Context-Dependent Competition in a Model Gut Bacterial Community

Understanding the ecological processes that generate complex community structures may provide insight into the establishment and maintenance of a normal microbial community in the human gastrointestinal tract, yet very little is known about how biotic interactions influence community dynamics in this system. Here, we use natural strains of Escherichia coli and a simplified model microbiota to demonstrate that the colonization process on the strain level can be context dependent, in the sense that the outcome of intra-specific competition may be determined by the composition of the background community. These results are consistent with previous models for competition between organisms where one competitor has adapted to low resource environments whereas the other is optimized for rapid reproduction when resources are abundant. The genomic profiles of E. coli strains representing these differing ecological strategies provide clues for deciphering the genetic underpinnings of niche adaptation within a single species. Our findings extend the role of ecological theory in understanding microbial systems and the conceptual toolbox for describing microbial community dynamics. There are few, if any, concrete examples of context-dependent competition on a single trophic level. However, this phenomenon can have potentially dramatic effects on which bacteria will successfully establish and persist in the gastrointestinal system, and the principle should be equally applicable to other microbial ecosystems.     

Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley

The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.     

Long-distance migration timing of Tringa sandpipers adjusted to recent climate change

Capsule Evidence for earlier spring migration of Tringa sandpipers after warmer winters, but no clear pattern concerning autumn migration timing.

Aim To analyse the timing of migration of three Tringa sandpipers between 1966 and 2002 with respect to recent global warming on a local and a hemispheric scale.

Methods I analysed long-term migration timing variation in Greenshank Tringa nebularia, Spotted Redshank T. erythropus and Wood Sandpiper T. glareola at four Central European staging sites. Variation in passage onset, median and end per migration period was analysed using stepwise regression with respect to variation in (i) local abundance, residence time and age-dependent abundance as an estimate of breeding success and (ii) climate at the staging sites, snowmelt at the presumed central breeding area and the North Atlantic Oscillation (NAO).

Results All three species consistently showed an overall spring migration advance and autumn migration delay. Autumn passage timing varied with both climatic conditions at the breeding area and breeding success, while in 43% of all cases spring passage correlated with local and hemispheric climate variation.

Conclusion The distinction between population dynamic and climatic effects on timing of autumn migration requires separate data for local adult and juvenile passage or a larger sample of sites. In spring, the data strongly suggest a flexible response of migration timing to local weather conditions and the hemispheric variation of the North Atlantic Oscillation. This indicates that even long-distance migrants are able to adjust their overall migration pattern to fluctuating environmental conditions on a phenotypic basis.     

Photosynthesis in relation to D1, PsaA and Rubisco in marine and brackish water ecotypes of Fucus vesiculosus and Fucus radicans (Phaeophyceae)

The aim of this study was to investigate photosynthetic differences between the marine, Norwegian Sea ecotype and the brackish, Bothnian Sea ecotype of F. vesiculosus and F. radicans and to see whether photosynthetic differences could be connected with the relative amounts of D1 protein (PSII), PsaA (PSI) protein and/or Rubisco. For this purpose, we tested if a higher photosynthetic maximum (P _max) in the Atlantic Ocean ecotype of F. vesiculosus relative to the Baltic Sea ecotype, and an increase of the P _max in Baltic Sea ecotype of F. vesiculosus at higher salinity, could be due to an increase in the relative amounts of Rubisco. The proteins have been evaluated on a relative basis. Immunoblot signals showed that the amount of Rubisco was higher in both ecotypes of F. vesiculosus than in F. radicans, but no differences could be detected between the two ecotypes of F. vesiculosus. The results suggest an uneven photosystem protein stoichiometry in Fucus, with more of the PSI protein PsaA relative to the PSII protein D1. The difference in P _max between the two ecotypes of F. vesiculosus might be related to the difficulties for the algae to adapt to the environment in Bothnian Sea.     

The Nitric-oxide Reductase from Paracoccus denitrificans Uses a Single Specific Proton Pathway

The NO reductase from Paracoccus denitrificans reduces NO to N₂O (2NO + 2H⁺ + 2e⁻ → N₂O + H₂O) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent NO reductase; cNOR). cNORs are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the O₂-reducing, proton-pumping respiratory enzymes. In contrast, although NO reduction is as exergonic as O₂ reduction, there are no protons pumped in cNOR, and in addition, protons needed for NO reduction are derived from the periplasmic solution (no contribution to the electrochemical gradient is made). cNOR thus only needs to transport protons from the periplasm into the active site without the requirement to control the timing of opening and closing (gating) of proton pathways as is needed in a proton pump. Based on the crystal structure of a closely related cNOR and molecular dynamics simulations, several proton transfer pathways were suggested, and in principle, these could all be functional. In this work, we show that residues in one of the suggested pathways (denoted pathway 1) are sensitive to site-directed mutation, whereas residues in the other proposed pathways (pathways 2 and 3) could be exchanged without severe effects on turnover activity with either NO or O₂. We further show that electron transfer during single-turnover reduction of O₂ is limited by proton transfer and can thus be used to study alterations in proton transfer rates. The exchange of residues along pathway 1 showed specific slowing of this proton-coupled electron transfer as well as changes in its pH dependence. Our results indicate that only pathway 1 is used to transfer protons in cNOR.     

Laminin Production and Basement Membrane Deposition by Mesenchymal Stem Cells upon Adipogenic Differentiation

The aim was to study laminin (LM) synthesis, integration, and deposition into the basement membrane (BM) during adipogenesis. Human bone marrow-derived mesenchymal stromal cells (MSCs) were induced along the adipogenic lineage. LM chain mRNA and protein levels were followed using quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence (IF) staining, transmission electron microscopy (TEM), and immunoprecipitation. MSCs produced low levels of LM mRNAs but were not surrounded by BM in IF and TEM imaging. LM-α4, LM-β1, and LM-γ1 mRNAs increased during adipogenesis 3.9-, 5.8-, and 2.8-fold by day 28. LM-411 was immunoprecipitated from the ECM of the differentiated cells. Immunostaining suggested deposition of LM-411 and some LM-421. BM build-up was probably organized in part by integrin (Int) α₆β₁. At day 28, TEM images revealed BM-like structures around fat droplet-containing cells. The first signs of BM formation and Int α₆β₁ were seen using IF imaging at day 14. Laminin-411 and Int α₆β₁ were expressed in vivo in mature human subcutaneous fat tissue. Undifferentiated human MSCs did not organize LM subunits into BM, whereas LM-411 and some LM-421 are precipitated in the BM around adipocytes. This is the first demonstration of LM-411 precipitation during hMSC adipogenesis around adipocytes as a structural scaffold and Int-regulated signaling element.     

Habitat structure alters top-down control in litter communities

The question whether top-down or bottom-up forces dominate trophic relationships, energy flow, and abundances within food webs has fuelled much ecological research with particular focus on soil litter ecosystems. Because litter simultaneously provides habitat structure and a basal resource, disentangling direct trophic and indirect non-trophic effects on different trophic levels remains challenging. Here, we focussed on short-term per capita interaction strengths of generalist predators (centipedes) on their microbi-detritivore prey (springtails) and addressed how the habitat structuring effects of the leaf litter modifies this interaction. We performed a series of laboratory functional response experiments where four levels of habitat structure were constructed by adding different amounts of leaf litter to the experimental arenas. We found that increased leaf litter reduced the consumption rate of the predator. We interpreted this as a dilution effect of the augmented habitat size provided by the increasing leaf litter surface available to the species. Dilution of the prey population decreased encounter rates, whereas the capture success was not affected. Interestingly, our results imply that top-down control by centipedes decreased with increasing resource supply for the microbi-detritivore prey (i.e. the leaf litter that simultaneously provides habitat structure). Therefore, effective top-down control of predators on microbi-detritvore populations seems unlikely in litter-rich ecosystems due to the non-trophic, habitat-structuring effect of the basal litter resource.     

GABI‐DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana

Owing to duplication events in its progenitor, more than 90% of the genes in the Arabidopsis thaliana genome are members of multigene families. A set of 2108 gene families, each consisting of precisely two unlinked paralogous genes, was identified in the nuclear genome of A. thaliana on the basis of sequence similarity. A systematic method for the creation of double knock‐out lines for such gene pairs, designated as DUPLO lines, was established and 200 lines are now publicly available. Their initial phenotypic characterisation led to the identification of seven lines with defects that emerge only in the adult stage. A further six lines display seedling lethality and 23 lines were lethal before germination. Another 14 lines are known to show phenotypes under non‐standard conditions or at the molecular level. Knock‐out of gene pairs with very similar coding sequences or expression profiles is more likely to produce a mutant phenotype than inactivation of gene pairs with dissimilar profiles or sequences. High coding sequence similarity and highly similar expression profiles are only weakly correlated, implying that promoter and coding regions of these gene pairs display different degrees of diversification.     

Investigation of acyclic uridine amide and 5′-amido nucleoside analogues as potential inhibitors of the Plasmodium falciparum dUTPase

Previously we have shown that trityl and diphenyl deoxyuridine derivatives and their acyclic analogues can inhibit Plasmodium falciparum dUTPase (PfdUTPase). We report the synthesis of conformationally restrained amide derivatives as inhibitors PfdUTPase, including both acyclic and cyclic examples. Activity was dependent on the orientation and location of the amide constraining group. In the case of the acyclic series, we were able to obtain amide-constrained analogues which showed similar or greater potency than the unconstrained analogues. Unfortunately these compounds showed lower selectivity in cellular assays.