THE ZOOSPORE OF CHLOROKYBUS ATMOPHYTICUS,A CHAROPHYTE WITH SARCINOID GROWTH HABIT

Chlorokybus atmophyticus has a sarcinoid growth habit and produces scale-covered zoospores. Flagella are laterally inserted and attached internally to a multilayered structure characteristic of the Charophyceae. There are two kinds of pyrenoid in each cell, a feature previously observed in only one scaly green flagellate. C. atmophyticus demonstrates that the sarcinoid growth habit arose independently at least twice in the green algae and cannot be used to define taxonomic groups unless combined with other criteria. It is further concluded that C. atmophyticus should be classified in a separate family Chlorokybaceae and a separate order Chloroky bales.     

The use of stable isotopes to trace small-scale movements by small fish species

Valuable biological information can be obtained by monitoring the movement of organisms. However, the choice of monitoring method becomes highly restricted when following small organisms (<100 mm), especially in aquatic ecosystems. Stable isotopes are being increasingly used in this respect but rarely at the local spatial scale, i.e. 10–1000 s of metres. We sought to identify movement of small fishes between a main river channel and its tributary. Little overlap in isotope baseline was detected between the two channels despite some temporal variability in δ¹⁵N of baseline indicator organisms in the main river. The individuals of two small cyprinid fish species (Leuciscus souffia and Alburnoides bipunctatus) of all the size classes (40–100 mm) caught within the tributary showed considerable heterogeneity in δ¹⁵N values. Classification and discriminant analysis on isotope-derived data distinguished two significantly different groups. Moreover, this result was supported by further sampling of fish caught in the main river (in May and December 2006). Alternative hypotheses, such as dietary differences, biological factors, temporal shifts and spatial differences in diet, did not explain δ¹⁵N variability. This application of stable isotopes at a relatively small spatial and temporal scales further demonstrates its potential as a tool for ecologists.     

Association of the colistin resistance gene mcr-1 with faecal pollution in water environments in Hanoi,Vietnam

Colistin is one of the antibiotics of last resort for human health. However, the dissemination of the plasmid-mediated colistin resistance gene mcr-1 is of great concern globally. In the One Health framework, the environment is an important component for managing antimicrobial resistance. However, little information is available concerning the prevalence of mcr-1 in water environments. We aimed to reveal the prevalence of mcr-1 in different water environments in Hanoi, Vietnam. Quantitative PCR was applied to detect mcr-1 in four urban drainages receiving untreated domestic wastewater, three rivers, five lakes and two groundwater samples. Urban drainages contained higher concentrations of mcr-1, suggesting that urban residents carry the gene. The class 1 integron-integrase gene was identified as a good surrogate of antibiotic resistance genes including mcr-1. A significant correlation was found between the levels of mcr-1 and the human-specific cross-assembly phage, which is an indicator of human faecal pollution. These results indicated that the primary source of mcr-1 in urban water environments is human faeces, which is consistent with the fact that most domestic wastewater is untreated in Hanoi. The control of untreated wastewater is critical for alleviating the spread of mcr-1 in water environments in Vietnam.     

In vivo neutralization of TNF-alpha promotes humoral autoimmunity by preventing the induction of CTL.

Neutralization of TNF-alpha in humans with rheumatoid arthritis or Crohn's disease has been associated with the development of humoral autoimmunity. To determine the effect of TNF-alpha neutralization on cell-mediated and humoral-mediated responses, we administered anti-TNF-alpha mAb to mice undergoing acute graft-vs-host disease (GVHD) using the parent-into-F(1) model. In vivo neutralization of TNF-alpha blocked the lymphocytopenic features characteristic of acute GVHD and induced a lupus-like chronic GVHD phenotype (lymphoproliferation and autoantibody production). These effects resulted from complete inhibition of detectable antihost CTL activity and required the presence of anti-TNF-alpha mAb for the first 4 days after parental cell transfer, indicating that TNF-alpha plays a critical role in the induction of CTL. Moreover, an in vivo blockade of TNF-alpha preferentially inhibited the production of IFN-gamma and blocked IFN-gamma-dependent up-regulation of Fas; however, cytokines such as IL-10, IL-6, or IL-4 were not inhibited. These results suggest that a therapeutic TNF-alpha blockade may promote humoral autoimmunity by selectively inhibiting the induction of a CTL response that would normally suppress autoreactive B cells.     

Biochemical Conservation and Evolution of Germacrene A Oxidase in Asteraceae

Sesquiterpene lactones are characteristic natural products in Asteraceae, which constitutes ∼8% of all plant species. Despite their physiological and pharmaceutical importance, the biochemistry and evolution of sesquiterpene lactones remain unexplored. Here we show that germacrene A oxidase (GAO), evolutionarily conserved in all major subfamilies of Asteraceae, catalyzes three consecutive oxidations of germacrene A to yield germacrene A acid. Furthermore, it is also capable of oxidizing non-natural substrate amorphadiene. Co-expression of lettuce GAO with germacrene synthase in engineered yeast synthesized aberrant products, costic acids and ilicic acid, in an acidic condition. However, cultivation in a neutral condition allowed the de novo synthesis of a single novel compound that was identified as germacrene A acid by gas and liquid chromatography and NMR analyses. To trace the evolutionary lineage of GAO in Asteraceae, homologous genes were further isolated from the representative species of three major subfamilies of Asteraceae (sunflower, chicory, and costus from Asteroideae, Cichorioideae, and Carduoideae, respectively) and also from the phylogenetically basal species, Barnadesia spinosa, from Barnadesioideae. The recombinant GAOs from these genes clearly showed germacrene A oxidase activities, suggesting that GAO activity is widely conserved in Asteraceae including the basal lineage. All GAOs could catalyze the three-step oxidation of non-natural substrate amorphadiene to artemisinic acid, whereas amorphadiene oxidase diverged from GAO displayed negligible activity for germacrene A oxidation. The observed amorphadiene oxidase activity in GAOs suggests that the catalytic plasticity is embedded in ancestral GAO enzymes that may contribute to the chemical and catalytic diversity in nature.     

Comparison of Directly Prepared and Cultured Cells in Karyotypic Analysis of All

An evaluation of methods for studying bone marrow obtained from patients with acute lymphoblastic leukemia indicates that both directly prepared and cultured cells are necessary for complete karyotypic analysis, but that both synchronized and unsynchronized cultures may not be necessary.     

Ammonium photo-production by heterocytous cyanobacteria: potentials and constraints

Over the last decades, production of microalgae and cyanobacteria has been developed for several applications, including novel foods, cosmetic ingredients and more recently biofuel. The sustainability of these promising developments can be hindered by some constraints, such as water and nutrient footprints. This review surveys data on N₂-fixing cyanobacteria for biomass production and ways to induce and improve the excretion of ammonium within cultures under aerobic conditions. The nitrogenase complex is oxygen sensitive. Nevertheless, nitrogen fixation occurs under oxic conditions due to cyanobacteria-specific characteristics. For instance, in some cyanobacteria, the vegetative cell differentiation in heterocyts provides a well-adapted anaerobic microenvironment for nitrogenase protection. Therefore, cell cultures of oxygenic cyanobacteria have been grown in laboratory and pilot photobioreactors (Dasgupta et al., 2010; Fontes et al., 1987; Moreno et al., 2003; Nayak & Das, 2013). Biomass production under diazotrophic conditions has been shown to be controlled by environmental factors such as light intensity, temperature, aeration rate, and inorganic carbon concentration, also, more specifically, by the concentration of dissolved oxygen in the culture medium. Currently, there is little information regarding the production of extracellular ammonium by heterocytous cyanobacteria. This review compares the available data on maximum ammonium concentrations and analyses the specific rate production in cultures grown as free or immobilized filamentous cyanobacteria. Extracellular production of ammonium could be coupled, as suggested by recent research on non-diazotrophic cyanobacteria, to that of other high value metabolites. There is little information available regarding the possibility for using diazotrophic cyanobacteria as cellular factories may be in regard of the constraints due to nitrogen fixation.     

Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Carbon System Measurements and Potential Climatic Drivers at a Site of Rapidly Declining Ocean pH

We explored changes in ocean pH in coastal Washington state, USA, by extending a decadal-scale pH data series, by reporting independent measures of dissolved inorganic carbon (DIC), spectrophotometric pH, and total alkalinity (TA), by exploring pH patterns over larger spatial scales, and by probing for long-term trends in environmental variables reflecting potentially important drivers of pH. We found that pH continued to decline in this area at a rapid rate, that pH exhibited high natural variability within years, that our measurements of pH corresponded well to spectrophotometric pH measures and expected pH calculated from DIC/TA, and that TA estimates based on salinity predicted well actual alkalinity. Multiple datasets reflecting upwelling, including water temperature, nutrient levels, phytoplankton abundance, the NOAA upwelling index, and data on local wind patterns showed no consistent trends over the period of our study. Multiple datasets reflecting precipitation change and freshwater runoff, including precipitation records, local and regional river discharge, salinity, nitrate and sulfate in rainwater, and dissolved organic carbon (DOC) in rivers also showed no consistent trends over time. Dissolved oxygen did not decline over time, indicating that long-term changes did not result from shifts in contributions of respiration to pH levels. These tests of multiple potential drivers of the observed rapid rate of pH decline indicate a primary role for inorganic carbon and suggest that geochemical models of coastal ocean carbon fluxes need increased investigation.