). Responses of mean surface air temperature and total precipitation to changes in the NAO index value are examined in a central European domain in both CanESM2-LE and CRCM5-LE via Pearson correlation coefficients and the change per unit index change for historical (1981-2010) and future (2070-2099) winters. Results show that statistically robust NAO patterns are found in the CanESM2-LE under current forcing conditions. NAO flow pattern reproductions in the CanESM2-LE trigger responses in the high-resolution CRCM5-LE that are comparable to reanalysis data. NAO-response relationships weaken in the future period, but their intermember spread shows no significant change. The results stress the value of single-model ensembles for the evaluation of internal variability by pointing out the large differences of NAO-response relationships among individual members. They also strengthen the validity of the nested ensemble for further impact modeling using RCM data only, since important large-scale teleconnections present in the driving data propagate properly to the fine-scale dynamics in the RCM

Assessing natural variability in RCM signals: comparison of a multi model EURO-CORDEX ensemble with a 50-member single model large ensemble

Uncertainties in climate model ensembles are still relatively large. Besides scenario and model response uncertainty, natural variability is another important source of uncertainty. To study regional natural variability on timescales of several decades and more, observations are often too sparse and short. Regional Climate Models (RCMs) can be used to overcome this lack of useful data at high spatial resolutions. In this study, we compare a new 50-member single RCM large ensemble (CRCM5-LE) with an ensemble of 22 EURO-CORDEX models for seasonal temperature and precipitation at 0.11° grid size over Europe—all driven by the RCP 8.5 scenario. This setup allows us to quantify the contribution of natural/model-internal variability on the total uncertainty of a multi-model ensemble. The variability of climate change signals within the two ensembles is compared for three future periods (2020–2049, 2040–069 and 2070–2099). Results show that the single model spread is usually smaller than the multi-model spread for temperature. Similar variabilities can mostly be found in the near future (and to a lesser extent in the mid future) during winter and spring, especially for northern and central parts of Europe. The contribution of internal variability is generally higher for precipitation. In the near future almost all seasons and regions show similar variabilities. In the mid and far future only fall, summer and spring still show similar variabilites. There is a significant decrease of the contribution of internal variability over time for both variables. However, even in the far future for most regions and seasons 25–75% of the overall variability can be explained by internal variability