Heat and moisture budgets from airborne measurements and high-resolution model simulations

High-resolution simulations with a mesoscale model are performed to estimate heat and moisture budgets of a well-mixed boundary layer. The model budgets are validated against energy budgets obtained from airborne measurements over heterogeneous terrain in Western Germany. Time rate of change, vertical divergence, and horizontal advection for an atmospheric column of air are estimated. Results show that the time trend of specific humidity exhibits some deficiencies, while the potential temperature trend is matched accurately. Furthermore, the simulated turbulent surface fluxes of sensible and latent heat are comparable to the measured fluxes, leading to similar values of the vertical divergence. The analysis of different horizontal model resolutions exhibits improved surface fluxes with increased resolution, a fact attributed to a reduced aggregation effect. Scale-interaction effects could be identified: while time trends and advection are strongly influenced by mesoscale forcing, the turbulent surface fluxes are mainly controlled by microscale processes

Protein-Binding Microarray Analysis of Tumor Suppressor AP2α Target Gene Specificity

Cheap and massively parallel methods to assess the DNA-binding specificity of transcription factors are actively sought, given their prominent regulatory role in cellular processes and diseases. Here we evaluated the use of protein-binding microarrays (PBM) to probe the association of the tumor suppressor AP2α with 6000 human genomic DNA regulatory sequences. We show that the PBM provides accurate relative binding affinities when compared to quantitative surface plasmon resonance assays. A PBM-based study of human healthy and breast tumor tissue extracts allowed the identification of previously unknown AP2α target genes and it revealed genes whose direct or indirect interactions with AP2α are affected in the diseased tissues. AP2α binding and regulation was confirmed experimentally in human carcinoma cells for novel target genes involved in tumor progression and resistance to chemotherapeutics, providing a molecular interpretation of AP2α role in cancer chemoresistance. Overall, we conclude that this approach provides quantitative and accurate assays of the specificity and activity of tumor suppressor and oncogenic proteins in clinical samples, interfacing genomic and proteomic assays

Nuclear factor I genomic binding associates with chromatin boundaries

BACKGROUND: The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequencing (ChIP-Seq), we performed a genome-wide mapping of NFI DNA binding sites in primary mouse embryonic fibroblasts. RESULTS: We found that in vivo and in vitro NFI DNA binding specificities are indistinguishable, as in vivo ChIP-Seq NFI binding sites matched predictions based on previously established position weight matrix models of its in vitro binding specificity. Combining ChIP-Seq with mRNA profiling data, we found that NFI preferentially associates with highly expressed genes that it up-regulates, while binding sites were under-represented at expressed but unregulated genes. Genomic binding also correlated with markers of transcribed genes such as histone modifications H3K4me3 and H3K36me3, even outside of annotated transcribed loci, implying NFI in the control of the deposition of these modifications. Positional correlation between + and - strand ChIP-Seq tags revealed that, in contrast to other transcription factors, NFI associates with a nucleosomal length of cleavage-resistant DNA, suggesting an interaction with positioned nucleosomes. In addition, NFI binding prominently occurred at boundaries displaying discontinuities in histone modifications specific of expressed and silent chromatin, such as loci submitted to parental allele-specific imprinted expression. CONCLUSIONS: Our data thus suggest that NFI nucleosomal interaction may contribute to the partitioning of distinct chromatin domains and to epigenetic gene expression regulation. NFI ChIP-Seq and input control DNA data were deposited at Gene Expression Omnibus (GEO) repository under accession number GSE15844. Gene expression microarray data for mouse embryonic fibroblasts are on GEO accession number GSE15871

Protein-binding microarrays: probing disease markers at the interface of proteomics and genomics.

DNA-binding proteins mediate a variety of crucial molecular functions, such as transcriptional regulation and chromosome maintenance, replication and repair, which in turn control cell division and differentiation. The roles of these proteins in disease are currently being investigated using microarray-based approaches. However, these assays can be difficult to adapt to routine diagnosis of complex diseases such as cancer. Here, we review promising alternative approaches involving protein-binding microarrays (PBMs) that probe the interaction of proteins from crude cell or tissue extracts with large collections of synthetic or natural DNA sequences. Recent studies have demonstrated the use of these novel PBM approaches to provide rapid and unbiased characterization of DNA-binding proteins as molecular markers of disease, for example cancer progression or infectious diseases

Verfahrensoptimierung einer Betriebswasserrecyclinganlage fuer die Lebensmittelindustrie am Beispiel Brauereiabwasser Abschlussbericht

In many fields of food industry there are high quantities of highly polluted waste waters. Generally, the waste waters come in batches, with differing concentrations of organic and anorganic substances which makes a satisfactory cleaning hardly possible. With the treatment methods which have been in use until now, it was impossible to treat the waste water to a degree which would have made it suitable for re-use within the system. To change this situation, the AquaTech Company has developed a new method. The method is characterized by the combination of a two-phase, anaerobic waste water treatment with several filtration phases. Using the AquaTech method helps to reduce the organic load thus helping to reduce the waste water tariff significantly. And, at the same time, a part of the waste water is cleaned to a degree which makes it possible to re-use it within the operational system. Another advantage is the saving of energy because the biogas developed within the process can be used for thermal and electrical purposes.In vielen Bereichen der Lebensmittelindustrie fallen erhebliche Mengen an hoch belasteten Abwaessern an. Die Abwaesser fallen in der Regel chargenweise mit stark schwankenden Konzentrationen an organischen und anorganischen Inhaltsstoffen an, so dass eine zufriedenstellende Reinigung nur schwer realisierbar ist. Insbesondere war eine weitergehende Aufbereitung des Abwassers zur innerbetrieblichen Wiederverwendung bei den bisher eingesetzten Behandlungsverfahren nicht moeglich. Um diesem Missstand entgegenzuwirken, hat die Firma AquaTec ein neues Verfahren entwickelt. Es zeichnet sich durch eine Kombination einer zweistufigen, anaeroben Abwasserbehandlung mit mehreren Filtrationsstufen aus. Durch das AquaTec-Verfahren wird zum einen die Schutzfracht (Organik) reduziert, wodurch die Abwassergebuehren wesentlich reduziert werden koennen. Zum anderen wird ein Teil des Abwassers so weit gereinigt, dass eine Wiederverwendung im Betrieb moeglich ist. Ein weiterer Vorteil ist die Einsparung von Energie, da das im Prozess anfallende Biogas thermisch und elektrisch verwertet werden kann. (orig.)SIGLEAvailable from TIB Hannover: F02B491 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekDeutsche Bundesstiftung Umwelt, Osnabrueck (Germany)DEGerman