Cryptogenic hepatitis patients have a higher Bartonella sp.-DNA detection in blood and skin samples than patients with non-viral hepatitis of known cause

BackgroundThis study aimed to assess the prevalence of Bartonella sp.-DNA detection in blood and skin samples from patients with non-viral end-stage liver disease awaiting liver transplantation.Methodology/Principal findingsBlood samples and healthy skin fragments from 50 patients were tested using microbiological and molecular methods. Fifteen patients had cryptogenic hepatitis (CH) and 35 had alcoholic, drug-induced or autoimmune liver disease. DNA was extracted from whole blood and liquid culture samples, isolates, and skin fragments. Thirteen of the 50 patients (26%) had Bartonella henselae DNA detection in their blood (9/50) and/or skin (5/50) samples. Colonies were isolated in 3/50 (6%) and infection was detected in 7/50 (14%) of the 50 patients. B. henselae-DNA detection was more prevalent in patients with CH than in other patients (p = 0.040). Of 39 patients followed-up for at least two years, a higher mortality rate was observed among patients with CH infected with B. henselae (p = 0.039).Conclusions/SignificanceFurther studies assessing the role of B. henselae infection in the pathogenesis of hepatitis patients must be urgently conducted.     

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.     

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.     

EZYprep LC‐coupled MALDI‐TOF/TOF MS: An improved matrix spray application for phosphopeptide characterisation

The quality of MALDI‐TOF mass spectrometric analysis is highly dependent on the matrix and its deposition strategy. Although different matrix‐deposition methods have specific advantages, one major problem in the field of proteomics, particularly with respect to quantitation, is reproducibility between users or laboratories. Compounding this is the varying crystal homogeneity of matrices depending on the deposition strategy used. Here, we describe a novel optimised matrix‐deposition strategy for LC‐MALDI‐TOF/TOF MS using an automated instrument that produces a nebulised matrix “mist” under controlled atmospheric conditions. Comparisons of this with previously reported strategies showed the method to be advantageous for the atypical matrix, 2,5‐DHB, and improved phosphopeptide ionisation when compared with deposition strategies for CHCA. This optimised DHB matrix‐deposition strategy with LC‐MALDI‐TOF/TOF MS, termed EZYprep LC, was subsequently optimised for phosphoproteome analysis and compared to LC‐ESI‐IT‐MS and a previously reported approach for phosphotyrosine identification and characterisation. These methods were used to map phosphorylation on epidermal growth factor‐stimulated epidermal growth factor receptor to gauge the sensitivity of the proposed method. EZYprep DHB LC‐MALDI‐TOF/TOF MS was able to identify more phosphopeptides and characterise more phosphorylation sites than the other two proteomic strategies, thus proving to be a sensitive approach for phosphoproteome analysis.     

Ecology,morphology and physiology of Chroothece richteriana (Rhodophyta,Stylonematophyceae) in the highly calcareous Río Chícamo,south-east Spain

The ecology of Chroothece was studied in the highly calcareous Río Chícamo, south-east Spain, in order to explain its success there, but rarity elsewhere. The river, which originates mainly from an underground aquifer, has water with high conductivity, sulphate and nitrate but low phosphate concentrations, the latter mainly organic. Chroothece occurs in mats and in lobed colonies reaching 4 cm in the broadest dimension. The colony surface consists of one layer of cells, each of which is attached to a stalk, which dichotomizes when the cell divides; stalks often extend to the colony base. The central region of many mat cells and almost all colony cells has a yellow to orange-brown colour, associated with the numerous lipid droplets densely covering the surface of the pyrenoid and arms of the star-shaped chloroplast. Field material and laboratory isolates indicate that stalk formation occurs under moderate P limitation and both stalks and cell sheath show high phosphatase activities. This also occurred in a culture collection strain maintained for 30 years in a very P-rich medium, but then transferred to a moderately P-limiting medium (c. 0.9 mg l^?1). We suggest that colony formation is initiated by aggregation of motile cells following P pulses in the water. Comparisons are made with Rivularia, a competitor in this nitrate-rich river, in spite of being a N₂-fixer. One difference is that Chroothece cells lie at the periphery of the colonies and are therefore exposed to maximum sunlight, whereas Rivularia trichomes grow inside colonies with photoprotection by scytonemin. However, the ability to withstand heavy grazing pressure may be an especially important factor favouring Rivularia here.     

Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation

Relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co‐occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar g_s temporal dynamics in response to drought. Further, whereas P. edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.     

Invasive cane toads are unique in shape but overlap in ecological niche compared to Australian native frogs

Invasive species are an important issue worldwide but predicting invasiveness, and the underlying mechanisms that cause it, is difficult. There are several primary hypotheses to explain invasion success. Two main hypothesis based on niche spaces stand out as alternative, although not exclusive. The empty niche hypothesis states that invaders occupy a vacant niche space in the recipient community, and the niche competition hypothesis states that invaders overlap with native species in niche space. Studies on trait similarity/dissimilarity between the invader and native species can provide information on their niche overlap. Here, we use the highly invasive and well‐studied cane toad (Rhinella marina) to test these two hypotheses in Australia, and assess its degree of overlap with native species in several niche dimensions. We compare extensive morphological and environmental data of this successful invader to 235 species (97%) of native Australian frogs. Our study is the first to document the significant morphological differences between the invasive cane toad and a continent‐wide frog radiation: despite significant environmental overlap, cane toads were distinct in body size and shape from most Australian frog species, suggesting that in addition to their previously documented phenotypic plasticity and wide environmental and trophic niche breadth, their unique shape also may have contributed to their success as an invasive species in Australia. Thus, the invasive success of cane toads in Australia may be explained through them successfully colonizing an empty niche among Australian anurans. Our results support that the cane toad's distinct morphology may have played a unique role in the invasiveness of this species in Australia, which coupled with a broad environmental niche breadth, would have boosted their ability to expand their distribution across Australia. We also propose RLLR (Relative limb length ratio) as a potentially useful measure of identifying morphological niche uniqueness and a potential measure of invasiveness potential in anuran amphibians.