Gene expression profiling reveals effects of Cimicifuga racemosa (L.) NUTT. (black cohosh) on the estrogen receptor positive human breast cancer cell line MCF-7

BACKGROUND: Extracts from the rhizome of Cimicifuga racemosa (black cohosh) are increasingly popular as herbal alternative to hormone replacement therapy (HRT) for the alleviation of postmenopausal disorders. However, the molecular mode of action and the active principles are presently not clear. Previously published data have been largely contradictory. We, therefore, investigated the effects of a lipophilic black cohosh rhizome extract and cycloartane-type triterpenoids on the estrogen receptor positive human breast cancer cell line MCF-7. RESULTS: Both extract and purified compounds clearly inhibited cellular proliferation. Gene expression profiling with the extract allowed us to identify 431 regulated genes with high significance. The extract induced expression pattern differed from those of 17beta-estradiol or the estrogen receptor antagonist tamoxifen. We observed a significant enrichment of genes in an anti-proliferative and apoptosis-sensitizing manner, as well as an increase of mRNAs coding for gene products involved in several stress response pathways. These functional groups were highly overrepresented among all regulated genes. Also several transcripts coding for oxidoreductases were induced, as for example the cytochrome P450 family members 1A1 and 1B1. In addition, some transcripts associated with antitumor but also tumor-promoting activity were regulated. Real-Time RT-PCR analysis of 13 selected genes was conducted after treatment with purified compounds - the cycloartane-type triterpene glycoside actein and triterpene aglycons - showing similar expression levels compared to the extract. CONCLUSION: No estrogenic but antiproliferative and proapoptotic gene expression was shown for black cohosh in MCF-7 cells at the transcriptional level. The effects may be results of the activation of different pathways. The cycloartane glycosides and - for the first time - their aglycons could be identified as an active principle in black cohosh

WISER Deliverable D3.3-2: The importance of invertebrate spatial and temporal variation for ecological status classification for European lakes

European lakes are affected by many human induced disturbances. In principle, ecological theories predict that the structure and functioning of benthic invertebrate assemblage (one of the Biological Quality Elements following the Water Framework Directive, WFD terminology) change in response to the level of disturbances, making this biological element suitable for assessing the status and management of lake ecosystems. In practice, to set up assessment systems based on invertebrates, we need to distiguish community changes that are related to human pressures from those that are inherent natural variability. This task is complicated by the fact that invertebrate communities inhabiting the littoral and the profundal zones of lakes are constrained by different factors and respond unevenly to distinct human disturbances. For example it is not clear yet how the invertebrates assemblages respond to watershed and shoreline alterations, nor the relative importance of spatial and temporal factors on assemblage dynamics and relative bioindicator values of taxa, the habitat constraints on species traits and other taxonomic and methodological limitations. The current lack of knowledge of basic features of invertebrate temporal and spatial variations is limiting the fulfillment of the EU-wide intercalibration of lake ecological quality assessment systems in Europe, and thus compromising the basis for setting the environmental objectives as required by the WFD. The aim of this deliverable is to provide a contribution towards the understanding of basic sources of spatial and temporal variation of lake invertebrate assemblages. The report is structured around selected case studies, manly involving the analysis of existing datasets collated within WISER. The case studies come from different European lake types in the Northern, Central, Alpine and Mediterranean regions. All chapters have an obvious applied objective and our aim is to provide to those dealing with WFD implementation at various levels useful information to consider when designing monitoring programs and / or invertebrate-based classification systems

Automatic and online pollen monitoring

BACKGROUND: Pollen are monitored in Europe by a network of about 400 pollen traps, all operated manually. To date, automated pollen monitoring has only been feasible in areas with limited variability in pollen species. There is a need for rapid reporting of airborne pollen as well as for alleviating the workload of manual operation. We report our experience with a fully automated, image recognition-based pollen monitoring system, BAA500. METHODS: The BAA500 sampled ambient air intermittently with a 3-stage virtual impactor at 60 m(3)/h in Munich, Germany. Pollen is deposited on a sticky surface that was regularly moved to a microscope equipped with a CCD camera. Images of the pollen were constructed and compared with a library of known samples. A Hirst-type pollen trap was operated simultaneously. RESULTS: Over 480,000 particles sampled with the BAA500 were both manually and automatically identified, of which about 46,000 were pollen. Of the automatically reported pollen, 93.3% were correctly recognized. However, compared with manual identification, 27.8% of the captured pollen were missing in the automatic report, with most reported as unknown pollen. Salix pollen grains were not identified satisfactorily. The daily pollen concentrations reported by a Hirst-type pollen trap and the BAA500 were highly correlated (r = 0.98). CONCLUSIONS: The BAA500 is a functional automated pollen counter. Its software can be upgraded, and so we expected its performance to improve upon training. Automated pollen counting has great potential for workload reduction and rapid online pollen reporting

Semiconductor nanostructure quantum ratchet for high efficiency solar cells

Conventional solar cell efficiencies are capped by the ~31% Shockley–Queisser limit because, even with an optimally chosen bandgap, some red photons will go unabsorbed and the excess energy of the blue photons is wasted as heat. Here we demonstrate a “quantum ratchet” device that avoids this limitation by inserting a pair of linked states that form a metastable photoelectron trap in the bandgap. It is designed both to reduce non-radiative recombination, and to break the Shockley–Queisser limit by introducing an additional “sequential two photon absorption” (STPA) excitation channel across the bandgap. We realise the quantum ratchet concept with a semiconductor nanostructure. It raises the electron lifetime in the metastable trap by ~104, and gives a STPA channel that increases the photocurrent by a factor of ~50%. This result illustrates a new paradigm for designing ultra-efficient photovoltaic devices

The role of turbulence in the hydraulic environment of benthic invertebrates

The role of turbulence in the dislodgment of benthic stream invertebrates from the riverbed was investigated experimentally in a laboratory flume. For the first time, technological advances allowed measuring the spatio-temporal patterns of turbulent flow around two free-moving invertebrates (Aeshna cyanea and Somatochlora flavomaculata). A specific methodology was developed for the analysis of turbulence around benthic invertebrates. The results confirmed two hypotheses: (i) on the contrary to sediment particles, invertebrates are not only sensitive to the peak values of the turbulent flow forcing but also to the temporal fluctuations in this flow forcing; and (ii) the dominant temporal fluctuations are not due to local turbulent structures of the size of the invertebrate, but to turbulent structures that scale with the flow depth and are inherited from upstream. In 15 of the 17 conducted tests, important turbulent events that scale with the flow depth accompanied by rapid temporal flow fluctuations occurred at the moment of dislodgement. The dominant forcing was consistently a threefold increase in shear stress, and was related to a sweep event in 12 of the 17 tests. Thereby, the increase in longitudinal velocity was typically about 40%, which led to a 100% increase in drag force in comparison with the time-averaged drag force. These results enable a new understanding of the detailed hydraulic conditions leading to passive drift of stream invertebrates. In addition, they open new perspectives to improve models predicting the distribution of benthic invertebrates based on hydrodynamics by accounting for turbulence

Neutrino oscillations in structured matter

A layered material structure in a monochromatic neutrino beam produces interference effects that could be used for the measurement of features of the neutrino mass matrix. The phenomenon would be most useful at high energies.Comment: 18 pp of which two figure

Hydraulically-actuated compliant revolute joint for medical robotic systems based on multimaterial additive manufacturing

IEEE International Conference on Robotics and Automation (ICRA), Montréal, Canada, janvier 2019 Research team : AV

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed

High-throughput Comparison, Functional Annotation, and Metabolic Modeling of Plant Genomes using the PlantSEED Resource

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes