Kurata, Nori; Yamazaki, Yukiko
The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.
Wang, Xiaoling; Liu, Xuepeng; Sun, Yuefeng; An, Juan; Zhang, Jing; Chen, Hongchao
Former studies, the methods for estimating the ventilation time are all empirical in construction schedule simulation. However, in many real cases of construction schedule, the many factors have impact on the ventilation time. Therefore, in this paper the 3D unsteady quasi-single phase models are proposed to optimize the ventilation time with different tunneling lengths. The effect of buoyancy is considered in the momentum equation of the CO transport model, while the effects of inter-phase drag, lift force, and virtual mass force are taken into account in the momentum source of the dust transport model. The prediction by the present model for airflow in a diversion tunnel is confirmed by the experimental values reported by Nakayama [Nakayama, In-situ measurement and simulation by CFD of methane gas distribution at a heading faces, Shigen-to-Sozai 114 (11) (1998) 769-775]. The construction ventilation of the diversion tunnel of XinTangfang power station in China is used as a case. The distributions of airflow, CO and dust in the diversion tunnel are analyzed. A theory method for GIS-based dynamic visual simulation for the construction processes of underground structure groups is presented that combines cyclic operation network simulation, system simulation, network plan optimization, and GIS-based construction processes' 3D visualization. Based on the ventilation time the construction schedule of the diversion tunnel is simulated by the above theory method.
Ishihama, Akira; Shimada, Tomohiro; Yamazaki, Yukiko
Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, ‘Transcription Profile of Escherichia coli’ (www.shigen.nig.ac.jp/ecoli/tec/). PMID:26843427
Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.
JOGMEC, as a member of research group for resources assessment of Research Consortium for Methane Hydrate Resources in Japan (MH21), is conducting resources assessment of methane hydrates (MHs) offshore surrounding Japan. The interpretation of 3-D seismic data acquired by geophysical vessel 'Shigen', which is owned by Agency for Natural Resources and Energy, are carried out. And MH concentrated zones are being extracted. This study is an introduction for the case example of interpretation of 3-D seismic data in the area which have not been drilled. The characteristic of 3-D seismic data in this study area shows fold structure, which undulates severalfold. In addition, some faults are interpreted, which does not show the large displacement, are seen. Bottom Simulating Reflector (BSR) is very visible continuously. Clear velocity contrast in the boundary between above and below of BSR and the high velocity anomaly above BSR are confirmed in the high density velocity analysis profile. MHs are assumed to exist in sand heterogeneously because the velocity distribution in the extracted zones is inhomogeneous. In the results of geomorphological analysis, channel deposits and mid submarine fan deposits, which are located above BSR, are presumed the sediments which bear sand. Thus the extracted zones are estimated MH concentrated zones. As above, even the area has not been drilled, the extraction of MH concentrated zones can be estimated by the interpretation of the seismic data, the result of the high density velocity analysis, and the distribution of sand by geomorphological analysis. These results will be useful for the plan of the future drilling programme. This introduction is the example of 3-D seismic survey area. It will become a useful information for 3-D seismic survey plan by performing similar interpretation in 2-D seismic survey lines.
Gok, Elcin; Polat, Orhan
Izmir metropolitan area is one of the biggest cities of Turkey in terms of population and industrial density. Amount of recordings and quality of located events increased since the new local seismic array, IzmirNET, was installed in 2008. Present study addresses to elucidate seismotectonics of Izmir vicinity by a new data set and reveal first results of seismological analysis obtained for 4.5 years. 930 small earthquakes are well located within less than 1.0 km horizontal error (RMS ≤ 0.15 s) over a total of 1421 recorded events. Data were processed by using SEISAN Earthquake Analysis Software implemented at SeismoLab of Dokuz Eylul University. The Orhanli-Tuzla Fault Zone and Izmir faults are capable of producing a destructive earthquake. Events show clear clusters around the Outer Bay of Izmir Gulf and Sigacik Bay. We also detected some dense clusters Sigacik Bay to the South, and in the outer bay of Izmir Gulf along NW-SE direction. We investigated kinematics of active faults around the Izmir and Foca areas by using 41 focal mechanism solutions from different algorithms. Foca is located 60 km in the NW direction of Izmir. Mechanisms generally resulted in pure normal or dominant normal faulting with minor strike-slip components in agreement with the kinematics of the other fault zones in Western Turkey. A stress tensor study using selected fault plane solution indicates that the study area is under extension regime in an N-S direction with 71° plunge for maximum compressive principal stress axis (S1), and closer to horizontals for intermediate (S2) and minimum compressive principal stress axis (S3).
Maria Mendez Martinez, Luz de; Portillo, Mercy
We studied the geographic area located in the central part of El Salvador, between the San Salvador Volcano (Quezaltepec) and Ilopango Lake. Its latitude is between 13 deg. 36' and 13 deg. 54', and longitude is between -89 deg. 18' and -88 deg. 57'. This area is directly affected by the WNW axis, the most prominent weak tectonic system in the region. Our research aimed to determine the focal mechanisms of seisms occurring in the studied area between 1994 and March 2005. Our analysis provided information about displacement types of the geological faults, using the wave impulse P method and computer applications ARCGIS and SEISAN, with the subroutine FOCMEC. Information of the studied seisms was obtained from the National Service of Territorial Studies (SNET) database. Geographic models used in the preparation of maps are from the geographic information system of the School of Physics at the University of El Salvador. The 37 focal mechanisms on the map of faults were identified in digital seismographs to determinate the arrival polarity of the wave P for each seism station. Data from the focal mechanisms were analyzed and correlated with their replications. The analysis allowed us to identify evidences to consider the fault continuity not reported by the last geological mission in El Salvador conducted in the 1970s. The fault continuity is located northwest of the studied geographical area, between San Salvador City and the San Salvador Volcano. The compression and strain axes for this area are two main horizontal force axes. The average orientation for the strain axis is NNE-SSW, and WNW-SEE for the compression axis. There is also important seismic activity in the Ilopango Lake and surrounding area. However, data did not allow us to make any inference. The tensors distribution resulted in a high dispersion corresponding to typical fauces models.
Perrot, J.; Goslin, J.; Dziak, R. P.; Haxel, J. H.; Maia, M. A.; Tisseau, C.; Royer, J.
The seismicity of the North Atlantic Ocean was recorded by the SIRENA array of 6 autonomous underwater hydrophones (AUH) moored within the SOFAR channel on the flanks of the Mid-Atlantic Ridge (MAR). The instruments were deployed north of the Azores Plateau between 40° and 50°N from June 2002 to September 2003. The low attenuation properties of the SOFAR channel for earthquake T-wave propagation result in a detection threshold reduction to a magnitude completeness level (Mc) of ~2.8, to be compared to a Mc~4.7 for MAR events recorded by land-based seismic networks. A spatio-temporal analysis was performed over the 1696 events localized inside the SIRENA array. For hydrophone-derived catalogs, the acoustic magnitude, or Source Level (SL), is used as a measure of earthquake size. The ''source level completeness'', above which the data set is complete, is SLc=208 dB. The SIRENA catalog was searched for swarms using the cluster software of the SEISAN distribution. A minimum SL of 210 dB was chosen to detect a possible mainshock, and all subsequent events within 40 days following the possible mainshock, located within a radius of 15 km from the mainshock were considered as events of the swarm. 15 km correspond to the maximum fault length in a slow-ridge context. 11 swarms with more than 15 events were detected along the MAR between 40°et 50°N during the SIRENA deployment. The maximum number of earthquakes in a swarm is 40 events. The SL vs. time distribution within each swarm allowed a first discrimination between the swarms occurring in a tectonic context and those which can be attributed to volcanic processes, the latter showing a more constant SL vs. time distribution. Moreover, the swarms occurring in a tectonic context show a "mainshock-afterschock" distribution of the cumulative number of events vs. time, fitting a Modified Omori Law. The location of tectonic and volcanic swarms correlates well with regions where a positive and negative Mantle Bouguer
Blanco Chia, J. F.; Poveda, E.; Pedraza, P.
The latest seismological equipment and data processing instrumentation installed at the Colombia Seismological Network (RSNC) are described. System configuration, network operation, and data management are discussed. The data quality and the new seismological products are analyzed. The main purpose of the network is to monitor local seismicity with a special emphasis on seismic activity surrounding the Colombian Pacific and Caribbean oceans, for early warning in case a Tsunami is produced by an earthquake. The Colombian territory is located at the South America northwestern corner, here three tectonic plates converge: Nazca, Caribbean and the South American. The dynamics of these plates, when resulting in earthquakes, is continuously monitored by the network. In 2012, the RSNC registered in 2012 an average of 67 events per day; from this number, a mean of 36 earthquakes were possible to be located well. In 2010 the network was also able to register an average of 67 events, but it was only possible to locate a mean of 28 earthquakes daily. This difference is due to the expansion of the network. The network is made up of 84 stations equipped with different kind of broadband 40s, 120s seismometers, accelerometers and short period 1s sensors. The signal is transmitted continuously in real-time to the Central Recording Center located at Bogotá, using satellite, telemetry, and Internet. Moreover, there are some other stations which are required to collect the information in situ. Data is recorded and processed digitally using two different systems, EARTHWORM and SEISAN, which are able to process and share the information between them. The RSNC has designed and implemented a web system to share the seismological data. This innovative system uses tools like Java Script, Oracle and programming languages like PHP to allow the users to access the seismicity registered by the network almost in real time as well as to download the waveform and technical details. The coverage
Rojas, W.; Camacho, E. I.; Marroquín, G.; Molina, E.; Talavera, E.; Benito, M. B.; Lindholm, C.
Central America (CA) is known as a seismically active region in which several historic destructive earthquakes have occurred. This fact has promoved the development of seismic hazard studies that provide necessary estimates for decision making and risk assessment efforts, requiring a complete and standardized seismic catalog. With this aim, several authors have contributed to the study of the historical seismicity of Central America (e.g. Grases, Feldaman; White y Harlow, 1993; White et al. 2004; Ambraseys y Adams, 2001; Peraldo y Montero, 1999), who complied historical data. A first catalogue was developed by Rojas (1993) that comprises the 1522 to 1993 period. This information was integrated in 2007, together with data from the International Seismological Centre (CASC) and the national catalogs of CA countries in a new regional catalogue. Since 2007 a continuous effort has been done in order to complete and update this CA earthquake catalog. In particular, two workshops were held in 2008 and 2011 in the Universidad Politécnica de Madrid (Spain), joining experts from the different CA countries who worked each one in its own catalogue covering the entire region and the border with northwestern Colombia and southern Mexico. These national catalogues were later integrated in a common regional catalogue in SEISAN format. At this aim it was necessary to solve some problems, like to avoid duplicity of events, specially close to the boundaries, to consider the different scales of magnitude adopted by different countries, to take into account the completeness by the different national networks, etc. Some solutions were adopted for obtaining a homogenized catalogue to Mw, containing historical and instrumental events with Mw > 3.5 from 1522 up to 2011. The catalogue updated to December 2007 was the basis for the first regional hazard study carried out by Benito et al., (2011) as part of the collaborative RESIS II project under coordination of NORSAR. The ones updated to
Ordaz, M.; Martinelli, F.; Meletti, C.; D'Amico, V.
CRISIS is a computer tool for probabilistic seismic hazard analysis (PSHA), whose development started in the late 1980's at the Instituto de Ingeniería, UNAM, Mexico. It started circulating outside the Mexican borders at the beginning of the 1990's, when it was first distributed as part of SEISAN tools. Throughout the years, CRISIS has been used for seismic hazard studies in several countries in Latin America (Mexico, Guatemala, Belize, El Salvador, Honduras, Nicaragua, Costa Rica, Panama, Colombia, Venezuela, Ecuador, Peru, Argentina and Chile), and in many other countries of the World. CRISIS has always circulated free of charge for non-commercial applications. It is worth noting that CRISIS has been mainly written by people that are, at the same time, PSHA practitioners. Therefore, the development loop has been relatively short, and most of the modifications and improvements have been made to satisfy the needs of the developers themselves. CRISIS has evolved from a rather simple FORTRAN code to a relatively complex program with a friendly graphical interface, able to handle a variety of modeling possibilities for source geometries, seismicity descriptions and ground motion prediction models (GMPM). We will describe some of the improvements made for the newest version of the code: CRISIS 2012.These improvements, some of which were made in the frame of the Italian research project INGV-DPC S2 (http://nuovoprogettoesse2.stru.polimi.it/), funded by the Dipartimento della Protezione Civile (DPC; National Civil Protection Department), include: A wider variety of source geometries A wider variety of seismicity models, including the ability to handle non-Poissonian occurrence models and Poissonian smoothed-seismicity descriptions. Enhanced capabilities for using different kinds of GMPM: attenuation tables, built-in models and generalized attenuation models. In the case of built-in models, there is, by default, a set ready to use in CRISIS, but additional custom GMPMs
Martín, R.; Carmona, E.; Almendros, J.; Serrano, I.; Villaseñor, A.; Galeano, J.
the seismic activity and an efficient seismo-volcanic surveillance. The data are processed and analyzed using the SEISAN database management software. In addition to the seismic network, we deployed a small-aperture seismic array south of Fumarole Bay. It is composed by 9 vertical and 1 three-component short-period stations. The 24-bit data acquisition system samples these 12 channels at 100 sps. There is also a permanent seismic station operating since 2008 and located near GdC, that is very useful for the preliminary evaluation of the seismicity at the start of the survey. This station is composed by a 16-s electrolytic seismometer (Eentec SP400) and a 24-bit datalogger (Eentec DR4000) sampling at 100 sps. During the 2010-2011 survey we identified 33 regional earthquakes, 80 volcano-tectonic (VT) earthquakes, and 929 long-period (LP) events. The volcanic alert system has remained green (the lowest level) at all times. The seismic activity has been similar to previous surveys and remained within limits that are normal for the island.
Yavuz, Evrim; Çaka, Deniz; Tunç, Berna; Woith, Heiko; Gottfried Lühr, Birger; Barış, Şerif
Attenuation characteristic of seismic waves was determined using coda Q in the frame of MARsite (MARsite has received funding from the European Union's Seventh Programme for research, technological development and demonstration under grant agreement No 308417). Data from 82 earthquakes recorded in 2013-2014 in the Armutlu Peninsula and its vicinity by 9 ARNET seismic stations were used for processing. The earthquake magnitudes (Ml) and depths vary from 1.5 to 3.7 and 1.2-16.9 km, respectively. Epicentral distances closer than 90 km were selected to ensure better signal-to-noise ratios. Lapse times between 20 seconds and 40 seconds at intervals of 5 seconds were used for the calculation of the coda wave quality factor. The coda windows were filtered at central frequencies of 1.5, 3, 6, 9 and 12 Hz bandpass filter. To obtain reliable results, only data with signal-to-noise ratios greater than 5 and correlation coefficents higher than 0.7 were used. The SEISAN software and one of its subroutines (CODAQ) were used for data processing and analyses. In the whole study area, Qc=(51±4)f^(0.91±0.04) for 20 seconds, Qc=(77±7)f^(0.80±0.04) for 30 seconds and Qc=(112±13)f^(0.72±0.06) for 40 seconds lapse times are obtained for coda wave quality factor. The observed quality factor is dependent on frequency and lapse time. The results indicate that the upper lithosphere is more heterogeneous and seismically more active than the lower lithosphere as expected in the region which is tectonically complex refering to the effects of the North Anatolian Fault Zone. By considering earthquake clusters and recorded stations, the scattering area was drawn. The intersection of the scattered areas for 20 seconds lapse time is covering all stations. Quality factor in 1 Hz and frequency dependent values were calculated separately and for the intersection of all scattered areas. Calculated Qo and n values of the intersection area are 50 and 0.89, respectively. Hence, the Qo and n values
Perrot, Julie; Cevatoglu, Melis; Cannat, Mathilde; Escartin, Javier; Maia, Marcia; Tisseau, Chantal; Dziak, Robert; Goslin, Jean
The seismicity of the South Atlantic Ocean has been recorded by the MARCHE network of 4 autonomous underwater hydrophones (AUH) moored within the SOFAR channel on the flanks of the Mid-Atlantic Ridge (MAR). The instruments were deployed south of the Azores Plateau between 32° and 39°N from July 2005 to August 2008. The low attenuation properties of the SOFAR channel for earthquake T-wave propagation result in a detection threshold reduction from a magnitude completeness level (Mc) of ~4.3 for MAR events recorded by the land-based seismic networks to Mc=2.1 using this hydrophone array. A spatio-temporal analysis has been performed among the 5600 events recorded inside the MARCHE array. Most events are distributed along the ridge between lat. 39°N on the Azores Platform and the Rainbow (36°N) segment. In the hydrophone catalogue, acoustic magnitude (Source Level, SL) is used as a measure of earthquake size. The source level above which the data set is complete is SLc=205 dB. We look for seismic swarms using the cluster software of the SEISAN package. The criterion used are a minimum SL of 210 to detect a possible mainshock, and a radius of 30 km and a time window of 40 days after this mainshock (Cevatoglu, 2010, Goslin et al., 2012). 7 swarms with more than 15 events are identified using this approach between 32°et 39°N of latitude. The maximum number of earthquake in a swarm is 57 events. This result differs from the study of Simao et al. (2010) as we processed a further year of data and selected sequences with fewer events. Looking at the distribution of the SL as a function of time after the mainshock, we discuss the possible mechanism of these earthquakes : tectonic events with a "mainshock-aftershock" distribution fitting a modified Omori law or volcanic events showing more constant SL values. We also present the geophysical setting of these 7 swarms, using gravity, bathymetry, and available local geological data. This study illustrates the potential of
Tectonics and earthquake source parameters in the Isthmus of Tehuantepec, Mexico- A microseismic study The Isthmus of Tehuantepec (IT) is located in southeastern Mexico where the Cocos, the Caribbean and the North American plates converge. The seismicity of the region has been recently studied, based on the recordings obtained during a microearthquake campaign carried out during the fall of 1995, preliminary results were presented previously (Chavez et al. EOS, 78, 46, 1997; EOS, 80, 46, 1999; EOS, 81, 48, 2000). Herewith, we present the latest results obtained from the processing, with the code SEISAN (Havskov, 1995, 1997), of about 200 events (out of more than 900) located with an RMS œ 0.5 s. The source parameters of 44 of them were estimated. Among other results, the following can be mentioned: 1) 30 percent of the located events are shallow (Hœ50 Km), 30percent with depths between 50 and 100 Km, and the rest with H3 100 Km; 2) The errors in their Latitudes, Longitudes and Depths best fitted the lognormal and inverse Gaussian distributions with standard deviations of about 5 Km; 3) The shallow seismic activity occurs mainly in the Tehuantepec Gulf, parallel to the Middle American Trench, as well as in the Central and Northern parts of the IT. Under the latter shallow events, we confirmed the existance of the so-called Central Seismic Cluster of the IT (Ponce et al., 1992) at a depth of about 120 Km and found another one south of Cuauthemoc (170 N, -950 W) at a depth of 100 Km; 4) The intense deformation undergoing in the Cocos plate in the IT region was also confirmed by the its gradual, but sustancial, inclination angle from west to east and south to north in the NE 450 direction (Burbach et al., 1984, Ponce et al. 1992); 5) From the 44 fault plane solutions (fps) found, about 46% were normal and the rest had a thrust fps. The events with a normal fps are located in the central and southern parts of the IT; 6) The T axis directions of the former are E-W, N