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  • 1
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    Anomalously high b-values in the south flank of Kilauea volcano, Hawaii: evidence for the distribution of magma below Kilauea's East rift zone (2001)
    In:  Journal of Volcanology and Geothermal Research, Reykjavík, Icelandic Meteorological Office, Ministry for the Environment, University of Iceland, vol. 106, no. 1-2, pp. 23-37, pp. L05306, (ISSN: 1340-4202)
    Details
    Publication Date: 2001
    Keywords: Seismicity ; Statistical investigations ; Gutenberg-Richter magnitude frequency b-value ; Volcanology ; Fault zone
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    BIBLIOGRAPHY SEISMOLOGY
  • 2
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    Reference-guided assembly of four diverse Arabidopsis thaliana genomes [Genetics] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-06-22
    Description: We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html.
    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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    Complex coastal change in response to autogenic basin infilling: An example from a sub-tropical Holocene strandplain (2016)
    Wiley
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    Publication Date: 2016-01-24
    Description: Thick bay-fill sequences that often culminate in strandplain development serve as important sedimentary archives of land–ocean interaction, although distinguishing between internal and external forcings is an ongoing challenge. This study employs sediment cores, ground-penetrating radar surveys, radiocarbon dates, palaeogeographic reconstructions and hydrodynamic modelling to explore the role of autogenic processes – notably a reduction in wave energy in response to coastal embayment infilling – in coastal evolution and shoreline morphodynamics. Following a regional 2 to 4 m highstand at ca 5.8 ka, the 75 km 2 Tijucas Strandplain in Southern Brazil built from fluvial sediments deposited into a semi-enclosed bay. Holocene regressive deposits are underlain by fluvial sands and a Pleistocene transgressive–regressive sequence, and backed by a highstand barrier island. The strandplain is immediately underlain by 5 to 16 m of seaward-thickening, fluvially derived, Holocene-age, basin-fill mud. Several trends are observed from the landward (oldest) to the seaward (youngest) sections of the strandplain: (i) the upper shoreface and foreshore become finer and thinner and shift from sand-dominated to mud-dominated; (ii) beachface slopes decrease from 〉11 o to ca 7 o ; and (iii) progradation rates increase from 0.4 m yr −1 to 1.8 m yr −1 . Hydrodynamic modelling demonstrates a correlation between progressive shoaling of Tijucas Bay driven by sea-level fall and sediment infilling and a decrease in onshore wave energy transport from 18 to 4 kW/m. The combination of allogenic (sediment supply, falling relative sea level and geology) and autogenic (decrease in wave energy due to bay shoaling) processes drove the development of a regressive system with characteristics that are rare, if not unique, in the Holocene and rock records. These findings demonstrate the complexities in architecture styles of highstand and regressive systems tracts. Furthermore, this article highlights the diverse internal and external processes and feedbacks responsible for the development of these intricate marginal marine sedimentary systems. This article is protected by copyright. All rights reserved.
    Print ISSN: 0037-0746
    Electronic ISSN: 1365-3091
    Topics: Geosciences
    Published by Wiley
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  • 4
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    Evidence for a transgressive barrier within a regressive strandplain system: Implications for complex coastal response to environmental change (2012)
    Wiley
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    Publication Date: 2012-09-05
    Description: Clastic, depositional strandplain systems have the potential to record changes in the primary drivers of coastal evolution: climate, sea-level, and the frequency of major meteorological and oceanographic events. This study seeks to use one such record from a southern Brazilian strandplain to highlight the potentially-complex nature of coastal sedimentological response to small changes in these drivers. Following a 2 to 4 m highstand at ca 5·8 ka in southern Brazil, falling sea-level reworked shelf sediment onshore, forcing coastal progradation, smoothing the irregular coastline and forming the 5 km wide Pinheira Strandplain, composed of ca 500 successive beach and dune ridges. Sediment cores, grab samples and 〉11 km of ground-penetrating radar profiles reveal that the strandplain sequence is composed of well-sorted, fine to very-fine quartz sand. Since the mid-Holocene highstand, the shoreline prograded at a rate of ca 1 to 2 m yr −1 through the deposition of a 4 to 6 m thick shoreface unit; a 1 to 3 m thick foreshore unit containing ubiquitous ridge and runnel facies; and an uppermost beach and foredune unit. However, the discovery of a linear, 100 m wide barrier ridge with associated washover units, a 3 to 4 m deep lagoon and 250 m wide tidal inlet within the strandplain sequence reveals a period of shoreline transgression at 3·3 to 2·8 ka during the otherwise regressive developmental history of the plain. The protected nature of Pinheira largely buffered it from changes in precipitation patterns, wave energy and fluvial sediment supply during the time of its formation. However, multiple lines of evidence indicate that a change in the rate of relative sea-level fall, probably due to either steric or ice-volume effects, may have affected this coastline. Thus, whereas these other potential drivers cannot be fully discounted, this study provides insights into the complexity of decadal-scale to millennial-scale coastal response to likely variability in sea-level change rates.
    Print ISSN: 0037-0746
    Electronic ISSN: 1365-3091
    Topics: Geosciences
    Published by Wiley
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  • 5
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    Allee effect promotes diversity in traveling waves [Ecology] (2012)
    National Academy of Sciences
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    Publication Date: 2012-06-06
    Description: Most mathematical studies on expanding populations have focused on the rate of range expansion of a population. However, the genetic consequences of population expansion remain an understudied body of theory. Describing an expanding population as a traveling wave solution derived from a classical reaction-diffusion model, we analyze the spatio-temporal evolution of its genetic structure. We show that the presence of an Allee effect (i.e., a lower per capita growth rate at low densities) drastically modifies genetic diversity, both in the colonization front and behind it. With an Allee effect (i.e., pushed colonization waves), all of the genetic diversity of a population is conserved in the colonization front. In the absence of an Allee effect (i.e., pulled waves), only the furthest forward members of the initial population persist in the colonization front, indicating a strong erosion of the diversity in this population. These results counteract commonly held notions that the Allee effect generally has adverse consequences. Our study contributes new knowledge to the surfing phenomenon in continuous models without random genetic drift. It also provides insight into the dynamics of traveling wave solutions and leads to a new interpretation of the mathematical notions of pulled and pushed waves.
    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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  • 6
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    Transmembrane orientation and possible role of the fusogenic peptide from parainfluenza virus 5 (PIV5) in promoting fusion [Biophysics and Computational Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-03-09
    Description: Membrane fusion is required for diverse biological functions ranging from viral infection to neurotransmitter release. Fusogenic proteins increase the intrinsically slow rate of fusion by coupling energetically downhill conformational changes of the protein to kinetically unfavorable fusion of the membrane–phospholipid bilayers. Class I viral fusogenic proteins have an N-terminal hydrophobic fusion peptide (FP) domain, important for interaction with the target membrane, plus a C-terminal transmembrane (C-term-TM) helical membrane anchor. The role of the water-soluble regions of fusogenic proteins has been extensively studied, but the contributions of the membrane-interacting FP and C-term-TM peptides are less well characterized. Typically, FPs are thought to bind to membranes at an angle that allows helix penetration but not traversal of the lipid bilayer. Here, we show that the FP from the paramyxovirus parainfluenza virus 5 fusogenic protein, F, forms an N-terminal TM helix, which self-associates into a hexameric bundle. This FP also interacts strongly with the C-term-TM helix. Thus, the fusogenic F protein resembles SNARE proteins involved in vesicle fusion by having water-soluble coiled coils that zipper during fusion and TM helices in both membranes. By analogy to mechanosensitive channels, the force associated with zippering of the water-soluble coiled-coil domain is expected to lead to tilting of the FP helices, promoting interaction with the C-term-TM helices. The energetically unfavorable dehydration of lipid headgroups of opposing bilayers is compensated by thermodynamically favorable interactions between the FP and C-term-TM helices as the coiled coils zipper into the membrane phase, leading to a pore lined by both lipid and protein.
    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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  • 7
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    Observation of a narrow structure in ^{1}H(γ,K_{S}^{0})X via interference with φ-meson production (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-03-27
    Description: Author(s): M. J. Amaryan, G. Gavalian, C. Nepali, M. V. Polyakov, Ya. Azimov, W. J. Briscoe, G. E. Dodge, C. E. Hyde, F. Klein, V. Kuznetsov, I. Strakovsky, and J. Zhang We report observation of a narrow peak structure at ∼ 1.54 GeV with a Gaussian width σ   = 6 MeV in the missing mass of K S in the reaction γ + p → p K S K L . The observed structure may be due to the interference between a strange (or antistrange) baryon resonance in the p K L system and the φ ( K S K L ) photoproducti... [Phys. Rev. C 85, 035209] Published Mon Mar 26, 2012
    Keywords: Hadronic Physics and QCD
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 8
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    In silico mapping of complex disease-related traits in mice (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-09
    Description: Experimental murine genetic models of complex human disease show great potential for understanding human disease pathogenesis. To reduce the time required for analysis of such models from many months down to milliseconds, a computational method for predicting chromosomal regions regulating phenotypic traits and a murine database of single nucleotide polymorphisms were developed. After entry of phenotypic information obtained from inbred mouse strains, the phenotypic and genotypic information is analyzed in silico to predict the chromosomal regions regulating the phenotypic trait.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grupe, A -- Germer, S -- Usuka, J -- Aud, D -- Belknap, J K -- Klein, R F -- Ahluwalia, M K -- Higuchi, R -- Peltz, G -- 1 R01 HG02322-01/HG/NHGRI NIH HHS/ -- R01 AR044659/AR/NIAMS NIH HHS/ -- R01 AR044659-07/AR/NIAMS NIH HHS/ -- T32HG-00044/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2001 Jun 8;292(5523):1915-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and Genomics, Roche Bioscience, Palo Alto, CA 94303, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11397946" target="_blank"〉PubMed〈/a〉
    Keywords: *Algorithms ; Animals ; Bone Density ; Chromosome Mapping/*methods ; Crosses, Genetic ; Databases, Factual ; *Disease Models, Animal ; Female ; Genetic Linkage ; Genotype ; Humans ; Linkage Disequilibrium ; Major Histocompatibility Complex/genetics ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred Strains ; Phenotype ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; *Quantitative Trait, Heritable ; Software
    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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  • 9
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    Scientific misconduct investigations: who should conduct them? (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-11-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klein, D F -- New York, N.Y. -- Science. 1991 Nov 15;254(5034):918.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1948072" target="_blank"〉PubMed〈/a〉
    Keywords: *Biomedical Research ; Federal Government ; *Fraud ; Government Agencies ; Government Regulation ; *Social Control, Formal ; United States
    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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  • 10
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    Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-07-19
    Description: Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly neutralizing HIV antibodies that occur naturally have been characterized. To determine whether these antibodies are part of a larger group of related molecules, we cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H (IgH) chain amino acids and arise independently from two related IgH genes. Comparison of the crystal structure of one of the antibodies to the broadly neutralizing antibody VRC01 revealed conservation of the contacts to the HIV spike.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" 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/PMC3351836/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheid, Johannes F -- Mouquet, Hugo -- Ueberheide, Beatrix -- Diskin, Ron -- Klein, Florian -- Oliveira, Thiago Y K -- Pietzsch, John -- Fenyo, David -- Abadir, Alexander -- Velinzon, Klara -- Hurley, Arlene -- Myung, Sunnie -- Boulad, Farid -- Poignard, Pascal -- Burton, Dennis R -- Pereyra, Florencia -- Ho, David D -- Walker, Bruce D -- Seaman, Michael S -- Bjorkman, Pamela J -- Chait, Brian T -- Nussenzweig, Michel C -- P01 AI081677/AI/NIAID NIH HHS/ -- P30 AI060354/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1633-7. doi: 10.1126/science.1207227. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764753" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/*immunology/metabolism ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/immunology/*metabolism ; Binding Sites ; Binding Sites, Antibody ; Cloning, Molecular ; Consensus Sequence ; Crystallography, X-Ray ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/*immunology/metabolism ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; Humans ; Immunoglobulin Fab Fragments/chemistry ; Immunoglobulin Heavy Chains/chemistry ; Immunoglobulin Light Chains/chemistry ; Molecular Mimicry ; Molecular Sequence Data ; Mutation ; Protein Conformation
    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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