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  • 1
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    Ground-Motion Prediction Equations for Subduction Interface Earthquakes in Japan Using Site Class and Simple Geometric Attenuation Functions (2016)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2016-07-26
    Description: We presented a set of ground-motion prediction equations (GMPEs) for the horizontal components of strong-motion records from subduction interface events in Japan. We assembled and processed in a consistent manner a large set of strong-motion records from reliably identified subduction interface events up to the end of 2012. The GMPEs were based on a set of simple geometric attenuation functions, and site class was based on site period as the site parameter. We adopted a bilinear magnitude-scaling function hinged at M w  7.1 and found that the magnitude-scaling rate for large events is much smaller than that for smaller events. To reliably determine the magnitude-scaling rate for events with M w ≥7.1, we used a set of strong-motion records obtained since 1968 to increase the number of records from large events. A small number of strong-motion records are from recording stations with inferred site classes using the response spectral ratio of the horizontal-to-vertical components or a geological description of the surface soil layers. The effect of site information quality for subduction interface events was examined using a goodness-of-fit parameter from a dataset with or without the sites having an inferred site class. The site information quality made a significant difference at all spectral periods, because the model fit improved significantly when the sites with inferred classes were excluded. We modeled the effect of volcanic zones using an anelastic attenuation coefficient applied to the horizontal portion of the seismic-wave travel distance within a set of assumed volcanic zones. The within-event residuals were approximately separated into within-site and between-site components, and the corresponding standard deviations were calculated using a random effects model. The between-site standard deviations vary significantly among site classes and with spectral periods. Online Material: Figures showing distributions of between-event and within-event residuals.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 2
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    Integrin activation and internalization on soft ECM as a mechanism of induction of stem cell differentiation by ECM elasticity [Cell Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-06-08
    Description: The mechanism by which ECM elasticity induces lineage specification of stem cells has not been clearly understood. Integrins are well-documented mechanosensors that are positioned at the beginning of the sensing pathway. By using an antibody specifically recognizing the active conformation of β1 integrin, we observed that β1 integrin activation in bone marrow mesenchymal stem cells (BMMSCs) was induced by soft substrate to a significantly greater degree than by stiff substrate. In contrast, however, the level of cell surface integrin on soft substrate was significantly lower than that on stiff substrate. Soft substrate markedly enhanced the internalization of integrin, and this internalization was mediated mainly through caveolae/raft-dependent endocytosis. The inhibition of integrin internalization blocked the neural lineage specification of BMMSCs on soft substrate. Furthermore, soft substrate also repressed the bone morphogenetic protein (BMP)/Smad pathway at least partially through integrin-regulated BMP receptor endocytosis. A theoretical analysis based on atomic force microscopy (AFM) data indicated that integrin–ligand complexes are more easily ruptured on soft substrate; this outcome may contribute to the enhancement of integrin internalization on soft substrate. Taken together, our results suggest that ECM elasticity affects integrin activity and trafficking to modulate integrin BMP receptor internalization, thus contributing to stem cell lineage specification.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    ChIP-seq reveals the global regulator AlgR mediating cyclic di-GMP synthesis in Pseudomonas aeruginosa (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-30
    Description: AlgR is a key transcriptional regulator required for the expression of multiple virulence factors, including type IV pili and alginate in Pseudomonas aeruginosa . However, the regulon and molecular regulatory mechanism of AlgR have yet to be fully elucidated. Here, among 157 loci that were identified by a ChIP-seq assay, we characterized a gene, mucR , which encodes an enzyme that synthesizes the intracellular second messenger cyclic diguanylate (c-di-GMP). A algR strain produced lesser biofilm than did the wild-type strain, which is consistent with a phenotype controlled by c-di-GMP. AlgR positively regulates mucR via direct binding to its promoter. A algR mucR double mutant produced lesser biofilm than did the single algR mutant, demonstrating that c-di-GMP is a positive regulator of biofilm formation. AlgR controls the levels of c-di-GMP synthesis via direct regulation of mucR . In addition, the cognate sensor of AlgR, FimS/AlgZ, also plays an important role in P. aeruginosa virulence. Taken together, this study provides new insights into the AlgR regulon and reveals the involvement of c-di-GMP in the mechanism underlying AlgR regulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    A Versatile and Highly Efficient Toolkit Including 102 Nuclear Markers for Vertebrate Phylogenomics, Tested by Resolving the Higher Level Relationships of the Caudata (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-16
    Description: Resolving difficult nodes for any part of the vertebrate tree of life often requires analyzing a large number of loci. Developing molecular markers that are workable for the groups of interest is often a bottleneck in phylogenetic research. Here, on the basis of a nested polymerase chain reaction (PCR) strategy, we present a universal toolkit including 102 nuclear protein-coding locus (NPCL) markers for vertebrate phylogenomics. The 102 NPCL markers have a broad range of evolutionary rates, which makes them useful for a wide range of time depths. The new NPCL toolkit has three important advantages compared with all previously developed NPCL sets: 1) the kit is universally applicable across vertebrates, with a PCR success rate of 94.6% in 16 widely divergent tested vertebrate species; 2) more than 90% of PCR reactions produce strong and single bands of the expected sizes that can be directly sequenced; and 3) all cleanup PCR reactions can be sequenced with only two specific universal primers. To test its actual phylogenetic utility, 30 NPCLs from this toolkit were used to address the higher level relationships of living salamanders. Of the 639 target PCR reactions performed on 19 salamanders and several outgroup species, 632 (98.9%) were successful, and 602 (94.1%) were directly sequenced. Concatenation and species-tree analyses on this 30-locus data set produced a fully resolved phylogeny and showed that Cryptobranchoidea (Cryptobranchidae + Hynobiidae) branches first within the salamander tree, followed by Sirenidae. Our experimental tests and our demonstration for a particular case show that our NPCL toolkit is a highly reliable, fast, and cost-effective approach for vertebrate phylogenomic studies and thus has the potential to accelerate the completion of many parts of the vertebrate tree of life.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Direct observation of the spatial and temporal dynamics of polaron diffusion in SrTiO_{3} (2013)
    American Physical Society (APS)
    Details
    Publication Date: 2013-06-06
    Description: Author(s): T. Kohmoto, D. Ikeda, X. Liang, and T. Moriyasu The generation, relaxation, and diffusion dynamics of optically induced lattice distortion in the relaxed excited state of SrTiO 3 are studied by using polarization spectroscopy with the pump-probe technique. The relaxed excited state is generated with a rise time on the order of 100 ps. Three kinds ... [Phys. Rev. B 87, 214301] Published Wed Jun 05, 2013
    Keywords: Dynamics, dynamical systems, lattice effects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: Transcription factors bind to the genome by forming specific contacts with the primary DNA sequence; however, RNA-binding proteins (RBPs) have greater scope to achieve binding specificity through the RNA secondary structure. It has been revealed that single nucleotide variants (SNVs) that alter RNA structure, also known as RiboSNitches, exhibit 3-fold greater local structure changes than replicates of the same DNA sequence, demonstrated by the fact that depletion of RiboSNitches could result in the alteration of specific RNA shapes at thousands of sites, including 3' UTRs, binding sites of microRNAs and RBPs. However, the network between SNVs and post-transcriptional regulation remains unclear. Here, we developed RBP-Var, a database freely available at http://www.rbp-var.biols.ac.cn/ , which provides annotation of functional variants involved in post-transcriptional interaction and regulation. RBP-Var provides an easy-to-use web interface that allows users to rapidly find whether SNVs of interest can transform the secondary structure of RNA and identify RBPs whose binding may be subsequently disrupted. RBP-Var integrates DNA and RNA biology to understand how various genetic variants and post-transcriptional mechanisms cooperate to orchestrate gene expression. In summary, RBP-Var is useful in selecting candidate SNVs for further functional studies and exploring causal SNVs underlying human diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Expanding CRISPR/Cas9 Genome Editing Capacity in Zebrafish Using SaCas9 (2016)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2016-08-10
    Description: The type II CRISPR/Cas9 system has been used widely for genome editing in zebrafish. However, the requirement for the 5'-NGG-3' protospacer-adjacent motif (PAM) of Cas9 from Streptococcus pyogenes (SpCas9) limits its targeting sequences. Here, we report that a Cas9 ortholog from Staphylococcus aureus (SaCas9), and its KKH variant, successfully induced targeted mutagenesis with high frequency in zebrafish. Confirming previous findings, the SpCas9 variant, VQR, can also induce targeted mutations in zebrafish. Bioinformatics analysis of these new Cas targets suggests that the number of available target sites in the zebrafish genome can be greatly expanded. Collectively, the expanded target repertoire of Cas9 in zebrafish should further facilitate the utility of this organism for genetic studies of vertebrate biology.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 8
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    Tree growth acceleration and expansion of alpine forests: The synergistic effect of atmospheric and edaphic change (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-09-01
    Description: Many forest ecosystems have experienced recent declines in productivity; however, in some alpine regions, tree growth and forest expansion are increasing at marked rates. Dendrochronological analyses at the upper limit of alpine forests in the Tibetan Plateau show a steady increase in tree growth since the early 1900s, which intensified during the 1930s and 1960s, and have reached unprecedented levels since 1760. This recent growth acceleration was observed in small/young and large/old trees and coincided with the establishment of trees outside the forest range, reflecting a connection between the physiological performance of dominant species and shifts in forest distribution. Measurements of stable isotopes (carbon, oxygen, and nitrogen) in tree rings indicate that tree growth has been stimulated by the synergistic effect of rising atmospheric CO 2 and a warming-induced increase in water and nutrient availability from thawing permafrost. These findings illustrate the importance of considering soil-plant-atmosphere interactions to understand current and anticipate future changes in productivity and distribution of forest ecosystems.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    A Summary of the BARREL Campaigns: Technique for studying electron precipitation (2015)
    Wiley
    Details
    Publication Date: 2015-05-17
    Description: The Balloon Array for Radiation belt Relativistic Electron Losses (BARREL) studies the loss of energetic electrons from Earth's radiation belts. BARREL's array of slowly drifting balloon payloads was designed to capitalize on magnetic conjunctions with NASA's Van Allen Probes. Two campaigns were conducted from Antarctica in 2013 and 2014. During the first campaign in January and February of 2013, there were three moderate geomagnetic storms with Sym-H min 〈 −40 nT. Similarly, two minor geomagnetic storms occurred during the second campaign, starting in December of 2013 and continuing on into February of 2014. Throughout the two campaigns, BARREL observed electron precipitation over a wide range of energies and exhibiting temporal structure from 100's of milliseconds to hours. Relativistic electron precipitation was observed in the dusk to midnight sector, and microburst precipitation was primarily observed near dawn. In this paper we review the two BARREL science campaigns and discuss the data products and analysis techniques as applied to relativistic electron precipitation observed on 19 January 2013.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
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    Centennial-scale climate variability during the past 2000 years on the central Tibetan Plateau (2015)
    Sage
    In: Holocene
    Details
    Publication Date: 2015-05-20
    Description: It is currently suggested that climate change on the northeastern Tibetan Plateau (TP) was influenced alternately by the monsoon and the Westerlies. However, the mechanisms driving Holocene climate change on the TP remain unclear, since the extent of the influence of individual atmospheric circulation systems has not yet been clearly defined because of the shortage of high-quality paleoclimatic records. This is especially true in the central TP, where only a few ice core and paleolimnological records are available. Here, we present a decadal-resolution temperature record from Dagze Co in the central TP for the past 2000 years, based on the unsaturation index of long-chain alkenones, using an updated temperature calibration, and a record of precipitation isotopes from compound-specific isotope ratios of leaf waxes. The centennial-scale variation of the temperature and precipitation isotope records captures well-known climatic events over the past 1000 years, for example, the ‘Little Ice Age’, which was cooler and drier than the ‘Medieval Warm Period’. However, the relationship between temperature and the precipitation isotope records differed during the interval at 2000–1000 cal. yr BP compared to the past 1000 years, probably because of changes in precipitation seasonality and the additional influence of the Westerlies on the central TP. In addition, the temperature records exhibit a prominent 210-year cyclicity, suggesting a possible influence of solar radiation on temperature variability.
    Print ISSN: 0959-6836
    Electronic ISSN: 1477-0911
    Topics: Geography , Geosciences
    Published by Sage
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