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Submarine fault scarps in the Sea of Marmara pull-apart (North Anatolian Fault): Implications for seismic hazard in Istanbul (2005)

R. Armijo ; N. Pondard ; B. Meyer ; [et al.]

In: Geochem. Geophys. Geosyst., Amsterdam, Elsevier Scientific Publishing Company, vol. 6, no. 6, pp. 1-29, pp. Q06009

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Publication Date: 2005

Description: Earthquake scarps associated with recent historical events have been found on the floor of the Sea of Marmara, along the North Anatolian Fault (NAF). The MAuto-Regressive Moving Average-processRASCARPS cruise using an unmanned submersible (ROV) provides direct observations to study the fine-scale morphology and geology of those scarps, their distribution, and geometry. The observations are consistent with the diversity of fault mechanisms and the fault segmentation within the north Marmara extensional step-over, between the strike-slip Ganos and Izmit faults. Smaller strike-slip segments and pull-apart basins alternate within the main step-over, commonly combining strike-slip and extension. Rapid sedimentation rates of 1-3 mm/yr appear to compete with normal faulting components of up to 6 mm/yr at the pull-apart margins. In spite of the fast sedimentation rates the submarine scarps are preserved and accumulate relief. Sets of youthful earthquake scarps extend offshore from the Ganos and Izmit faults on land into the Sea of Marmara. Our observations suggest that they correspond to the submarine ruptures of the 1999 Izmit (Mw 7.4) and the 1912 Ganos (Ms 7.4) earthquakes. While the 1999 rupture ends at the immediate eastern entrance of the extensional Cinarcik Basin, the 1912 rupture appears to have crossed the Ganos restraining bend into the Sea of Marmara floor for 60 km with a right-lateral slip of 5 m, ending in the Central Basin step-over. From the Gulf of Saros to Marmara the total 1912 rupture length is probably about 140 km, not 50 km as previously thought. The direct observations of submarine scarps in Marmara are critical to defining barriers that have arrested past earthquakes as well as defining a possible segmentation of the contemporary state of loading. Incorporating the submarine scarp evidence modifies substantially our understanding of the current state of loading along the NAF next to Istanbul. Coulomb stress modeling shows a zone of maximum loading with at least 4-5 m of slip deficit encompassing the strike-slip segment 70 km long between the Cinarcik and Central Basins. That segment alone would be capable of generating a large-magnitude earthquake (Mw 7.2). Other segments in Marmara appear less loaded. FROTH

Keywords: Earthquake hazard ; Turkey ; Fault zone ; NAF ; G3 ; G-cubed ; AGU ; Ucarkus ; Lepinay ; Cagatay ; Cakir ; Structural geology ; 7230 ; Seismology: ; Seismicity ; and ; tectonics ; Oezalaybey ; Ozalaybey ; Lefevre ; 7223 ; Earthquake ; interaction, ; forecasting, ; and ; prediction ; morphology ; submersible ; 8110 ; Tectonophysics: ; Continental ; tectonics: ; general ; 1766 ; 1894 ; 1912 ; 1999 ; Earthquake

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Upper-crustal structure of the Central Andes inferred from dip curvature analysis of isostatic residual gravity. Deformation Processes of the Andes (2006)

U. Riller ; H.-J. Götze ; S. Schmidt ; [et al.]

In: Frontiers in Earth Sciences, Springer: Berlin, Heidelberg, pp. 327-336

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Publication Date: 2006

Keywords: TF II ; Task Force II ; New tectonic causes of volcano failure

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BIBLIOGRAPHY ILP

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A new class of homoserine lactone quorum-sensing signals (2008)

A. L. Schaefer ; E. P. Greenberg ; C. M. Oliver ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 454(7204): 595-9. doi: 10.1038/nature07088.

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Publication Date: 2008-06-20

Description: Quorum sensing is a term used to describe cell-to-cell communication that allows cell-density-dependent gene expression. Many bacteria use acyl-homoserine lactone (acyl-HSL) synthases to generate fatty acyl-HSL quorum-sensing signals, which function with signal receptors to control expression of specific genes. The fatty acyl group is derived from fatty acid biosynthesis and provides signal specificity, but the variety of signals is limited. Here we show that the photosynthetic bacterium Rhodopseudomonas palustris uses an acyl-HSL synthase to produce p-coumaroyl-HSL by using environmental p-coumaric acid rather than fatty acids from cellular pools. The bacterium has a signal receptor with homology to fatty acyl-HSL receptors that responds to p-coumaroyl-HSL to regulate global gene expression. We also found that p-coumaroyl-HSL is made by other bacteria including Bradyrhizobium sp. and Silicibacter pomeroyi. This discovery extends the range of possibilities for acyl-HSL quorum sensing and raises fundamental questions about quorum sensing within the context of environmental signalling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schaefer, Amy L -- Greenberg, E P -- Oliver, Colin M -- Oda, Yasuhiro -- Huang, Jean J -- Bittan-Banin, Gili -- Peres, Caroline M -- Schmidt, Silke -- Juhaszova, Katarina -- Sufrin, Janice R -- Harwood, Caroline S -- England -- Nature. 2008 Jul 31;454(7204):595-9. doi: 10.1038/nature07088. Epub 2008 Jun 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Washington, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563084" target="_blank"〉PubMed〈/a〉

Keywords: 4-Butyrolactone/*analogs & derivatives/chemistry/metabolism ; Bacterial Proteins/genetics/isolation & purification/*metabolism ; Base Sequence ; Biological Assay ; Coumaric Acids/*metabolism ; Gene Expression Regulation, Bacterial ; *Quorum Sensing ; Regulon ; Rhodopseudomonas/enzymology/genetics/*growth & development/*metabolism ; Sequence Alignment ; *Signal Transduction

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Proportionally more deleterious genetic variation in European than in African populations (2008)

K. E. Lohmueller ; A. R. Indap ; S. Schmidt ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 451(7181): 994-7. doi: 10.1038/nature06611.

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Publication Date: 2008-02-22

Description: Quantifying the number of deleterious mutations per diploid human genome is of crucial concern to both evolutionary and medical geneticists. Here we combine genome-wide polymorphism data from PCR-based exon resequencing, comparative genomic data across mammalian species, and protein structure predictions to estimate the number of functionally consequential single-nucleotide polymorphisms (SNPs) carried by each of 15 African American (AA) and 20 European American (EA) individuals. We find that AAs show significantly higher levels of nucleotide heterozygosity than do EAs for all categories of functional SNPs considered, including synonymous, non-synonymous, predicted 'benign', predicted 'possibly damaging' and predicted 'probably damaging' SNPs. This result is wholly consistent with previous work showing higher overall levels of nucleotide variation in African populations than in Europeans. EA individuals, in contrast, have significantly more genotypes homozygous for the derived allele at synonymous and non-synonymous SNPs and for the damaging allele at 'probably damaging' SNPs than AAs do. For SNPs segregating only in one population or the other, the proportion of non-synonymous SNPs is significantly higher in the EA sample (55.4%) than in the AA sample (47.0%; P 〈 2.3 x 10(-37)). We observe a similar proportional excess of SNPs that are inferred to be 'probably damaging' (15.9% in EA; 12.1% in AA; P 〈 3.3 x 10(-11)). Using extensive simulations, we show that this excess proportion of segregating damaging alleles in Europeans is probably a consequence of a bottleneck that Europeans experienced at about the time of the migration out of Africa.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923434/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923434/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lohmueller, Kirk E -- Indap, Amit R -- Schmidt, Steffen -- Boyko, Adam R -- Hernandez, Ryan D -- Hubisz, Melissa J -- Sninsky, John J -- White, Thomas J -- Sunyaev, Shamil R -- Nielsen, Rasmus -- Clark, Andrew G -- Bustamante, Carlos D -- P50 GM065509/GM/NIGMS NIH HHS/ -- P50 GM065509-070006/GM/NIGMS NIH HHS/ -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-03/HG/NHGRI NIH HHS/ -- R01 HL072904/HL/NHLBI NIH HHS/ -- England -- Nature. 2008 Feb 21;451(7181):994-7. doi: 10.1038/nature06611.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18288194" target="_blank"〉PubMed〈/a〉

Keywords: Africa/ethnology ; Alleles ; Computational Biology ; Emigration and Immigration ; Europe/ethnology ; Exons/genetics ; Genome, Human/*genetics ; Heterozygote ; Homozygote ; Humans ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/*genetics ; United States

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Optical manipulation of nanoparticles and biomolecules in sub-wavelength slot waveguides (2009)

A. H. Yang ; S. D. Moore ; B. S. Schmidt ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 457(7225): 71-5. doi: 10.1038/nature07593.

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Publication Date: 2009-01-06

Description: The ability to manipulate nanoscopic matter precisely is critical for the development of active nanosystems. Optical tweezers are excellent tools for transporting particles ranging in size from several micrometres to a few hundred nanometres. Manipulation of dielectric objects with much smaller diameters, however, requires stronger optical confinement and higher intensities than can be provided by these diffraction-limited systems. Here we present an approach to optofluidic transport that overcomes these limitations, using sub-wavelength liquid-core slot waveguides. The technique simultaneously makes use of near-field optical forces to confine matter inside the waveguide and scattering/adsorption forces to transport it. The ability of the slot waveguide to condense the accessible electromagnetic energy to scales as small as 60 nm allows us also to overcome the fundamental diffraction problem. We apply the approach here to the trapping and transport of 75-nm dielectric nanoparticles and lambda-DNA molecules. Because trapping occurs along a line, rather than at a point as with traditional point traps, the method provides the ability to handle extended biomolecules directly. We also carry out a detailed numerical analysis that relates the near-field optical forces to release kinetics. We believe that the architecture demonstrated here will help to bridge the gap between optical manipulation and nanofluidics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Allen H J -- Moore, Sean D -- Schmidt, Bradley S -- Klug, Matthew -- Lipson, Michal -- Erickson, David -- England -- Nature. 2009 Jan 1;457(7225):71-5. doi: 10.1038/nature07593.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19122638" target="_blank"〉PubMed〈/a〉

Keywords: Bacteriophage lambda/genetics ; DNA, Viral/*analysis ; Electrons ; Kinetics ; Micromanipulation/instrumentation/*methods ; Nanoparticles/*analysis ; *Optical Tweezers ; Optics and Photonics/*instrumentation/*methods

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

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Transcriptome complexity in a genome-reduced bacterium (2009)

M. Guell ; V. van Noort ; E. Yus ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 326(5957): 1268-71. doi: 10.1126/science.1176951.

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Publication Date: 2009-12-08

Description: To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously undescribed, mostly noncoding transcripts, 89 of them in antisense configuration to known genes. We identified 341 operons, of which 139 are polycistronic; almost half of the latter show decaying expression in a staircase-like manner. Under various conditions, operons could be divided into 447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guell, Marc -- van Noort, Vera -- Yus, Eva -- Chen, Wei-Hua -- Leigh-Bell, Justine -- Michalodimitrakis, Konstantinos -- Yamada, Takuji -- Arumugam, Manimozhiyan -- Doerks, Tobias -- Kuhner, Sebastian -- Rode, Michaela -- Suyama, Mikita -- Schmidt, Sabine -- Gavin, Anne-Claude -- Bork, Peer -- Serrano, Luis -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1268-71. doi: 10.1126/science.1176951.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965477" target="_blank"〉PubMed〈/a〉

Keywords: Base Sequence ; *Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; *Genome, Bacterial ; Molecular Sequence Data ; Mycoplasma pneumoniae/*genetics/metabolism ; Oligonucleotide Array Sequence Analysis ; Operon ; RNA, Antisense/genetics/metabolism ; RNA, Bacterial/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Untranslated/analysis/*genetics ; *Transcription, Genetic

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Complement factor H variant increases the risk of age-related macular degeneration (2005)

J. L. Haines ; M. A. Hauser ; S. Schmidt ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 308(5720): 419-21. doi: 10.1126/science.1110359.

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Publication Date: 2005-03-12

Description: Age-related macular degeneration (AMD) is a leading cause of visual impairment and blindness in the elderly whose etiology remains largely unknown. Previous studies identified chromosome 1q32 as harboring a susceptibility locus for AMD. We used single-nucleotide polymorphisms to interrogate this region and identified a strongly associated haplotype in two independent data sets. DNA resequencing of the complement factor H gene within this haplotype revealed a common coding variant, Y402H, that significantly increases the risk for AMD with odds ratios between 2.45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haines, Jonathan L -- Hauser, Michael A -- Schmidt, Silke -- Scott, William K -- Olson, Lana M -- Gallins, Paul -- Spencer, Kylee L -- Kwan, Shu Ying -- Noureddine, Maher -- Gilbert, John R -- Schnetz-Boutaud, Nathalie -- Agarwal, Anita -- Postel, Eric A -- Pericak-Vance, Margaret A -- AG11268/AG/NIA NIH HHS/ -- EY015216/EY/NEI NIH HHS/ -- EY12118/EY/NEI NIH HHS/ -- M01 RR-00095/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):419-21. Epub 2005 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15761120" target="_blank"〉PubMed〈/a〉

Keywords: Aged ; Alleles ; Binding Sites ; C-Reactive Protein/metabolism ; Case-Control Studies ; Chromosomes, Human, Pair 1/genetics ; Complement Activation ; Complement Factor H/analysis/*genetics/physiology ; Gene Frequency ; Genetic Predisposition to Disease ; *Genetic Variation ; Genotype ; Haplotypes ; Heparin/metabolism ; Humans ; Linkage Disequilibrium ; Macular Degeneration/*genetics ; Odds Ratio ; *Polymorphism, Single Nucleotide ; Risk Factors ; Sequence Analysis, DNA ; Smoking

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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