Quantitative and Dynamic Catalogs of Proteins Released during Apoptotic and Necroptotic Cell Death

The inflammatory functions of the cytokine tumor necrosis factor (TNF) rely on its ability to induce cytokine production and to induce cell death. Caspase-dependent and caspase-independent pathways-apoptosis and necroptosis, respectively-regulate immunogenicity by the release of distinct sets of cellular proteins. To obtain an unbiased, systems-level understanding of this important process, we here applied mass spectrometry-based proteomics to dissect protein release during apoptosis and necroptosis. We report hundreds of proteins released from human myeloid cells in time course experiments. Both cell death types induce receptor shedding, but only apoptotic cells released nucleosome components. Conversely, necroptotic cells release lysosomal components by activating lysosomal exocytosis at early stages of necroptosis-induced membrane permeabilization and show reduced release of conventionally secreted cytokines

Molecular Evolution of a MicroRNA Cluster

Many of the known microRNAs are encoded in polycistronic transcripts. Here, we reconstruct the evolutionary history of the mir17 microRNA clusters which consist of miR-17, miR-18, miR-19a, miR-19b, miR-20, miR-25, miR-92, miR-93, miR-106a, and miR-106b. The history of this cluster is governed by an initial phase of local (tandem) duplications, a series of duplications of entire clusters and subsequent loss of individual microRNAs from the resulting paralogous clusters. The complex history of the mir17 microRNA family appears to be closely linked to the early evolution of the vertebrate lineage

Comparative promoter region analysis powered by CORG

BACKGROUND: Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely determines gene expression. In vertebrates, transcription start sites and surrounding regulatory elements are often poorly defined. To support promoter analysis, we present CORG , a framework for studying upstream regions including untranslated exons (5' UTR). DESCRIPTION: The automated annotation of promoter regions integrates information of two kinds. First, statistically significant cross-species conservation within upstream regions of orthologous genes is detected. Pairwise as well as multiple sequence comparisons are computed. Second, binding site descriptions (position-weight matrices) are employed to predict conserved regulatory elements with a novel approach. Assembled EST sequences and verified transcription start sites are incorporated to distinguish exonic from other sequences. As of now, we have included 5 species in our analysis pipeline (man, mouse, rat, fugu and zebrafish). We characterized promoter regions of 16,127 groups of orthologous genes. All data are presented in an intuitive way via our web site. Users are free to export data for single genes or access larger data sets via our DAS server . The benefits of our framework are exemplarily shown in the context of phylogenetic profiling of transcription factor binding sites and detection of microRNAs close to transcription start sites of our gene set. CONCLUSION: The CORG platform is a versatile tool to support analyses of gene regulation in vertebrate promoter regions. Applications for CORG cover a broad range from studying evolution of DNA binding sites and promoter constitution to the discovery of new regulatory sequence elements (e.g. microRNAs and binding sites)

The Fire and Smoke Model Evaluation Experiment - A plan for integrated, large fire-atmosphere field campaigns

The Fire and Smoke Model Evaluation Experiment (FASMEE) is designed to collect integrated observations from large wildland fires and provide evaluation datasets for new models and operational systems. Wildland fire, smoke dispersion, and atmospheric chemistry models have become more sophisticated, and next-generation operational models will require evaluation datasets that are coordinated and comprehensive for their evaluation and advancement. Integrated measurements are required, including ground-based observations of fuels and fire behavior, estimates of fire-emitted heat and emissions fluxes, and observations of near-source micrometeorology, plume properties, smoke dispersion, and atmospheric chemistry. To address these requirements the FASMEE campaign design includes a study plan to guide the suite of required measurements in forested sites representative of many prescribed burning programs in the southeastern United States and increasingly common high-intensity fires in the western United States. Here we provide an overview of the proposed experiment and recommendations for key measurements. The FASMEE study provides a template for additional large-scale experimental campaigns to advance fire science and operational fire and smoke models

Observation of the superconducting proximity effect in Nb/InAs and NbNx/InAs by Raman scattering

URL:http://link.aps.org/doi/10.1103/PhysRevB.66.134530 DOI:10.1103/PhysRevB.66.134530High-quality thin Nb and NbN films (60-100 Å) are grown on (100) n+-InAs (n=1019cm-3) substrates by dc-magnetron sputter deposition. Studies of the electronic properties of interfaces between the superconductor and the semiconductor are done by Raman scattering measurements. The superconducting proximity effect at superconductor-semiconductor interfaces is observed through its impact on inelastic light scattering intensities originating from the near-interface region of InAs. The InAs longitudinal optical phonon LO mode (237cm-1) and the plasmon-phonon coupled modes L- (221cm-1) and L+ (1100 to 1350cm-1), for n+=1×1019-2×1019cm-3 are measured. The intensity ratio of the LO mode (associated with the near-surface charge accumulation region, in InAs) to that of the L- mode (associated with bulk InAs), is observed to increase by up to 40% below the superconducting transition temperature. This temperature-dependent change in light scattering properties is only observed with high quality superconducting films and when the superconductor and the semiconductor are in good electrical contact. A few possible mechanisms of the observed effect are proposed.We gratefully acknowledge support from the United States Department of Energy through Materials Research Laboratory~Grant No. DEFG02-96ER45439! ~I.V.R., A.C.A., L.H.G., T.A.T., J.F.D., P.W.B., J.F.K.!, and from the United States Department of Energy through Midwest Superconductivity Consortium ~MISCON! ~Grant No. DE FG02-90ER45427! and the NSF ~Grant No. DMR 96-23827! ~S.W.H., P.F.M.!. SEM, XRD, XPS, and RBS materials characterizations were performed at the Center for Microanalysis of Materials and Microfabrication Center at Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana- Champaign ~Grant No. DE FG02-96ER45439!. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin company, for the United States Department of Energy under Contract No. DE-AC04-94AL85000

The expansion of the metazoan microRNA repertoire

BACKGROUND: MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript. RESULTS: We identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and deuterostomes and might be related to the advent of bilaterians. A second large wave of innovations maps to the branch leading to the vertebrates. The third significant outburst of miRNA innovation coincides with placental (eutherian) mammals. In addition, we observe the expected expansion of the microRNA inventory due to genome duplications in early vertebrates and in an ancestral teleost. The non-local duplications in the vertebrate ancestor are predated by local (tandem) duplications leading to the formation of about a dozen ancient microRNA clusters. CONCLUSION: Our results suggest that microRNA innovation is an ongoing process. Major expansions of the metazoan miRNA repertoire coincide with the advent of bilaterians, vertebrates, and (placental) mammals

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products

Analgesia and functional outcome after total knee arthroplasty: periarticular infiltration vs continuous femoral nerve block

BACKGROUND: Capacity to ambulate represents an important milestone in the recovery process after total knee arthroplasty (TKA). The purpose of this study was to determine the analgesic effect of two analgesic techniques and their impact on functional walking capacity as a measure of surgical recovery. METHODS: Forty ASA II-III subjects undergoing TKA were enrolled in a randomized, double-blind, single-centre study receiving 48 h postoperative analgesia with either periarticular infiltration of local anaesthetic (Group I) or continuous femoral nerve block (Group F). Breakthrough pain relief was achieved with patient-controlled analgesia (PCA) morphine. The main outcome was postoperative morphine consumption. Early (postoperative days 1-3) and late (6 weeks) functional walking capacity (2 and 6 min walk tests, 2MWT and 6MWT, respectively), degree of physical activity (CHAMPS), health-related quality of life (SF-12), and clinical indicators of knee function (WOMAC, Knee Society evaluation, and range of motion) were measured. RESULTS: Patients in Group F used the PCA less (P=0.02) to achieve adequate analgesia. Postoperative 2MWT was similar in both groups (P=0.27). Six weeks after surgery, recovery of 6MWT, physical activity, and knee function were significantly improved in Group F (P<0.05). Preoperative walking capacity, physical activity and early total walking time were the independent predictors of early recovery. Distance and time spent walking were the predictors of functional walking exercise capacity at 6 weeks after surgery. CONCLUSIONS: Femoral block is associated with lower opioid consumption and a better recovery at 6 weeks than periarticular infiltration. Early postoperative activity measures (2MWT and walking time) were proved to be possible indicators of knee function recovery at 6 weeks after surgery

Non-coding RNA annotation of the genome of Trichoplax adhaerens

A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs—in particular rRNAs, tRNAs and some snRNAs—we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome