The Microaerophile SPirillum volutans: Cultivation on Complex Liquid and Solid Media

Spirillum volutans grows only under microaerobic conditions in a peptone-succinate-salts broth, but can grow aerobically when the peptone is replaced by vitamin-free acid-hydrolyzed casein broth. The addition of potassium metabisulfite, norepinephrine, catalase or superoxide dismutase (SOD) permitted aerobic growth in peptone-succinate-salts broth. A combination of catalase and SOD had a synergistic effect. S. volutans lacked catalase and had only a low level of peroxidase activity, but did possess SOD activity (12 to 14 U/mg of protein). The organism was found to be extraordinarily sensitive to exogenous hydrogen peroxide. Illumination of peptone-succinate-salts broth generated hydrogen peroxide and rendered the medium inhibitory to growth. A combination of catalase and SOD prevented this inhibition. Growth of S. volutans on solid media, not previously possible, was accomplished by the use of vitamin-free acid-hydrolyzed casein and peptone-succinate-salts agar media; maximum growth responses were dependent on the following combination of factors: addition of bisulfite, catalase, or SOD, protection of the media from illumination, incubation in a highly humid atmosphere, and incubation under atmospheres of 12% oxygen or less. The results indicate that the microaerophilic nature of S. volutans is attributable largely to the high sensitivity of the organism to exogenous hydrogen peroxide and, to a lesser extent, superoxide radicals occurring in the culture medium.     

Temperature,hydrochemistry and plankton in Wicken Brickpits, 1930–1931

Temperature, selected chemical constituents and plankton were analysed from three depths, fortnightly, by day and occasionally by night, in two flooded brickpits, between May 1930 and August 1931.Br was 3.3 m deep, with clear water and little weed; III was only 1.8 m deep, with thick submerged weed, more sheltered than Br and becoming eutrophic. Neither had direct inflow nor outlet. Both conformed to the second order for dimictic lakes, with summer and winter stratification, leading, for varying periods, to stagnation marked by pH between 6.6 and 7.2 and O₂ much depleted or absent at the bottom.During stagnation, release of SiO₂, soluble inorganic phosphate-P, ammonium ions and bases from the bottom was shown by sampling water close to the mud. This finding preceded the definition of redox potential by others.Thermistor temperature measurements, used for the first time, showed comparable summer gradients in both ponds: on windy days these were usually sigmoid, with discontinuity at various depths, or else nearly isothermal; on calm days, they were exponential, when transmission of heat, from surface to bottom, was apparently due to radiation alone, without water circulation. Stability was then high.Diatoms were abundant in both ponds; but planktonic Rotifera and Crustacea differed in the two, apart fromDiaptomus gracilis, which was dominant in both.     

Physiological Adaptations in Response to Environmental Stress During an N2-Fixing Anabaena Bloom

Anabaena spiroides has the ability to maintain intense biomass production for extensive periods in the epilimnion of a small eutrophic lake characterized by conditions shown to cause photooxidative death in a number of other phytoplankton. By the enhancement of carotenoid synthesis chlorophyll a was protected from photooxidation and prevented from catalyzing other photooxidative reactions within the cells. By temporally separating CO₂ and N₂ fixation, maximum utilization of photosynthetically active radiation was achieved. Because CO₂ fixation was more sensitive than N₂ fixation to a high oxygen concentration, the former was maximized during morning hours, before the afternoon buildup of dissolved oxygen. The diurnal partitioning of carbon and N₂ fixation has two additional advantages; possible competition for reductant-generating compounds is minimized, and adequate endogenous pools of carbon skeletons are assured to accept newly fixed ammonia. Hence, Anabaena, far from undergoing photooxidative death, appears to utilize a physiological strategy which allows optimization of radiant energy use for reductive processes and dominance of surface waters and shading of deeper phytoplankton during summer blooms.     

Genome‐wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis

Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context. Previous studies have shown that a protein complex, the ASI1‐AIPP1‐EDM2 (AAE) complex, participates in polyadenylation regulation of several intronic heterochromatin‐containing genes. However, the genome‐wide functions of AAE are still unknown. Here, we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome‐wide level and preferentially interacts with genetic heterochromatin. Polyadenylation (poly(A) sequencing reveals that AAE complex has a substantial influence on poly(A) site usage of heterochromatin‐containing genes, including not only intronic heterochromatin‐containing genes but also the genes showing overlap with heterochromatin. Intriguingly, AAE is also involved in the alternative splicing regulation of a number of heterochromatin‐overlapping genes, such as the disease resistance gene RPP4. We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation. In addition to conferring RNA processing regulation at genic heterochromatin‐containing genes, AAE also targets some transposable elements (TEs) outside of genes (including TEs sandwiched by genes and island TEs) for epigenetic silencing. Our results reveal new functions of AAE in RNA processing and epigenetic silencing, and thus represent important advances in epigenetic regulation.     

Infection intensity-dependent accuracy of reagent strip for the diagnosis of Schistosoma haematobium and estimation of treatment prevalence thresholds

BackgroundReagent strip to detect microhematuria as a proxy for Schistosoma haematobium infections has been considered an alternative to urine filtration for individual diagnosis and community-based estimates of treatment needs for preventive chemotherapy. However, the diagnostic accuracy of reagent strip needs further investigation, particularly at low infection intensity levels.MethodsWe used existing data from a study conducted in Tanzania that employed urine filtration and reagent strip testing for S. haematobium in two villages, including a baseline and six follow-up surveys after praziquantel treatment representing a wide range of infection prevalence. We developed a Bayesian model linking individual S. haematobium egg count data based on urine filtration to reagent strip binary test results available on multiple days and estimated the relation between infection intensity and sensitivity of reagent strip. Furthermore, we simulated data from 3,000 hypothetical populations with varying mean infection intensity to infer on the relation between prevalence observed by urine filtration and the interpretation of reagent strip readings.Principal findingsReagent strip showed excellent sensitivity even for single measurement reaching 100% at around 15 eggs of S. haematobium per 10 ml of urine when traces on reagent strip were considered positive. The corresponding specificity was 97%. When traces were considered negative, the diagnostic accuracy of the reagent strip was equivalent to urine filtration data obtained on a single day. A 10% and 50% urine filtration prevalence based on a single day sampling corresponds to 11.2% and 48.6% prevalence by reagent strip, respectively, when traces were considered negative, and 17.6% and 57.7%, respectively, when traces were considered positive.Conclusions/SignificanceTrace results should be included in reagent strip readings when high sensitivity is required, but excluded when high specificity is needed. The observed prevalence of reagent strip results, when traces are considered negative, is a good proxy for prevalence estimates of S. haematobium infection by urine filtration on a single day.     

Species specificity and intraspecific variation in the chemical profiles of Heliconius butterflies across a large geographic range

In many animals, mate choice is important for the maintenance of reproductive isolation between species. Traits important for mate choice and behavioral isolation are predicted to be under strong stabilizing selection within species; however, such traits can also exhibit variation at the population level driven by neutral and adaptive evolutionary processes. Here, we describe patterns of divergence among androconial and genital chemical profiles at inter‐ and intraspecific levels in mimetic Heliconius butterflies. Most variation in chemical bouquets was found between species, but there were also quantitative differences at the population level. We found a strong correlation between interspecific chemical and genetic divergence, but this correlation varied in intraspecific comparisons. We identified “indicator” compounds characteristic of particular species that included compounds already known to elicit a behavioral response, suggesting an approach for identification of candidate compounds for future behavioral studies in novel systems. Overall, the strong signal of species identity suggests a role for these compounds in species recognition, but with additional potentially neutral variation at the population level.     

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Genome‐scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between and within metabolic pathways. The developed method and model are expected to increase the use of model‐based design in metabolic engineering.     

Climate and land use changes will degrade the configuration of the landscape for titi monkeys in eastern Brazil

Land use changes have profound effects on populations of Neotropical primates, and ongoing climate change is expected to aggravate this scenario. The titi monkeys from eastern Brazil (Callicebus personatus group) have been particularly affected by this process, with four of the five species now allocated to threatened conservation status categories. Here, we estimate the changes in the distribution of these titi monkeys caused by changes in both climate and land use. We also use demographic‐based, functional landscape metrics to assess the magnitude of the change in landscape conditions for the distribution predicted for each species. We built species distribution models (SDMs) based on maximum entropy for current and future conditions (2070), allowing for different global circulation models and contrasting scenarios of glasshouse gas concentrations. We refined the SDMs using a high‐resolution map of habitat remnants. We then calculated habitat availability and connectivity based on home‐range size and the dispersal limitations of the individual, in the context of a predicted loss of 10% of forest cover in the future. The landscape configuration is predicted to be degraded for all species, regardless of the climatic settings. This include reductions in the total cover of forest remnants, patch size and functional connectivity. As the landscape configuration should deteriorate severely in the future for all species, the prevention of further loss of populations will only be achieved through habitat restoration and reconnection to counteract the negative effects for these and several other co‐occurring species.