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  • 1
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    Automatic detection of low-frequency earthquakes (LFEs) based on a beamformed network response (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-16
    Description: Low-frequency earthquakes (LFEs), which frequently originate from multiplet-generating sources that are closely linked with tectonic tremor in subduction zones around the world, are difficult to observe and characterize due to their low signal-to-noise ratios. This obstacle can be sidestepped by detecting and then stacking all of the multiplets of a master LFE event, or template, using a matched-filter search; the difficulty however lies in finding an LFE event to use as a template. We implement here an automated beamforming algorithm to detect LFEs within the Mexican subduction zone that can then be used as templates in a matched-filter search. Seismograms recorded on a network of seismic stations are aligned to match the moveout of a potential source at depth and their energies are then summed; any spikes in the summed energy indicate an event originating from that potential source. We apply this method to a 1-d test case and we are able to detect 381 unique, potential LFE templates. We then compare our method to a previously introduced LFE detection scheme based on multiplet correlations for three test cases and find that the two methods are complementary.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 2
    Electronic Resource
    Electronic Resource
    Lipid Metabolism (1967)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 36 (1967), S. 247-270 
    Details
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bi.36.070167.001335
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    The Regulation of Glutamine Synthesis in Microorganisms (1970)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Microbiology 24 (1970), S. 501-524 
    Details
    ISSN: 0066-4227
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.mi.24.100170.002441
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular Approaches to The Study of Fertilization (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 50 (1981), S. 815-843 
    Details
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.bi.50.070181.004123
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    Paper (German National Licenses)
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  • 5
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    Genomic Data from Extinct North American Camelops Revise Camel Evolutionary History (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-20
    Description: Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicuñas). These results contradict previous morphology-based phylogenetic models for Camelops , which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Phylogenetic Estimation of Timescales Using Ancient DNA: The Effects of Temporal Sampling Scheme and Uncertainty in Sample Ages (2013)
    Oxford University Press
    Details
    Publication Date: 2013-01-19
    Description: In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci (2013)
    Oxford University Press
    Details
    Publication Date: 2013-02-06
    Description: Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Pycellerator: an arrow-based reaction-like modelling language for biological simulations (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-06
    Description: Motivation: We introduce Pycellerator, a Python library for reading Cellerator arrow notation from standard text files, conversion to differential equations, generating stand-alone Python solvers, and optionally running and plotting the solutions. All of the original Cellerator arrows, which represent reactions ranging from mass action, Michales–Menten–Henri (MMH) and Gene-Regulation (GRN) to Monod–Wyman–Changeaux (MWC), user defined reactions and enzymatic expansions (KMech), were previously represented with the Mathematica extended character set. These are now typed as reaction-like commands in ASCII text files that are read by Pycellerator, which includes a Python command line interface (CLI), a Python application programming interface (API) and an iPython notebook interface. Results: Cellerator reaction arrows are now input in text files. The arrows are parsed by Pycellerator and translated into differential equations in Python, and Python code is automatically generated to solve the system. Time courses are produced by executing the auto-generated Python code. Users have full freedom to modify the solver and utilize the complete set of standard Python tools. The new libraries are completely independent of the old Cellerator software and do not require Mathematica. Availability and implementation: All software is available (GPL) from the github repository at https://github.com/biomathman/pycellerator/releases . Details, including installation instructions and a glossary of acronyms and terms, are given in the Supplementary information . Contact: bruce.e.shapiro@csun.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-31
    Description: Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recent western European neandertals (〈48 kyr) constitute a tightly defined group with low mitochondrial genetic variation in comparison with both eastern and older (〉48 kyr) European neandertals. Using control region sequences, Bayesian demographic simulations provide higher support for a model of population fragmentation followed by separate demographic trajectories in subpopulations over a null model of a single stable population. The most parsimonious explanation for these results is that of a population turnover in western Europe during early Marine Isotope Stage 3, predating the arrival of anatomically modern humans in the region.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Structural complexity of Dengue virus untranslated regions: cis-acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome (2013)
    Oxford University Press
    Details
    Publication Date: 2013-05-04
    Description: The Dengue virus (DENV) genome contains multiple cis -acting elements required for translation and replication. Previous studies indicated that a 719-nt subgenomic minigenome (DENV-MINI) is an efficient template for translation and (–) strand RNA synthesis in vitro . We performed a detailed structural analysis of DENV-MINI RNA, combining chemical acylation techniques, Pb 2+ ion-induced hydrolysis and site-directed mutagenesis. Our results highlight protein-independent 5'–3' terminal interactions involving hybridization between recognized cis -acting motifs. Probing analyses identified tandem dumbbell structures (DBs) within the 3' terminus spaced by single-stranded regions, internal loops and hairpins with embedded GNRA-like motifs. Analysis of conserved motifs and top loops (TLs) of these dumbbells, and their proposed interactions with downstream pseudoknot (PK) regions, predicted an H-type pseudoknot involving TL1 of the 5' DB and the complementary region, PK2. As disrupting the TL1/PK2 interaction, via ‘flipping’ mutations of PK2, previously attenuated DENV replication, this pseudoknot may participate in regulation of RNA synthesis. Computer modeling implied that this motif might function as autonomous structural/regulatory element. In addition, our studies targeting elements of the 3' DB and its complementary region PK1 indicated that communication between 5'–3' terminal regions strongly depends on structure and sequence composition of the 5' cyclization region.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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