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  • 1
    Electronic Resource
    Electronic Resource
    Mineralogy and geochemistry of the Au-Ag ore deposits of the South Korean Peninsula (1986)
    Springer
    Mineralium deposita 21 (1986), S. 234-243 
    Details
    ISSN: 1432-1866
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract Pyrite and arsenopyrite are the predominant ore minerals in the Korean Au-Ag deposits of this study. The X Ni py , X Co py , X Ni apy , and X Co apy values range between 100 and 3,000 ppm, 200 and 6,000 ppm, 200 and 8,200 ppm, and 100 and 10,200 ppm, respectively. Most X Ni py /X Co py values fall in the field lower than values varying 0.16–1.30. Arsenopyrite also tends to prefer cobalt rather than nickel showing X Ni apy /X Co apy values between 0.20 and 1.40. The concentrations of minor elements in ores and gangue minerals vary 1–55 ppm Au and 1–1,120 ppm Ag for the former and 4–57 ppm Ni and 2–45 ppm Co for the latter. The Au/Ag ratio in ore has a good correlation to the Ni/Co ratio of arsenopyrite to gangue. The (Ni/Co)py-(Ni/Co)gangue and (Ni/Co)apy-(Ni/Co)gangue diagrams revealed that the values from the Korean Au-Ag deposits plot in the field lower than 900 °C which is the lowermost temperature determined by previous partitioning experiments.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00199806
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  • 2
    Electronic Resource
    Electronic Resource
    Effect of nitrogen source on biosynthesis of rapamycin by Streptomyces hygroscopicus (1997)
    Springer
    Journal of industrial microbiology and biotechnology 19 (1997), S. 83-86 
    Details
    ISSN: 1476-5535
    Keywords: Keywords: nitrogen nutrition; biosynthesis; rapamycin; immunosuppressants; Streptomyces hygroscopicus; macrolides; lysine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Six non-amino acid nitrogen compounds were examined as nitrogen source for growth of Streptomyces hygroscopicus and biosynthesis of rapamycin. Of the nitrogen sources studied, ammonium sulfate was the best with respect to formation of rapamycin, and supported cell growth comparable to the organic nitrogen sources used in the control chemically defined medium, ie, aspartate, arginine plus histidine. In the new chemically defined medium, which is buffered with 200 mM 2-(N-morpholino)ethanesulfonic acid to prevent decline of pH during fermentation, an ammonium sulfate concentration of 40 mM was optimal for biosynthesis of rapamycin. Rapamycin production increased by more than 30% on both volumetric and specific bases as compared to the previous medium containing the three amino acids as nitrogen source.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/sj.jim.2900434
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  • 3
    Electronic Resource
    Electronic Resource
    C-terminal polypeptides are necessary and sufficient for in vivo targeting of transiently-expressed proteins to peroxisomes in suspension-cultured plant cells (1996)
    Springer
    Protoplasma 195 (1996), S. 156-167 
    Details
    ISSN: 1615-6102
    Keywords: Chloramphenicol acetyltransferase ; Cotton ; Malate synthase ; Microprojectile bombardment ; Peroxisome targeting signals ; Suspension-cultured cells ; Tobacco
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The potential of tobacco BY-2 suspension-cultured cells for examining in vivo targeting and import of proteins into plant peroxisomes was shown recently in our laboratory. In the current study, the necessity and sufficiency of putative C-terminal targeting signals on cottonseed malate synthase and bacterial chloramphenicol acetyl-transferase (CAT) were examined in BY-2 cells. Cotton suspension cells also were evaluated as another in vivo peroxisome targeting system. Ultrastructural views of BY-2 cells showed that the peroxisomes were relatively small (0.1-0.3 μm diameter), a characteristic of so-called “unspecialized” peroxisomes, Peroxisomes in cotton and tobacco cells were identified with anti-cottonseed catalase IgGs as distinct immunofluorescent particles clearly distinguishable from abundant immunofluorescent mitochondria and plastids, marked with antibodies to β-ATPase and stearoyl-ACP Δ 9 desaturase, respectively. The C-terminal ser-lys-leu (SKL) motif is a well-established peroxisome targeting signal (PTS 1) for mammals and yeasts, but not for plants. Antiserum raised against SKL peptides recognized proteins only in peroxisomes in cotton and tobacco cells. The necessity of SKL-COOH for targeting of proteins to plant peroxisomes had not been demonstrated; we showed that SKL-COOH was necessary for directing cottonseed malate synthase to BY-2 peroxisomes. KSRM-COOH, a conservative modification of SKL-COOH, was shown by others to be sufficient for redirecting CAT in stably-transformed Arabidopsis plants to the leaf peroxisomes. Here we show with the same CAT constructs (e.g., pMON316CAT-KSRM) that KSRM is sufficient for targeting transiently-expressed passenger proteins to unspecialized BY-2 peroxisomes. These results provide new direct evidence for the necessity of SKL-COOH (a type 1 PTS) and sufficiency of a conservative modification of the PTS 1 (KSRM-COOH) for in vivo, heterologous targeting of proteins to plant peroxisomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01279194
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  • 4
    Electronic Resource
    Electronic Resource
    Stress concentration at a sharp edge in contact problems (1972)
    Springer
    Journal of elasticity 2 (1972), S. 109-112 
    Details
    ISSN: 1573-2681
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00046059
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  • 5
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    Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-14
    Description: Understanding the evolution of Australia’s extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39–52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46–50 and 40–45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak ), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-02
    Description: Protein–peptide interactions are involved in a wide range of biological processes and are attractive targets for therapeutic purposes because of their small interfaces. Therefore, effective protein–peptide docking techniques can provide the basis for potential therapeutic applications by enabling an atomic-level understanding of protein interactions. With the increasing number of protein–peptide structures deposited in the protein data bank, the prediction accuracy of protein-peptide docking can be enhanced by utilizing the information provided by the database. The GalaxyPepDock web server, which is freely accessible at http://galaxy.seoklab.org/pepdock , performs similarity-based docking by finding templates from the database of experimentally determined structures and building models using energy-based optimization that allows for structural flexibility. The server can therefore effectively model the structural differences between the template and target protein–peptide complexes. The performance of GalaxyPepDock is superior to those of the other currently available web servers when tested on the PeptiDB set and on recently released complex structures. When tested on the CAPRI target 67, GalaxyPepDock generates models that are more accurate than the best server models submitted during the CAPRI blind prediction experiment.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-17
    Description: Molecular evolutionary rate estimates have been shown to depend on the time period over which they are estimated. Factors such as demographic processes, calibration errors, purifying selection, and the heterogeneity of substitution rates among sites (RHAS) are known to affect the accuracy with which rates of evolution are estimated. We use mathematical modeling and Bayesian analyses of simulated sequence alignments to explore how mutational hotspots can lead to time-dependent rate estimates. Mathematical modeling shows that underestimation of molecular rates over increasing time scales is inevitable when RHAS is ignored. Although a gamma distribution is commonly used to model RHAS, we show that when the actual RHAS deviates from a gamma-like distribution, rates can either be under- or overestimated in a time-dependent manner. Simulations performed under different scenarios of RHAS confirm the mathematical modeling and demonstrate the impacts of time-dependent rates on estimates of divergence times. Most notably, erroneous rate estimates can have narrow credibility intervals, leading to false confidence in biased estimates of rates, and node ages. Surprisingly, large errors in estimates of overall molecular rate do not necessarily generate large errors in divergence time estimates. Finally, we illustrate the correlation between time-dependent rate patterns and differential saturation between quickly and slowly evolving sites. Our results suggest that data partitioning or simple nonparametric mixture models of RHAS significantly improve the accuracy with which node ages and substitution rates can be estimated.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Age-dependent gait abnormalities in mice lacking the Rnf170 gene linked to human autosomal-dominant sensory ataxia (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-01
    Description: Really interesting new gene (RING) finger protein 170 (RNF170) is an E3 ubiquitin ligase known to mediate ubiquitination-dependent degradation of type-I inositol 1,4,5-trisphosphate receptors (ITPR1). It has recently been demonstrated that a point mutation of RNF170 gene is linked with autosomal-dominant sensory ataxia (ADSA), which is characterized by an age-dependent increase of walking abnormalities, a rare genetic disorder reported in only two families. Although this mutant allele is known to be dominant, the functional identity thereof has not been clearly established. Here, we generated mice lacking Rnf170 ( Rnf170 –/– ) to evaluate the effect of its loss of function in vivo . Remarkably, Rnf170 –/– mice began to develop gait abnormalities in old age (12 months) in the form of asynchronous stepping between diagonal limb pairs with a fixed step sequence during locomotion, while age-matched wild-type mice showed stable gait patterns using several step sequence repertoires. As reported in ADSA patients, they also showed a reduced sensitivity for proprioception and thermal nociception. Protein blot analysis revealed that the amount of Itpr1 protein was significantly elevated in the cerebellum and spinal cord but intact in the cerebral cortex in Rnf170 –/– mice. These results suggest that the loss of Rnf170 gene function mediates ADSA-associated phenotypes and this gives insights on the cure of patients with ADSA and other age-dependent walking abnormalities.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-20
    Description: Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Rad61/Wpl1 (Wapl), a cohesin regulator, controls chromosome compaction during meiosis (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-21
    Description: Meiosis-specific cohesin, required for the linking of the sister chromatids, plays a critical role in various chromosomal events during meiotic prophase I, such as chromosome morphogenesis and dynamics, as well as recombination. Rad61/Wpl1 (Wapl in other organisms) negatively regulates cohesin functions. In this study, we show that meiotic chromosome axes are shortened in the budding yeast rad61/wpl1 mutant, suggesting that Rad61/Wpl1 negatively regulates chromosome axis compaction. Rad61/Wpl1 is required for efficient resolution of telomere clustering during meiosis I, indicating a positive effect of Rad61/Wpl1 on the cohesin function required for telomere dynamics. Additionally, we demonstrate distinct activities of Rad61/Wpl1 during the meiotic recombination, including its effects on the efficient processing of intermediates. Thus, Rad61/Wpl1 both positively and negatively regulates various cohesin-mediated chromosomal processes during meiosis.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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