Croatian mayflies (Insecta,Ephemeroptera): species diversity and distribution patterns

Knowledge of the mayfly biodiversity in the Balkan Peninsula is still far from complete. Compared to the neighbouring countries, the mayfly fauna in Croatia is very poorly known. Situated at the crossroads of central and Mediterranean Europe and the Balkan Peninsula, Croatia is divided into two ecoregions: Dinaric western Balkan and Pannonian lowland. Mayflies were sampled between 2003 and 2013 at 171 sites, and a total of 66 species was recorded. Combined with the literature data, the Croatian mayfly fauna reached a total of 79 taxa. Of these, 29 species were recorded for the first time in Croatia while 15 species were not previously recorded in Dinaric western Balkan ecoregion. Based on the mayfly assemblage, sampling sites were first structured by ecoregion and then by habitat type. In comparison with the surrounding countries, the Croatian mayfly fauna is the most similar to the Hungarian and Bosnian fauna. Some morphologically interesting taxa such as Baetis cf. nubecularis Eaton, 1898 and Rhithrogena from the diaphana group were recorded. Ephemera cf. parnassiana Demoulin, 1958, the species previously recorded only from Greece, was also recorded.     

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

BackgroundWhile large-scale cancer genomic projects are comprehensively characterizing the mutational spectrum of various cancers, so far little attention has been devoted to either define the antigenicity of these mutations or to characterize the immune responses they elicit. Here we present a strategy to characterize the immunophenotypes and the antigen-ome of human colorectal cancer.ResultsWe apply our strategy to a large colorectal cancer cohort (n = 598) and show that subpopulations of tumor-infiltrating lymphocytes are associated with distinct molecular phenotypes. The characterization of the antigenome shows that a large number of cancer-germline antigens are expressed in all patients. In contrast, neo-antigens are rarely shared between patients, indicating that cancer vaccination requires individualized strategy. Analysis of the genetic basis of the tumors reveals distinct tumor escape mechanisms for the patient subgroups. Hypermutated tumors are depleted of immunosuppressive cells and show upregulation of immunoinhibitory molecules. Non-hypermutated tumors are enriched with immunosuppressive cells, and the expression of immunoinhibitors and MHC molecules is downregulated. Reconstruction of the interaction network of tumor-infiltrating lymphocytes and immunomodulatory molecules followed by a validation with 11 independent cohorts (n = 1,945) identifies BCMA as a novel druggable target. Finally, linear regression modeling identifies major determinants of tumor immunogenicity, which include well-characterized modulators as well as a novel candidate, CCR8, which is then tested in an orthologous immunodeficient mouse model.ConclusionsThe immunophenotypes of the tumors and the cancer antigenome remain widely unexplored, and our findings represent a step toward the development of personalized cancer immunotherapies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0620-6) contains supplementary material, which is available to authorized users.     

A method for detecting the effect of magnetic field on activity changes of neuronal populations of Morimus funereus (Coleoptera, Cerambycidae)

Modification of a new method for detecting changes in the activities of neuronal population and the nearest neuron is described. Preliminary measurements of the influence of a static magnetic field (2 mT) on neuronal population activity on eight individuals of an endangered insect species Morimus funereus are included. Five minutes exposure produced both excitatory (5/8) and inhibitory (3/8) effect on the activity of neuronal population of M. funereus antennal lobe. However, when the reversibility of induced effects was quantitatively analyzed, our results showed that they were prevailingly irreversible: (7/8) for the population, (6/8) for the nearest neuron.     

Genetic Architecture of Ear Fasciation in Maize (Zea mays) under QTL Scrutiny

Maize ear fasciation

Knowledge of the genes affecting maize ear inflorescence may lead to better grain yield modeling. Maize ear fasciation, defined as abnormal flattened ears with high kernel row number, is a quantitative trait widely present in Portuguese maize landraces.

Material and Methods

Using a segregating population derived from an ear fasciation contrasting cross (consisting of 149 F_2:3 families) we established a two location field trial using a complete randomized block design. Correlations and heritabilities for several ear fasciation-related traits and yield were determined. Quantitative Trait Loci (QTL) involved in the inheritance of those traits were identified and candidate genes for these QTL proposed.

Results and Discussion

Ear fasciation broad-sense heritability was 0.73. Highly significant correlations were found between ear fasciation and some ear and cob diameters and row number traits. For the 23 yield and ear fasciation-related traits, 65 QTL were identified, out of which 11 were detected in both environments, while for the three principal components, five to six QTL were detected per environment. Detected QTL were distributed across 17 genomic regions and explained individually, 8.7% to 22.4% of the individual traits or principal components phenotypic variance. Several candidate genes for these QTL regions were proposed, such as bearded-ear1, branched silkless1, compact plant1, ramosa2, ramosa3, tasselseed4 and terminal ear1. However, many QTL mapped to regions without known candidate genes, indicating potential chromosomal regions not yet targeted for maize ear traits selection.

Conclusions

Portuguese maize germplasm represents a valuable source of genes or allelic variants for yield improvement and elucidation of the genetic basis of ear fasciation traits. Future studies should focus on fine mapping of the identified genomic regions with the aim of map-based cloning.     

TAMEE: data management and analysis for tissue microarrays

Background  

With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories.     

Endogenous Gibberellin Profile During Christmas Rose (Helleborus niger L.) Flower and Fruit Development

Gibberellins (GAs) were identified and quantified during flower and fruit development in the Christmas rose (Helleborus niger L.), a native of southeastern Europe with a long international horticultural tradition. Physiologically, the plant differs from popular model species in two major respects: (1) following anthesis, the initially white or rose perianth (formed in this species by the sepals) turns green and persists until fruit ripening, and (2) the seed is shed with an immature embryo, a miniature endosperm, and a prominent perisperm as the main storage tissue. GA₁ and GA₄ were identified by full-scan mass spectra as the major bioactive GAs in sepals and fruit. LC-MS/MS system in accord with previously verified protocols also afforded analytical data on 12 precursors and metabolites of GAs. In the fruit, GA₄ peaked during rapid pericarp growth and embryo development and GA₁ peaked during the subsequent period of rapid nutrient accumulation in the seeds and continued pericarp enlargement. In the sepals, the flux through the GA biosynthetic pathway was highest prior to the light green stage when the photosynthetic system was induced. Unfertilized, depistillated, and deseeded flowers became less green than the seed-bearing controls; chlorophyll accumulation could be restored by applying GA₁, GA₄, and, less efficiently, GA₃ to the deseeded fruit. The sepals of unfertilized and depistillated flowers indeed contained very low levels of GA₄ and gradually decreasing levels of GA₁. However, the concentrations of their precursors and metabolites were less affected. These data suggest that a signal(s) from the fruit stimulates GA biosynthesis in the sepals resulting in greening. The fruit-derived GAs appear to be mainly involved in pericarp growth and seed development.