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  • 1
    Publication Date: 2016-07-22
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
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  • 2
    Publication Date: 2015-10-20
    Description: Field mapping and lidar analysis of surface faulting patterns expressed in flights of geologically similar fluvial terraces at the well-known Branch River and Saxton River sites along the Wairau (Alpine) and Awatere strike-slip faults, South Island, New Zealand, reveal that fault-related deformation patterns expressed in the topography at these sites are markedly less structurally complex along the higher-displacement (hundreds of kilometers), structurally mature Wairau fault than along the Awatere fault (~13–20 km total slip). These differences, which are generally representative of the surface traces of these faults, provide direct evidence that surface faulting becomes structurally simpler with increasing cumulative fault offset. We also examine the degree to which off-fault deformation (OFD) is expressed in the landscape at the Saxton River site along the less structurally mature Awatere fault. Significantly greater amounts of OFD are discernible as a wide damage zone (~460 m fault-perpendicular width) in older (ca. 15 ka), more-displaced (64–74 m) fluvial terraces than in younger (ca. 1–7 ka), less-displaced (〈55 m) terraces; no OFD is discernible in the lidar data on the least-displaced (〈35 m) terraces. From this, we infer that OFD becomes progressively more geomorphically apparent with accumulating displacement. These observations imply that (1) the processes that accommodate OFD are active during each earthquake, but may not be evident in deposits that have experienced relatively small displacements; (2) structures accommodating OFD will become progressively geomorphically clearer with increasing displacement; (3) geomorphic measurements of overall fault zone width taken in deposits that have experienced small displacements will be underestimates; and (4) fault slip rates based on geomorphic surface offsets will be underestimates for immature faults if based solely on measurements along the high-strain fault core.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
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  • 3
    Publication Date: 2015-01-30
    Description: The Alpine fault in south Westland, New Zealand, releases strains of Pacific–Australian relative plate motion in large earthquakes with an average interevent spacing of ~330 years. A new record of earthquake recurrence has been developed at Hokuri Creek, with evidence for 22 events. The youngest Hokuri Creek earthquake overlaps in time and is believed to be the same as the oldest of another site about 100 km to the northwest near Haast. The combined record spans the last 7900 years and includes 24 events. We study the recurrence rate and conditional probability of ground ruptures from this record using a new likelihood-based approach for estimation of recurrence model parameters. Paleoseismic parameter estimation includes both dating and natural recurrence uncertainties. Lognormal and Brownian passage time (BPT) models are considered. The likelihood surface has distribution location and width parameters as axes, the mean and standard deviation of the log recurrence for the lognormal, and the mean and coefficient of variation for the BPT. The maximum-likelihood (ML) point gives the parameters most likely to have given rise to the data. The ML point, 50-year conditional probabilities of a ground-rupturing earthquake are 26.8% and 26.1% for the lognormal and BPT models, respectively. Contours of equal likelihood track the parameter pairs that are equally probable to have given rise to the observed data. Conditional probabilities on the lognormal 95% boundary around the ML point range from 18.2% to 35.8%. An empirical distribution model completely based on past recurrence times gives a similar conditional probability of 27.1% (9.6%–50.2%). In contrast, the time-independent conditional probability estimate of 13.6% (8.8%–19.1%) is about half that of the time-dependent models. A nonparametric test of earthquake recurrence at Hokuri Creek indicates that time-dependent recurrence models best represent the southern Alpine fault of the South Island, New Zealand.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
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  • 4
    Publication Date: 2012-09-01
    Description: The dextral-reverse Alpine fault is the major onshore plate-boundary structure between the Australian and Pacific plates in New Zealand. No previous study of the central portion of the 200-km-long central segment has provided on-fault evidence for the most recent event (MRE). Using lidar (light detection and ranging) data coupled with field mapping, we recognized the main trace of the Alpine fault north of Gaunt Creek (South Island) as a north-striking fault scarp. We enhanced a natural exposure that revealed evidence for repeated late Holocene thrust fault movement. The north-northwest–striking fault zone is characterized by a distinct 5–50-cm-thick clay fault-gouge layer juxtaposing hanging-wall bedrock (mylonites and cataclasites) over unconsolidated late Holocene footwall colluvium. The bedrock is cut by a strath terrace and overlain by mid-Holocene (ca. 5400 calibrated 14 C yr B.P.) alluvial terrace, which has been faulted repeatedly and is conformably overlain by undeformed late Holocene colluvium and alluvium. An unfaulted peat at the base of the scarp is buried by post-MRE alluvium and yields a calibrated 2 radiocarbon age of A.D. 1710–1930, which dates the MRE as post-1709. Our data are consistent with sparse on-fault data, and validate earlier off-fault records that suggest an A.D. 1717 MRE. The 1717 event had a moment magnitude of M w 8.1 ± 0.1, based on the 380-km-long surface rupture. Because the fault has not ruptured for ~300 yr, it is likely approaching the end of its seismic cycle and poses a significant seismic hazard to New Zealand.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
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  • 5
    Publication Date: 2012-05-16
    Description: More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ70 (including phoP, slyA, and invF) from which we identified the −10 and −35 motifs of σ70-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    Publication Date: 2010-02-13
    Description: To feed the several billion people living on this planet, the production of high-quality food must increase with reduced inputs, but this accomplishment will be particularly challenging in the face of global environmental change. Plant breeders need to focus on traits with the greatest potential to increase yield. Hence, new technologies must be developed to accelerate breeding through improving genotyping and phenotyping methods and by increasing the available genetic diversity in breeding germplasm. The most gain will come from delivering these technologies in developing countries, but the technologies will have to be economically accessible and readily disseminated. Crop improvement through breeding brings immense value relative to investment and offers an effective approach to improving food security.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tester, Mark -- Langridge, Peter -- New York, N.Y. -- Science. 2010 Feb 12;327(5967):818-22. doi: 10.1126/science.1183700.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian Centre for Plant Functional Genomics, University of Adelaide, South Australia SA 5064, Australia. mark.tester@acpfg.com.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20150489" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*methods ; *Biotechnology ; *Breeding ; Crops, Agricultural/*genetics/growth & development ; Developing Countries ; Environment ; Food, Genetically Modified ; Genes, Plant ; Genetic Markers ; Genetic Techniques ; Genetic Variation ; Genotype ; Phenotype
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Nature Publishing Group (NPG)
    Publication Date: 2012-11-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Langridge, Peter -- England -- Nature. 2012 Nov 29;491(7426):678-80. doi: 10.1038/491678a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23192142" target="_blank"〉PubMed〈/a〉
    Keywords: *Bread ; Genome, Plant/*genetics ; Triticum/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2013-07-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McCouch, Susan -- Baute, Gregory J -- Bradeen, James -- Bramel, Paula -- Bretting, Peter K -- Buckler, Edward -- Burke, John M -- Charest, David -- Cloutier, Sylvie -- Cole, Glenn -- Dempewolf, Hannes -- Dingkuhn, Michael -- Feuillet, Catherine -- Gepts, Paul -- Grattapaglia, Dario -- Guarino, Luigi -- Jackson, Scott -- Knapp, Sandra -- Langridge, Peter -- Lawton-Rauh, Amy -- Lijua, Qui -- Lusty, Charlotte -- Michael, Todd -- Myles, Sean -- Naito, Ken -- Nelson, Randall L -- Pontarollo, Reno -- Richards, Christopher M -- Rieseberg, Loren -- Ross-Ibarra, Jeffrey -- Rounsley, Steve -- Hamilton, Ruaraidh Sackville -- Schurr, Ulrich -- Stein, Nils -- Tomooka, Norihiko -- van der Knaap, Esther -- van Tassel, David -- Toll, Jane -- Valls, Jose -- Varshney, Rajeev K -- Ward, Judson -- Waugh, Robbie -- Wenzl, Peter -- Zamir, Daniel -- England -- Nature. 2013 Jul 4;499(7456):23-4. doi: 10.1038/499023a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cornell University, Ithaca, New York, USA. mccouch@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823779" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/genetics ; Agriculture/economics/*methods/*trends ; Biodiversity ; Biological Specimen Banks ; Breeding ; Crops, Agricultural/genetics ; Food Supply/*statistics & numerical data ; Genes, Plant ; Humans ; Phenotype ; Seeds/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2012-10-19
    Description: Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉International Barley Genome Sequencing Consortium -- Mayer, Klaus F X -- Waugh, Robbie -- Brown, John W S -- Schulman, Alan -- Langridge, Peter -- Platzer, Matthias -- Fincher, Geoffrey B -- Muehlbauer, Gary J -- Sato, Kazuhiro -- Close, Timothy J -- Wise, Roger P -- Stein, Nils -- BB/100663X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2012 Nov 29;491(7426):711-6. doi: 10.1038/nature11543. Epub 2012 Oct 17.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23075845" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing/genetics ; Codon, Nonsense/genetics ; Crops, Agricultural/genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics ; Hordeum/classification/*genetics ; Molecular Sequence Annotation ; Physical Chromosome Mapping ; Polymorphism, Single Nucleotide/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; *Sequence Analysis, DNA ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2014-07-22
    Description: Environmental constraints severely restrict crop yields in most production environments, and expanding the use of variation will underpin future progress in breeding. In semi-arid environments boron toxicity constrains productivity, and genetic improvement is the only effective strategy for addressing the problem. Wheat breeders have sought and used available genetic diversity from landraces to maintain yield in these environments; however, the identity of the genes at the major tolerance loci was unknown. Here we describe the identification of near-identical, root-specific boron transporter genes underlying the two major-effect quantitative trait loci for boron tolerance in wheat, Bo1 and Bo4 (ref. 2). We show that tolerance to a high concentration of boron is associated with multiple genomic changes including tetraploid introgression, dispersed gene duplication, and variation in gene structure and transcript level. An allelic series was identified from a panel of bread and durum wheat cultivars and landraces originating from diverse agronomic zones. Our results demonstrate that, during selection, breeders have matched functionally different boron tolerance alleles to specific environments. The characterization of boron tolerance in wheat illustrates the power of the new wheat genomic resources to define key adaptive processes that have underpinned crop improvement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pallotta, Margaret -- Schnurbusch, Thorsten -- Hayes, Julie -- Hay, Alison -- Baumann, Ute -- Paull, Jeff -- Langridge, Peter -- Sutton, Tim -- England -- Nature. 2014 Oct 2;514(7520):88-91. doi: 10.1038/nature13538. Epub 2014 Jul 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia [2]. ; 1] Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia [2] Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank Department, Corrensstrasse 3, D-06466 Gatersleben, Germany [3]. ; Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia. ; School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25043042" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*drug effects/genetics ; Alleles ; Boron/*pharmacology ; Carrier Proteins/*genetics ; Drug Tolerance ; Gene Duplication/genetics ; Genes, Plant/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plant Roots/drug effects/genetics/metabolism ; Polyploidy ; Quantitative Trait Loci/genetics ; RNA, Messenger/analysis/genetics ; RNA, Plant/analysis/genetics ; Soil/*chemistry ; Triticum/classification/*drug effects/*genetics/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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