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  • 1
    Publication Date: 2016-07-07
    Description: Cryoconite granules are aggregations of microorganisms with mineral particles that form on glacier surfaces. To understand the processes by which the granules develop, this study focused on the altitudinal distribution of the granules and photosynthetic microorganisms on the glacier, bacterial community variation with granules size and environmental factors affecting the growth of the granules. Size-sorted cryoconite granules collected from five different sites on Qaanaaq Glacier were analyzed. C and N contents were significantly higher in large (diameter greater than 250 μm) granules than in smaller (diameter 30–249 μm) granules. Bacterial community structures, based on 16S rRNA gene amplicon sequencing, were different between the smaller and larger granules. The filamentous cyanobacterium Phormidesmis priestleyi was the dominant bacterial species in larger granules. Multivariate analysis suggests that the abundance of mineral particles on the glacier surface is the main factor controlling growth of these cyanobacteria. These results show that the supply of mineral particles on the glacier enhances granule development, that P. priestleyi is likely the key species for primary production and the formation of the granules and that the bacterial community in the granules changes over the course of the granule development.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
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  • 2
    Publication Date: 2015-01-13
    Description: The store-operated Ca 2+ release-activated Ca 2+ (CRAC) channel is activated by diminished luminal Ca 2+ levels in the endoplasmic reticulum and sarcoplasmic reticulum (SR), and constitutes one of the major Ca 2+ entry pathways in various tissues. Tubular aggregates (TAs) are abnormal structures in the skeletal muscle, and although their mechanism of formation has not been clarified, altered Ca 2+ homeostasis related to a disordered SR is suggested to be one of the main contributing factors. TA myopathy is a hereditary muscle disorder that is pathologically characterized by the presence of TAs. Recently, dominant mutations in the STIM1 gene, encoding a Ca 2+ sensor that controls CRAC channels, have been identified to cause tubular aggregate myopathy (TAM). Here, we identified heterozygous missense mutations in the ORAI1 gene, encoding the CRAC channel itself, in three families affected by dominantly inherited TAM with hypocalcemia. Skeletal myotubes from an affected individual and HEK293 cells expressing mutated ORAI1 proteins displayed spontaneous extracellular Ca 2+ entry into cells without diminishment of luminal Ca 2+ or the association with STIM1. Our results indicate that STIM1-independent activation of CRAC channels induced by dominant mutations in ORAI1 cause altered Ca 2+ homeostasis, resulting in TAM with hypocalcemia.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 3
    Publication Date: 2015-07-09
    Description: Motivation: The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell–cell interactions and spatially restricted signalling events. A tightly coupled cell-based mechano-regulatory simulation tool is therefore required. Results: We developed an open-source software framework for morphogenetic problems. The environment offers core functionalities for the tissue and signalling models. In addition, the software offers great flexibility to add custom extensions and biologically motivated processes. Cells are represented as highly resolved, massless elastic polygons; the viscous properties of the tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used to model the interaction between the viscous and elastic properties of the cells, thus extending on the IBCell model. The fluid and signalling processes are solved using the Lattice Boltzmann method. As application examples we simulate signalling-dependent tissue dynamics. Availability and implementation: The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html Contact: simon.tanaka@bsse.ethz.ch or dagmar.iber@bsse.ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 4
    Publication Date: 2012-10-12
    Description: We have used transient electron-beam-induced current (EBIC) to map minority carrier lifetime distributions in multicrystalline Silicon (mc-Si). In this technique, the electron beam from a scanning transmission electron microscope was on–off modulated while the sample was scanned. The resulting transient EBIC was analyzed to form a lifetime map. An analytical function was introduced as part of the analysis in determining this map. We have verified this approach using numerical simulations and have reproduced a lifetime map for an mc-Si wafer.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2015-12-02
    Description: In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2014-01-24
    Description: Animals cloned by somatic cell nuclear transfer (SCNT) provide a unique model for understanding the mechanisms of nuclear epigenetic reprograming to a state of totipotency. Though many phenotypic abnormalities have been demonstrated in cloned animals, the underlying mechanisms are not well understood. In this study, we performed transcriptome-wide allelic expression analyses in brain and placental tissues of cloned mice. We found that Gab1 , Sfmbt2 and Slc38a4 showed loss of imprinting in all cloned mice analyzed, which might be involved in placentomegaly of cloned mice. These three genes did not require de novo DNA methylation in growing oocytes for the establishment of imprinting, implying the involvement of a de novo DNA methylation-independent mechanism. Loss of Dlk1 - Dio3 imprinting was also observed in nearly half of cloned mouse embryos and showed a strong correlation with embryonic lethality. Our findings are essential to understand the underlying mechanisms of developmental abnormalities of cloned animals. We also emphasize that particular attention should be paid to specific imprinted genes for therapeutic and agricultural applications of SCNT.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2014-03-27
    Description: Glioblastomas frequently harbour genetic lesions that stimulate the activity of mammalian target of rapamycin complex 1 (mTORC1). Loss of heterozygosity of tuberous sclerosis complex 1 ( TSC1 ) or TSC2 , which together form a critical negative regulator of mTORC1, is also seen in glioblastoma; however, it is not known how loss of the TSC complex affects the development of malignant gliomas. Here we investigated the role of Tsc1 in gliomagenesis in mice. Tsc1 deficiency up-regulated mTORC1 activity and suppressed the proliferation of neural stem/progenitor cells (NSPCs) in a serial neurosphere-forming assay, suggesting that Tsc1 -deficient NSPCs have defective self-renewal activity. The neurosphere-forming capacity of Tsc1 -deficient NSPCs was restored by p16 Ink4a p19 Arf deficiency. Combined Tsc1 and p16 Ink4a p19 Arf deficiency in NSPCs did not cause gliomagenesis in vivo . However, in a glioma model driven by an active mutant of epidermal growth factor receptor (EGFR), EGFRvIII, loss of Tsc1 resulted in an earlier onset of glioma development. The mTORC1 hyperactivation by Tsc1 deletion accelerated malignant phenotypes, including increased tumour mass and enhanced microvascular formation, leading to intracranial haemorrhage. These data demonstrate that, although mTORC1 hyperactivation itself may not be sufficient for gliomagenesis, it is a potent modifier of glioma development when combined with oncogenic signals.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 8
    Publication Date: 2014-11-07
    Description: The 127 station NorthEast China Extended SeiSmic Array (NECESSArray) provides large quantities of high quality seismic data in northeast China that allow us to resolve lateral variations of Lg Q or crustal attenuation at 1 Hz ( Q o ) to 2.0° or greater. Using the reverse two-station/event method with 11 642 Lg path-amplitudes from 78 crustal earthquakes, we obtain a 2-D tomographic image of Lg Q o with values ranging from ~50 to 1400. A high degree of detail in the lateral variation of Lg attenuation is revealed in our tomographic image. High Q o regions are found in the Great Xing'an, Lesser Xing'an and Songen-Zhangguangcai Ranges. Low Q o regions are observed in the Songliao, Sanjiang and Erlian Basins. The lowest Q o is found near the Wudalianchi volcanic field and other Quaternary volcanic fields, the southern Songliao Basin, the western edge of the Erlian Basin and the Sanjiang Basin. Low Q o values are measured for paths that cross sedimentary basins with thick, unconsolidated sediments. Most of the high Lg attenuation in the Songliao Basin correlates reasonably well with low crustal Rayleigh wave phase velocity anomalies. The highest attenuating regions also correlate well with regions of Holocene volcanism.
    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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  • 9
    Publication Date: 2014-12-25
    Description: We examine P -wave velocity structure at the base of the mantle beneath the western Pacific, near the western edge of the Pacific Large-Low Shear Velocity Province (LLSVP), using high-quality seismograms provided by a large-scale mobile broad-band seismic observation in northeastern China (the NECESSArray project). Forward modelling using the reflectivity method is conducted to explain the variation of P -wave traveltimes as a function of epicentral distance near the core shadow zone. Additionally, PcP–P traveltimes are examined to enlarge the survey area. As a result, a rapid variation of P -wave velocity is detected at the base of the mantle. Regions of thin (20–50 km thick) and low velocity (–2 to –5 per cent) layers at the base of the mantle are intersected by an 80-km-thick region with a high velocity (+2 per cent). A slightly fast region exists at the northwest of the region with the thin low-velocity layer. These layers are typically separated by several hundred kilometres and would be difficult to explain by thermal effects alone. These observations suggest that very complicated thermochemical reactions occur near the edge of the Pacific LLSVP.
    Keywords: Seismology
    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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  • 10
    Publication Date: 2014-08-03
    Description: We have fabricated a simple detector for backscattered electrons (BSEs) and incorporated the detector into a scanning transmission electron microscope (STEM) sample holder. Our detector was made from a 4-mm 2 Si chip. The fabrication procedure was easy, and similar to a standard transmission electron microscopy (TEM) sample thinning process based on ion milling. A TEM grid containing particle objects was fixed to the detector with a silver paste. Observations were carried out using samples of Au and latex particles at 75 and 200 kV. Such a detector provides an easy way to obtain BSE images in an STEM.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
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