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Comment on "Bias correction, quantile mapping, and downscaling: revisiting the inflation issue"
(2014)
In a recent paper, Maraun describes the adverse effects of quantile mapping on downscaling. He argues that when large-scale GCM variables are rescaled directly to small-scale fields or even station data, genuine small-scale covariability is lost and replaced by uniform variability inherited from the larger scales. This leads to a misrepresentation mainly of areal means and long-term trends. This comment acknowledges the former point, although the argument is relatively old, but disagrees with the latter, showing that grid-size long-term trends can be different from local trends. Finally, because it is partly incorrectly addressed, some clarification is added regarding the inflation issue, stressing that neither randomization nor inflation is free of unverified assumptions.
In aquatic environments, community dynamics of bacteria, especially actively growing bacteria (AGB), are tightly linked with dissolved organic matter (DOM) quantity and quality. We analyzed the community dynamics of DNA-synthesizing and accordingly AGB by linking an improved bromodeoxyuridine immunocytochemistry approach with fluorescence-activated cell sorting (BrdU-FACS). FACS-sorted cells of even oligotrophic ecosystems in winter were characterized by 16S rRNA gene analysis. In incubation experiments, we examined community shifts of AGB in response to the addition of N-acetyl-glucosamine (NAG), one of the most abundant aminosugars in aquatic systems. Our improved BrdU-FACS analysis revealed that AGB winter communities of oligotrophic Lake Stechlin (northeastern Germany) substantially differ from those of total bacteria and consist of Alpha-, Beta-, Gamma-, Deltaproteobacteria, Actinobacteria, Candidatus OP10 and Chloroflexi. AGB populations with different BrdU-fluorescence intensities and cell sizes represented different phylotypes suggesting that single-cell growth potential varies at the taxon level. NAG incubation experiments demonstrated that a variety of widespread taxa related to Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Planctomycetes, Spirochaetes, Verrucomicrobia and Chloroflexi actively grow in the presence of NAG. The BrdU-FACS approach enables detailed phylogenetic studies of AGB and, thus, to identify those phylotypes which are potential key players in aquatic DOM cycling.
Background
The Amazon molly, Poecilia formosa (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring.
Here we provide and describe the first de novo assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly Poecilia mexicana. The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique.
Results
83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63% resp. 57% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly.
Conclusions
We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome (de novo). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research.
A novel method that optimizes the screening for antibody-secreting hapten-specific hybridoma cells by using flow cytometry is described. Cell clones specific for five different haptens were analyzed. We selectively double stained and analyzed fixed hybridoma cells with fluorophore-labeled haptens to demonstrate the target-selectivity, and with a fluorophore-labeled anti-mouse IgG antibody to characterize the level of surface expression of membrane-bound IgGs. ELISA measurements with the supernatants of the individual hybridoma clones revealed that antibodies from those cells, which showed the highest fluorescence intensities in the flow cytometric analysis, also displayed the highest affinities for the target antigens. The fluorescence intensity of antibody-producing cells corresponded well with the produced antibodies' affinities toward their respective antigens. Immunohistochemical staining verified the successful double labeling of the cells. Our method makes it possible to perform a high-throughput screening for hybridoma cells, which have both an adequate IgG production rate and a high target affinity. (C) 2014 Elsevier B.V. All rights reserved.
Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di-and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.
This study aims to compare impacts of climate change on streamflow in four large representative African river basins: the Niger, the Upper Blue Nile, the Oubangui and the Limpopo. We set up the eco-hydrological model SWIM (Soil and Water Integrated Model) for all four basins individually. The validation of the models for four basins shows results from adequate to very good, depending on the quality and availability of input and calibration data.
For the climate impact assessment, we drive the model with outputs of five bias corrected Earth system models of Coupled Model Intercomparison Project Phase 5 (CMIP5) for the representative concentration pathways (RCPs) 2.6 and 8.5. This climate input is put into the context of climate trends of the whole African continent and compared to a CMIP5 ensemble of 19 models in order to test their representativeness. Subsequently, we compare the trends in mean discharges, seasonality and hydrological extremes in the 21st century. The uncertainty of results for all basins is high. Still, climate change impact is clearly visible for mean discharges but also for extremes in high and low flows. The uncertainty of the projections is the lowest in the Upper Blue Nile, where an increase in streamflow is most likely. In the Niger and the Limpopo basins, the magnitude of trends in both directions is high and has a wide range of uncertainty. In the Oubangui, impacts are the least significant. Our results confirm partly the findings of previous continental impact analyses for Africa. However, contradictory to these studies we find a tendency for increased streamflows in three of the four basins (not for the Oubangui). Guided by these results, we argue for attention to the possible risks of increasing high flows in the face of the dominant water scarcity in Africa. In conclusion, the study shows that impact intercomparisons have added value to the adaptation discussion and may be used for setting up adaptation plans in the context of a holistic approach.
Comparing thermal wave function methods for multi-configuration time-dependent Hartree simulations
(2014)
We compare two methods for creating stochastic temperature wave functions that can be used for Multi-Configuration Time-Dependent Hartree (MCTDH) simulations. In the first method, the MCTDH coefficients are chosen randomly, while the other method uses a single Hartree product of random single-particle functions (SPFs). We find that using random SPFs dramatically improves convergence for a model system for surface sticking.