3D Ultrastructure of the Cochlear Outer Hair Cell Lateral Wall Revealed By Electron Tomography.

Outer Hair Cells (OHCs) in the mammalian cochlea display a unique type of voltage-induced mechanical movement termed electromotility, which amplifies auditory signals and contributes to the sensitivity and frequency selectivity of mammalian hearing. Electromotility occurs in the OHC lateral wall, but it is not fully understood how the supramolecular architecture of the lateral wall enables this unique form of cellular motility. Employing electron tomography of high-pressure frozen and freeze-substituted OHCs, we visualized the 3D structure and organization of the membrane and cytoskeletal components of the OHC lateral wall. The subsurface cisterna (SSC) is a highly prominent feature, and we report that the SSC membranes and lumen possess hexagonally ordered arrays of particles. We also find the SSC is tightly connected to adjacent actin filaments by short filamentous protein connections. Pillar proteins that join the plasma membrane to the cytoskeleton appear as variable structures considerably thinner than actin filaments and significantly more flexible than actin-SSC links. The structurally rich organization and rigidity of the SSC coupled with apparently weaker mechanical connections between the plasma membrane (PM) and cytoskeleton reveal that the membrane-cytoskeletal architecture of the OHC lateral wall is more complex than previously appreciated. These observations are important for our understanding of OHC mechanics and need to be considered in computational models of OHC electromotility that incorporate subcellular features

BikeNet: Preventing theft, building community

This report discusses the Save the Bike Project and the BikeNet App, and the ways it helps prevent and recover stolen bikes.Ope

Paleoseismological data from a new trench across the El Camp Fault(Catalan Coastal Ranges, NE Iberian Peninsula)

The El Camp Fault (Catalan Coastal Ranges, NE Iberian Peninsula) is a slow slipping normal fault whose seismic potential has only recently been recognised. New geomorphic and trench investigations were carried out during a training course across the El Camp Fault at the La Porquerola alluvial fan site. A new trench (trench 8) was dug close to a trench made previously at this site (trench 4). With the aid of two long topographic profiles across the fault scarp we obtained a vertical slip rate ranging between 0.05 and 0.08 mm/yr. At the trench site, two main faults, which can be correlated between trenches 8 and 4, make up the fault zone. Using trench analysis three paleoseismic events were identified, two between 34.000 and 125.000 years BP (events 3 and 2) and another event younger than 13 500 years BP (event 1), which can be correlated, respectively, with events X (50.000- 125.000 years BP), Y (35.000-50.000 years BP) and Z (3000-25.000 years BP). The last seismic event at the La Porquerola alluvial fan site is described for the first time, but with some uncertainties

Protein P7 of the Cystovirus φ6 Is Located at the Three-Fold Axis of the Unexpanded Procapsid

The objective of this study was to determine the location of protein P7, the RNA packaging factor, in the procapsid of the φ6 cystovirus. A comparison of cryo-electron microscopy high-resolution single particle reconstructions of the φ6 complete unexpanded procapsid, the protein P2-minus procapsid (P2 is the RNA directed RNA-polymerase), and the P7-minus procapsid, show that prior to RNA packaging the P7 protein is located near the three-fold axis of symmetry. Difference maps highlight the precise position of P7 and demonstrate that in P7-minus particles the P2 proteins are less localized with reduced densities at the three-fold axes. We propose that P7 performs the mechanical function of stabilizing P2 on the inner protein P1 shell which ensures that entering viral single-stranded RNA is replicated

Zn2+ ion surface enrichment in doped iron oxide nanoparticles leads to charge carrier density enhancement

Here, we report the development of monodisperse Zn-doped iron oxide nanoparticles (NPs) with different amounts of Zn (ZnxFe3-xO4, 0 < x < 0.43) by thermal decomposition of a mixture of zinc and iron oleates. The as-synthesized NPs show a considerable fraction of wüstite (FeO) which is transformed to spinel upon 2 h oxidation of the NP reaction solutions. At any Zn doping amounts, we observed the enrichment of the NP surface with Zn2+ ions, which is enhanced at higher Zn loadings. Such a distribution of Zn2+ ions is attributed to the different thermal decomposition profiles of Zn and Fe oleates, with Fe oleate decomposing at much lower temperature than that of Zn oleate. The decomposition of Zn oleate is, in turn, catalyzed by a forming iron oxide phase. The magnetic properties were found to be strongly dependent on the Zn doping amounts, showing the saturation magnetization to decrease by 9 and 20% for x = 0.05 and 0.1, respectively. On the other hand, X-ray photoelectron spectroscopy near the Fermi level demonstrates that the Zn0.05Fe2.95O4 sample displays a more metallic character (a higher charge carrier density) than undoped iron oxide NPs, supporting its use as a spintronic material

Metal oxide–zeolite composites in transformation of methanol to hydrocarbons : do iron oxide and nickel oxide matter?

The methanol-to-hydrocarbon (MTH) reaction has received considerable attention as utilizing renewable sources of both value-added chemicals and fuels becomes a number one priority for society. Here, for the first time we report the development of hierarchical zeolites (ZSM-5) containing both iron oxide and nickel oxide nanoparticles. By modifying the iron oxide (magnetite, Fe3O4) amounts, we are able to control the catalyst activity and the product distribution in the MTH process. At the medium Fe3O4 loading, the major fraction is composed of C9–C11 hydrocarbons (gasoline fraction). At the higher Fe3O4 loading, C1–C4 hydrocarbons prevail in the reaction mixture, while at the lowest magnetite loading the major component is the C5–C8 hydrocarbons. Addition of Ni species to Fe3O4–ZSM-5 leads to the formation of mixed Ni oxides (NiO/Ni2O3) positioned either on top of or next to Fe3O4 nanoparticles. This modification allowed us to significantly improve the catalyst stability due to diminishing coke formation and disordering of the coke formed. The incorporation of Ni oxide species also leads to a higher catalyst activity (up to 9.3 g(methanol)/(g(ZSM-5) × h)) and an improved selectivity (11.3% of the C5–C8 hydrocarbons and 23.6% of the C9–C11 hydrocarbons), making these zeolites highly promising for industrial applications

Three-Dimensional Structure of the Enveloped Bacteriophage Φ12: An Incomplete T = 13 Lattice Is Superposed on an Enclosed T = 1 Shell

BACKGROUND:Bacteriophage phi12 is a member of the Cystoviridae, a unique group of lipid containing membrane enveloped bacteriophages that infect the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola. The genomes of the virus species contain three double-stranded (dsRNA) segments, and the virus capsid itself is organized in multiple protein shells. The segmented dsRNA genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the Cystoviridae similar to the Reoviridae. METHODOLOGY/PRINCIPAL FINDINGS:We present structural studies of cystovirus phi12 obtained using cryo-electron microscopy and image processing techniques. We have collected images of isolated phi12 virions and generated reconstructions of both the entire particles and the polymerase complex (PC). We find that in the nucleocapsid (NC), the phi12 P8 protein is organized on an incomplete T = 13 icosahedral lattice where the symmetry axes of the T = 13 layer and the enclosed T = 1 layer of the PC superpose. This is the same general protein-component organization found in phi6 NC's but the detailed structure of the entire phi12 P8 layer is distinct from that found in the best classified cystovirus species phi6. In the reconstruction of the NC, the P8 layer includes protein density surrounding the hexamers of P4 that sit at the 5-fold vertices of the icosahedral lattice. We believe these novel features correspond to dimers of protein P7. CONCLUSIONS/SIGNIFICANCE:In conclusion, we have determined that the phi12 NC surface is composed of an incomplete T = 13 P8 layer forming a net-like configuration. The significance of this finding in regard to cystovirus assembly is that vacancies in the lattice could have the potential to accommodate additional viral proteins that are required for RNA packaging and synthesis

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin