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  • 1
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    An Exploration into Fern Genome Space (2015)
    Oxford University Press
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    Publication Date: 2015-09-19
    Description: Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to 2X) for six fern species from the Polypodiales ( Ceratopteris , Pteridium , Polypodium , Cystopteris ), Cyatheales ( Plagiogyria ), and Gleicheniales ( Dipteris ). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Improved Results of Impossible Differential Cryptanalysis on Reduced FOX (2016)
    Oxford University Press
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    Publication Date: 2016-03-29
    Description: FOX is a family of block ciphers published in 2004 and several attacks on reduced FOX have been published, and the best known attacks are on 7-round FOX64 and 5-round FOX128. In this paper, we present impossible differential attacks on 8-round FOX64 and 6-round FOX128 with various techniques such as the multiple differentials, the state-test technique, the quick sort method and the early abort technique. For 8-round FOX64, the data complexity and the time complexity is $2^{42}$ and $2^{239.54}$ one-round encryptions, respectively, and the memory required is $2^{44}$ bytes. For 6-round FOX128, the data complexity and the time complexity is $2^{75}$ and $2^{209.55}$ one-round encryptions, respectively, and the memory required is $2^{77}$ bytes.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 3
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    Constraining FeLoBAL outflows from absorption line variability (2015)
    Oxford University Press
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    Publication Date: 2015-08-27
    Description: Iron low-ionization broad absorption lines (FeLoBALs) trace a rare class of quasar outflows with large column densities and potentially large kinetic energies that might be important for ‘feedback’ to galaxy evolution. In order to probe the physical properties of these outflows, we conducted a multiple-epoch, absorption line variability study of 12 FeLoBAL quasars spanning a redshift range of 0.7 ≤  z  ≤ 1.9 over rest-frame time-scales of ~10 d to 7.6 yr. We detect absorption line variability with ≥8 confidence in 3 out of the 12 sources in our sample over time-scales of ~0.6 to 7.6 yr. Variable wavelength intervals are associated with ground- and excited-state Fe  ii multiplets, the Mg  ii 2796, 2803 doublet, Mg  i 2852, and excited-state Ni  ii multiplets. The observed variability along with evidence of saturation in the absorption lines favours transverse motions of gas across the line of sight as the preferred scenario, and allows us to constrain the outflow distance from the supermassive black hole to be 69, 7, and 60 pc for our three variable sources. In combination with other studies, these results suggest that the outflowing gas in FeLoBAL quasars resides on a range of scales and includes matter within tens of parsecs of the central source.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content (2016)
    Oxford University Press
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    Publication Date: 2016-08-27
    Description: Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution. Here we examine four loci ( psbA , ycf2 , rps7 , and rps12 exon 2–3) that were translocated from the SC into the IR during fern evolution. We use a model-based method, within a phylogenetic context, to test for substitution rate shifts. All four loci show a significant, 2- to 3-fold deceleration in their substitution rate following translocation into the IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we show that after translocation, the GC content of the third codon position and of the noncoding regions is significantly increased, implying that gene conversion within the IR is GC-biased. Taken together, our results suggest that the IR region not only reduces substitution rates, but also impacts nucleotide composition. This finding highlights a potential vulnerability of correlating substitution rate heterogeneity with organismal life history traits without knowledge of the underlying genome structure.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Long-term photometry of IC 348 with the Young Exoplanet Transit Initiative network (2016)
    Oxford University Press
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    Publication Date: 2016-08-24
    Description: We present long-term photometric observations of the young open cluster IC 348 with a baseline time-scale of 2.4 yr. Our study was conducted with several telescopes from the Young Exoplanet Transit Initiative (YETI) network in the Bessel R band to find periodic variability of young stars. We identified 87 stars in IC 348 to be periodically variable; 33 of them were unreported before. Additionally, we detected 61 periodic non-members of which 41 are new discoveries. Our wide field of view was the key to those numerous newly found variable stars. The distribution of rotation periods in IC 348 has always been of special interest. We investigate it further with our newly detected periods but we cannot find a statistically significant bimodality. We also report the detection of a close eclipsing binary in IC 348 composed of a low-mass stellar component ( M 0.09 M ) and a K0 pre-main-sequence star ( M 2.7 M ). Furthermore, we discovered three detached binaries among the background stars in our field of view and confirmed the period of a fourth one.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Eastern Baltic cod in distress: biological changes and challenges for stock assessment (2015)
    Oxford University Press
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    Publication Date: 2015-10-22
    Description: The eastern Baltic (EB) cod ( Gadus morhua ) stock was depleted and overexploited for decades until the mid-2000s, when fishing mortality rapidly declined and biomass started to increase, as shown by stock assessments. These positive developments were partly assigned to effective management measures, and the EB cod was considered one of the most successful stock recoveries in recent times. In contrast to this optimistic view, the analytical stock assessment failed in 2014, leaving the present stock status unclear. Deteriorated quality of some basic input data for stock assessment in combination with changes in environmental and ecological conditions has led to an unusual situation for cod in the Baltic Sea, which poses new challenges for stock assessment and management advice. A number of adverse developments such as low nutritional condition and disappearance of larger individuals indicate that the stock is in distress. In this study, we (i) summarize the knowledge of recent changes in cod biology and ecosystem conditions, (ii) describe the subsequent challenges for stock assessment, and (iii) highlight the key questions where answers are urgently needed to understand the present stock status and provide scientifically solid support for cod management in the Baltic Sea.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 7
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    Intact neuronal function in Rheb1 mutant mice: implications for TORC1-based treatments (2015)
    Oxford University Press
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    Publication Date: 2015-05-20
    Description: Target of rapamycin complex 1 (TORC1) is an important regulator of neuronal function. However, whereas a modest activation of the TORC1 signaling pathway has been shown to affect synaptic plasticity, learning and memory, the effect of TORC1 hypo-activation is less clear. This knowledge is particularly important since TORC1 inhibitors may hold great promise for treating a variety of disorders, including developmental disorders, aging-related disorders, epilepsy and cancer. Such treatments are likely to be long lasting and could involve treating young children. Hence, it is pivotal that the effects of sustained TORC1 inhibition on brain development and cognitive function are determined. Here, we made use of constitutive and conditional Rheb1 mutant mice to study the effect of prolonged and specific reduction in the TORC1 pathway. We show that Rheb1 mutant mice show up to 75% reduction in TORC1 signaling, but develop normally and show intact synaptic plasticity and hippocampus-dependent learning and memory. We discuss our findings in light of current literature in which the effect of pharmacological inhibition of TORC1 is studied in the context of synaptic plasticity and learning. We conclude that in contrast to TORC1 hyper-activity, cognitive function is not very sensitive to sustained and specific down-regulation of TORC1 activity.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Optical and Sunyaev-Zel'dovich observations of a new sample of distant rich galaxy clusters in the ROSAT All Sky (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-23
    Description: Finding a sample of the most massive clusters with redshifts z  〉 0.6 can provide an interesting consistency check of the cold dark matter (CDM) model. Here, we present results from our search for clusters with 0.6   z   1.0 where the initial candidates were selected by cross-correlating the ROSAT All Sky Survey (RASS) faint and bright source catalogues with red galaxies from the Sloan Digital Sky Survey DR8. Our survey thus covers 10 000 deg 2 , much larger than previous studies of this kind. Deeper follow-up observations in three bands using the William Herschel Telescope and the Large Binocular Telescope were performed to confirm the candidates, resulting in a sample of 44 clusters for which we present richnesses and red sequence redshifts, as well as spectroscopic redshifts for a subset. At least two of the clusters in our sample are comparable in richness to RCS2- J 232727.7–020437, one of the richest systems discovered to date. We also obtained new observations with the Combined Array for Research in Millimeter Astronomy for a subsample of 21 clusters. For 11 of those we detect the Sunyaev–Zel'dovich effect signature. The Sunyaev–Zel'dovich signal allows us to estimate M 200 and check for tension with the cosmological standard model. We find no tension between our cluster masses and the CDM model.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Expression of progerin in aging mouse brains reveals structural nuclear abnormalities without detectible significant alterations in gene expression, hippocampal stem cells or behavior (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-10
    Description: Hutchinson–Gilford progeria syndrome (HGPS) is a segmental progeroid syndrome with multiple features suggestive of premature accelerated aging. Accumulation of progerin is thought to underlie the pathophysiology of HGPS. However, despite ubiquitous expression of lamin A in all differentiated cells, the HGPS mutation results in organ-specific defects. For example, bone and skin are strongly affected by HGPS, while the brain appears to be unaffected. There are no definite explanations as to the variable sensitivity to progeria disease among different organs. In addition, low levels of progerin have also been found in several tissues from normal individuals, but it is not clear if low levels of progerin contribute to the aging of the brain. In an attempt to clarify the origin of this phenomenon, we have developed an inducible transgenic mouse model with expression of the most common HGPS mutation in brain, skin, bone and heart to investigate how the mutation affects these organs. Ultrastructural analysis of neuronal nuclei after 70 weeks of expression of the LMNA c.1824C〉T mutation showed severe distortion with multiple lobulations and irregular extensions. Despite severe distortions in the nuclei of hippocampal neurons of HGPS animals, there were only negligible changes in gene expression after 63 weeks of transgenic expression. Behavioral analysis and neurogenesis assays, following long-term expression of the HGPS mutation, did not reveal significant pathology. Our results suggest that certain tissues are protected from functional deleterious effects of progerin.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Reproducing the spectral energy distribution of PKS 1424+240: the role of automatic photon quenching (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-28
    Description: We present a one-zone homogeneous self-consistent model for the multiwavelength emission features of PKS 1424+240 that allows the effects of automatic photon quenching to be studied. In the model, a steady -ray injection rate in the source is assumed and the non-linear time-dependent kinematic equations describing the evolution of both electrons and photons are then acquired; these self-consistently involve photon–photon interaction, synchrotron radiation of electron/positron pairs, inverse Compton scattering and synchrotron self-absorption. The model is applied to reproduce the multiwavelength spectrum of PKS 1424+240; our results indicate that the observed spectral energy distribution (SED) of PKS 1424+240 can be reproduced well in the case of both electron injection and photon injection. The injected electrons mainly influence the SED over radio, optical and X-ray bands and the SED in the high-energy -ray band is determined mainly by automatic photon quenching; in particular, the break form of the spectrum in the energy range ≥ a few GeV is caused by this. It should be noted that the observed SED from X-ray to -ray bands can be reproduced only through quenching, provided the observed data in the optical band are produced through some other mechanism, e.g. electron synchrotron radiation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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