Responses of aquatic macrophyte cover and productivity to flooding variability on the Amazon floodplain

Macrophyte net primary productivity (NPP) is a significant but understudied component of the carbon budget in large Amazonian floodplains. Annual NPP is determined by the interaction between stem elongation (vertical growth) and plant cover changes (horizontal expansion), each affected differently by flood duration and amplitude. Therefore, hydrological changes as predicted for the Amazon basin could result in significant changes in annual macrophyte NPP. This study investigates the responses of macrophyte horizontal expansion and vertical growth to flooding variability, and its possible effects on the contribution of macrophytes to the carbon budget of Amazonian floodplains. Monthly macrophyte cover was estimated using satellite imagery for the 2003–2004 and 2004–2005 hydrological years, and biomass was measured in situ between 2003 and 2004. Regression models between macrophyte variables and river‐stage data were used to build a semiempirical model of macrophyte NPP as a function of water level. Historical river‐stage records (1970–2011) were used to simulate variations in NPP, as a function of annual flooding. Vertical growth varied by a factor of ca. 2 over the simulated years, whereas minimum and maximum annual cover varied by ca. 3.5 and 1.5, respectively. Results suggest that these processes act in opposite directions to determine macrophyte NPP, with larger sensitivity to changes in vertical growth, and thus maximum flooding levels. Years with uncommonly large flooding amplitude resulted in the highest NPP values, as both horizontal expansion and vertical growth were enhanced under these conditions. Over the simulated period, annual NPP varied by ca. 1.5 (1.06–1.63 TgC yr^?1). A small increasing trend in flooding amplitude, and by extension NPP, was observed for the studied period. Variability in growth rates caused by local biotic and abiotic factors, and the lack of knowledge on macrophyte physiological responses to extreme hydrological conditions remain the major sources of uncertainty.     

Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation

We recently described the presence of large chromosomal segments resulting from independent horizontal gene transfer (HGT) events in the genome of Saccharomyces cerevisiae strains, mostly of wine origin. We report here evidence for the amplification of one of these segments, a 17 kb DNA segment from Zygosaccharomyces bailii, in the genome of S. cerevisiae strains. The copy number, organization and location of this region differ considerably between strains, indicating that the insertions are independent and that they are post-HGT events. We identified eight different forms in 28 S. cerevisiae strains, mostly of wine origin, with up to four different copies in a single strain. The organization of these forms and the identification of an autonomously replicating sequence functional in S. cerevisiae, strongly suggest that an extrachromosomal circular DNA (eccDNA) molecule serves as an intermediate in the amplification of the Z. bailii region in yeast genomes. We found little or no sequence similarity at the breakpoint regions, suggesting that the insertions may be mediated by nonhomologous recombination. The diversity between these regions in S. cerevisiae represents roughly one third the divergence among the genomes of wine strains, which confirms the recent origin of this event, posterior to the start of wine strain expansion. This is the first report of a circle-based mechanism for the expansion of a DNA segment, mediated by nonhomologous recombination, in natural yeast populations.     

Appearances can be deceptive: different diversification patterns within a group of Mediterranean earthworms (Oligochaeta, Hormogastridae)

Many recent studies on invertebrates have shown how morphology not always captures the true diversity of taxa, with cryptic speciation often being discussed in this context. Here, we show how diversification patterns can be very different in two clades of closely related earthworms in the genus Hormogaster stressing the risk of using nonspecific substitution rate values across taxa. On the one hand, the Hormogaster elisae species complex, endemic to the central Iberian Peninsula, shows morphological stasis. On the other hand, a clade of Hormogaster from the NE Iberian Peninsula shows an enormous morphological variability, with 15 described morphospecies. The H. elisae complex, however, evolves faster genetically, and this could be explained by the harsher environmental conditions to which it is confined—as detected in this study, that is, sandier and slightly poorer soils with lower pH values than those of the other species in the family. These extreme conditions could be at the same time limiting morphological evolution and thus be responsible for the observed morphological stasis in this clade. Contrarily, Hormogaster species from the NE Iberian Peninsula, although still inhabiting harsher milieu than other earthworm groups, have had the opportunity to evolve into a greater morphological disparity. An attempt to delimit species within this group following the recently proposed general mixed Yule‐coalescent method showed a higher number of entities than expected under the morphospecies concept, most probably due to the low vagility of these animals, which considerably limits gene flow between distant conspecific populations, but also because of the decoupling between morphological and genetic evolution in the H. elisae complex.     

Accurate flow cytometric membrane potential measurement in bacteria using diethyloxacarbocyanine and a ratiometric technique.

BACKGROUND: Membrane potential (MP) plays a critical role in bacterial physiology. Existing methods for MP estimation by flow cytometry are neither accurate nor precise, due in part to the heterogeneity of size of the particles analyzed. The ratio of a size- and MP-sensitive measurement, and an MP-independent, size-sensitive measurement, should provide a better estimate of MP. METHODS: Flow cytometry and spectrofluorometry were used to detect red (488 --> 600 nm) fluorescence associated with aggregates of diethyloxacarbocyanine (DiOC2(3)), which, in the monomeric state, is normally green (488 --> 530 nm) fluorescent. RESULTS: In bacteria incubated with 30 microM dye, aggregate formation increases with the magnitude of the interior-negative membrane potential. Green fluorescence from stained bacteria predominantly reflects particle size, and is relatively independent of MP, whereas red fluorescence is highly dependent on both MP and size. The ratio of red to green fluorescence provides a measure of MP that is largely independent of cell size, with a low coefficient of variation (CV). Calibration with valinomycin and potassium demonstrates that the method is accurate over the range from -50 mV through -120 mV; it also accurately tracks reversible reductions in MP produced by incubation at 4 degrees C and washing in glucose-free medium. CONCLUSIONS: The ratiometric technique for MP estimation using DiOC2(3) is substantially more accurate and precise than those previously available, and may be useful in studies of bacterial physiology and in investigations of the effects of antibiotics and other agents on microorganisms.     

Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees

Background  

Tropical rain forests are the most diverse terrestrial ecosystems on the planet. How this diversity evolved remains largely unexplained. In Africa, rain forests are situated in two geographically isolated regions: the West-Central Guineo-Congolian region and the coastal and montane regions of East Africa. These regions have strong floristic affinities with each other, suggesting a former connection via an Eocene pan-African rain forest. High levels of endemism observed in both regions have been hypothesized to be the result of either 1) a single break-up followed by a long isolation or 2) multiple fragmentation and reconnection since the Oligocene. To test these hypotheses the evolutionary history of endemic taxa within a rain forest restricted African lineage of the plant family Annonaceae was studied. Molecular phylogenies and divergence dates were estimated using a Bayesian relaxed uncorrelated molecular clock assumption accounting for both calibration and phylogenetic uncertainties.     

Beta-catenin triggers nuclear factor kappaB-dependent up-regulation of hepatocyte inducible nitric oxide synthase

Disruption of cell-to-cell contacts, as observed in many pathophysiological conditions, prime hepatocytes for compensatory hyperplastic response that involves induction of several genes, including proto-oncogenes and other gene targets of beta-catenin signaling pathway. By using cultured hepatocytes and experimental models of adherens junction disruption we have investigated changes in beta-catenin subcellular localization and their relationships with inducible nitric oxide synthase (iNOS) expression. Two experimental models were employed: (a) rat hepatocytes obtained by collagenase liver perfusion within the first 48 h of culture; (b) 48-h old cultured hepatocytes, transiently transfected or not with a plasmid encoding for dominant/negative inhibitory kappa B-alpha, exposed to ethylene glycol-bis-(2-aminoethylether)-N,N,N',N'-tetraacetic acid/LiCl treatment. beta-Catenin signaling and cellular localization, iNOS expression and nuclear factor kappaB involvement, were investigated using morphological, cell and molecular biology techniques. E-cadherin-mediated disruption of cell-to-cell contacts induces early beta-catenin translocation from membrane to cytoplasm and nuclear compartments, events that are followed by up-regulation of c-myc, cyclin D1 and beta-transducin repeat-containing protein expression. This, in turn, resulted eventually in iNOS induction that was mechanistically related to nuclear factor kappaB activation, as unequivocally shown in cells expressing dominant negative inhibitory kappa B-alpha. Our data indicate that E-cadherin disassembly and concomitant inactivation of glycogen synthase kinase-3beta result in nuclear factor kappaB-dependent induction of iNOS in hepatocytes.     

Microsatellite markers for the drought-resistant earthworm Hormogaster elisae

We developed and characterized 10 highly polymorphic microsatellite loci from a simple sequence repeat-enriched genomic DNA library of the earthworm Hormogaster elisae. Characterization of these loci using 26 individuals revealed eight to 25 alleles per locus and high levels of heterozygosity. These loci will be used for paternity analysis and population genetic studies.