Winter−spring transition in the subarctic Atlantic: microbial response to deep mixing and pre-bloom production

In temperate, subpolar and polar marine systems, the classical perception is that diatoms initiate the spring bloom and thereby mark the beginning of the productive season. Contrary to this view, we document an active microbial food web dominated by pico- and nanoplankton prior to the diatom bloom, a period with excess nutrients and deep convection of the water column. During repeated visits to stations in the deep Iceland and Norwegian basins and the shallow Shetland Shelf (26 March to 29 April 2012), we investigated the succession and dynamics of photosynthetic and heterotrophic microorganisms. We observed that the early phytoplankton production was followed by a decrease in the carbon:nitrogen ratio of the dissolved organic matter in the deep mixed stations, an increase in heterotrophic prokaryote (bacteria) abundance and activity (indicated by the high nucleic acid:low nucleic acid bacteria ratio), and an increase in abundance and size of heterotrophic protists. The major chl a contribution in the early winter-spring transition was found in the fraction 50 µm) were stimulated by deep mixing later in the period, while picophytoplankton were unaffected by mixing; both physical and biological reasons for this development are discussed herein

Genes Linked to Production of Secondary Metabolites in Talaromyces atroroseus Revealed Using CRISPR-Cas9

The full potential of fungal secondary metabolism has until recently been impeded by the lack of universal genetic tools for most species. However, the emergence of several CRISPR-Cas9-based genome editing systems adapted for several genera of filamentous fungi have now opened the doors for future efforts in discovery of novel natural products and elucidation and engineering of their biosynthetic pathways in fungi where no genetic tools are in place. So far, most studies have focused on demonstrating the performance of CRISPR-Cas9 in various fungal model species, and recently we presented a versatile CRISPR-Cas9 system that can be successfully applied in several diverse Aspergillus species. Here we take it one step further and show that our system can be used also in a phylogenetically distinct and largely unexplored species from the genus of Talaromyces. Specifically, we exploit CRISPR-Cas9-based genome editing to identify a new gene in T. atroroseus responsible for production of polyketide-nonribosomal peptide hybrid products, hence, linking fungal secondary metabolites to their genetic origin in a species where no genetic engineering has previously been performed

Linker Flexibility Facilitates Module Exchange in Fungal Hybrid PKS-NRPS Engineering

Polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) each give rise to a vast array of complex bioactive molecules with further complexity added by the existence of natural PKS-NRPS fusions. Rational genetic engineering for the production of natural product derivatives is desirable for the purpose of incorporating new functionalities into pre-existing molecules, or for optimization of known bioactivities. We sought to expand the range of natural product diversity by combining modules of PKS-NRPS hybrids from different hosts, hereby producing novel synthetic natural products. We succeeded in the construction of a functional cross-species chimeric PKS-NRPS expressed in Aspergillus nidulans. Module swapping of the two PKS-NRPS natural hybrids CcsA from Aspergillus clavatus involved in the biosynthesis of cytochalasin E and related Syn2 from rice plant pathogen Magnaporthe oryzae lead to production of novel hybrid products, demonstrating that the rational re-design of these fungal natural product enzymes is feasible. We also report the structure of four novel pseudo pre-cytochalasin intermediates, niduclavin and niduporthin along with the chimeric compounds niduchimaeralin A and B, all indicating that PKS-NRPS activity alone is insufficient for proper assembly of the cytochalasin core structure. Future success in the field of biocombinatorial synthesis of hybrid polyketide-nonribosomal peptides relies on the understanding of the fundamental mechanisms of inter-modular polyketide chain transfer. Therefore, we expressed several PKS-NRPS linker-modified variants. Intriguingly, the linker anatomy is less complex than expected, as these variants displayed great tolerance with regards to content and length, showing a hitherto unreported flexibility in PKS-NRPS hybrids, with great potential for synthetic biology-driven biocombinatorial chemistry

Assessing social, emotional, and intercultural competences of students and school staff. A systematic literature review

The inclusion of social, emotional, and intercultural competences (SEI) in academic contexts has been supported by international organizations, such as the European Union, the United Nations, and the OECD, since the early 2000s. However, little information is yet available regarding the assessment of these competences. This paper shares the findings of a systematic literature review that produced an inventory of existing tools for the assessment of SEI competences of students and school staff. This is the first time assessment tools for these three competences have been concurrently reviewed. An interdisciplinary and international research team conducted this systematic literature review in the databases of ERIC, PsycInfo, PSYNDEX, Scopus, and Web of Science. Out of 13,963 articles, 149 assessment tools were examined and processed. In addition to the instrument analysis and a detailed description of the procedure, this article shows the basic theoretical concepts, as well as the limitations, of such a review. It was found that 1) the majority of the discovered instruments rely on self-reported survey and inventory data, 2) of the three competences, intercultural competence had the fewest relevant instruments, and 3) very few tools have been created to assess all three competences together. From this review, it is apparent that a wider variety of assessment tools (other than self-reports), as well as more comprehensive tools (e.g. qualitative analysis of vignettes) for the assessment of all three SEI competences, should be developed to meet international demand. The results of the literature review are available and freely accessible in the form of an assessment catalogue. (DIPF/Orig.

Methotrexate polyglutamate levels and co-distributions in childhood acute lymphoblastic leukemia maintenance therapy

PurposeMethotrexate polyglutamates (MTXpg) facilitate incorporation of thioguanine nucleotides into DNA (DNA-TG, the primary cytotoxic thiopurine metabolite and outcome determinant in MTX/6-mercaptopurine treatment of childhood ALL). We hypothesized that mapping erythrocyte levels of MTXpg with 1-6 glutamates and their associations with DNA-TG formation would facilitate future guidelines for maintenance therapy dosing.Methods and resultsSummed MTX with 1-6 glutamates resolved by LCMS [median (interquartile): 5.47 (3.58-7.69) nmol/mmol hemoglobin] was in agreement with total MTX by radio ligand assay. In 16,389 blood samples from 1426 ALL maintenance therapy patients, MTXpg3 21.0 (15.2-27.4)% was the predominant metabolite, and MTXpg1 (the maternal drug) constituted 38.6 (27.2-50.2)% of MTXpg1-6. All subsets correlated; the strongest associations were between metabolites with similar polyglutamate lengths. Correlations of MTXpg1 with MTXpg2 and MTXpg3,4,5,6 were r(s)=0.68 and r(s)=0.25-0.42, respectively. Intercorrelations of MTXpg3,4,5,6 were all r(s)0.51. MTXpg4 accounted for 29.8 (24.7-33.3)% of MTXpg3-6, yet explained 96% of the summed MTXpg3-6 variation. MTXpg1-4, MTXpg1-6, MTXpg2-6 and MTXpg3 were all associated with DNA-TG levels (pPeer reviewe

Heterogeneous distribution of plankton within the mixed layer and its implications for bloom formation in tropical seas

Intensive sampling at the coastal waters of the central Red Sea during a period of thermal stratification, prior to the main seasonal bloom during winter, showed that vertical patches of prokaryotes and microplankton developed and persisted for several days within the apparently density uniform upper layer. These vertical structures were most likely the result of in situ growth and mortality (e.g., grazing) rather than physical or behavioural aggregation. Simulating a mixing event by adding nutrient-rich deep water abruptly triggered dense phytoplankton blooms in the nutrient-poor environment of the upper layer. These findings suggest that vertical structures within the mixed layer provide critical seeding stocks that can rapidly exploit nutrient influx during mixing, leading to winter bloom formation

Identification of known and novel recurrent viral sequences in data from multiple patients and multiple cancers

Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified