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  • Oxford University Press  (86)
  • American Association for the Advancement of Science (AAAS)  (46)
  • International Union of Crystallography  (11)
  • 1
    Publikationsdatum: 2015-10-18
    Beschreibung: Dicer-2 is the central player for small interfering RNA biogenesis in the Drosophila RNA interference (RNAi) pathway. Intriguingly, we found that Dicer-2 has an unconventional RNAi-independent function that positively modulates Toll immune signaling, which defends against Gram-positive bacteria, fungi, and some viruses, in both cells and adult flies. The loss of Dicer-2 expression makes fruit flies more susceptible to fungal infection. We further revealed that Dicer-2 posttranscriptionally modulates Toll signaling because Dicer-2 is required for the proper expression of Toll protein but not for Toll protein stability or Toll mRNA transcription. Moreover, Dicer-2 directly binds to the 3' untranslated region (3'UTR) of Toll mRNA via its PAZ (Piwi/Argonaute/Zwille) domain and is required for protein translation mediated by Toll 3'UTR. The loss of Toll 3'UTR binding activity makes Dicer-2 incapable of promoting Toll signaling. These data indicate that the interaction between Dicer-2 and Toll mRNA plays a pivotal role in Toll immune signaling. In addition, we found that Dicer-2 is also required for the Toll signaling induced by two different RNA viruses in Drosophila cells. Consequently, our findings uncover a novel RNAi-independent function of Dicer-2 in the posttranscriptional regulation of Toll protein expression and signaling, indicate an unexpected intersection of the RNAi pathway and the Toll pathway, and provide new insights into Toll immune signaling, Drosophila Dicer-2, and probably Dicer and Dicer-related proteins in other organisms.
    Digitale ISSN: 2375-2548
    Thema: Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2014-03-13
    Beschreibung: Natural transformation (NT) in bacteria is a complex process, including binding, uptake, transport and recombination of exogenous DNA into the chromosome, consequently generating genetic diversity and driving evolution. DNA processing protein A (DprA), which is distributed among virtually all bacterial species, is involved in binding to the internalized single-stranded DNA (ssDNA) and promoting the loading of RecA on ssDNA during NTs. Here we present the structures of DNA_processg_A (DprA) domain of the Helicobacter pylori DprA (HpDprA) and its complex with an ssDNA at 2.20 and 1.80 Å resolutions, respectively. The complex structure revealed for the first time how the conserved DprA domain binds to ssDNA. Based on structural comparisons and binding assays, a unique ssDNA-binding mode is proposed: the dimer of HpDprA binds to ssDNA through two small, positively charged binding pockets of the DprA domains with classical Rossmann folds and the key residue Arg52 is re-oriented to ‘open’ the pocket in order to accommodate one of the bases of ssDNA, thus enabling HpDprA to grasp substrate with high affinity. This mode is consistent with the oligomeric composition of the complex as shown by electrophoretic mobility-shift assays and static light scattering measurements, but differs from the direct polymeric complex of Streptococcus pneumoniae DprA–ssDNA.
    Print ISSN: 0305-1048
    Digitale ISSN: 1362-4962
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2018-09-21
    Beschreibung: Perovskite solar cells (PSCs) have witnessed rapidly rising power conversion efficiencies, together with advances in stability and upscaling. Despite these advances, their limited stability and need to prove upscaling remain crucial hurdles on the path to commercialization. We summarize recent advances toward commercially viable PSCs and discuss challenges that remain. We expound the development of standardized protocols to distinguish intrinsic and extrinsic degradation factors in perovskites. We review accelerated aging tests in both cells and modules and discuss the prediction of lifetimes on the basis of degradation kinetics. Mature photovoltaic solutions, which have demonstrated excellent long-term stability in field applications, offer the perovskite community valuable insights into clearing the hurdles to commercialization.
    Schlagwort(e): Physics, Applied, Chemistry, Online Only
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Geologie und Paläontologie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2016-07-21
    Beschreibung: An exact analytical solution is presented for the effective dynamic transverse shear modulus in a heterogeneous fluid-filled porous solid containing cylindrical inclusions. The complex and frequency-dependent properties of the dynamic shear modulus are caused by the physical mechanism of mesoscopic-scale wave-induced fluid flow whose scale is smaller than wavelength but larger than the size of pores. Our model consists of three phases: a long cylindrical inclusion, a cylindrical shell of poroelastic matrix material with different mechanical and/or hydraulic properties than the inclusion and an outer region of effective homogeneous medium of laterally infinite extent. The behavior of both the inclusion and the matrix is described by Biot's consolidation equations, whereas the surrounding effective medium which is used to describe the effective transverse shear properties of the inner poroelastic composite is assumed to be a viscoelastic solid whose complex transverse shear modulus needs to be determined. The determined effective transverse shear modulus is used to quantify the S -wave attenuation and velocity dispersion in heterogeneous fluid-filled poroelastic rocks. The calculation shows the relaxation frequency and relative position of various fluid saturation dispersion curves predicted by this study exhibit very good agreement with those of a previous 2-D finite-element simulation. For the double-porosity model (inclusions having a different solid frame than the matrix but the same pore fluid as the matrix) the effective shear modulus also exhibits a size-dependent characteristic that the relaxation frequency moves to lower frequencies by two orders of magnitude if the radius of the cylindrical poroelastic composite increases by one order of magnitude. For the patchy-saturation model (inclusions having the same solid frame as the matrix but with a different pore fluid from the matrix), the heterogeneity in pore fluid cannot cause any attenuation in the transverse shear modulus at all. A comparison with the case of spherical inclusions illustrates that the transverse shear modulus for the cylindrical inclusion exhibits more S -wave attenuation than spherical inclusions.
    Schlagwort(e): Seismology
    Print ISSN: 0956-540X
    Digitale ISSN: 1365-246X
    Thema: Geologie und Paläontologie
    Publiziert von Oxford University Press im Namen von The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2013-09-18
    Beschreibung: This paper is concerned with the issue of passivity analysis for switched generalized neural networks (SGNNs). Parametric uncertainty is considered and assumed to be time-variant and norm bounded. We first give the passivity condition for SGNNs without uncertainties, and then extend the result to the cases with time-varying parametric uncertainties both in network parameters and output matrices. By using the Lyapunov–Krasovskii functional and some analysis techniques, the passivity criteria are presented in terms of linear matrix inequalities. Two numerical examples are given to show the effectiveness of the theoretical results.
    Print ISSN: 0265-0754
    Digitale ISSN: 1471-6887
    Thema: Mathematik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2016-09-02
    Beschreibung: Motivation: How chromatin folds in three-dimensional (3D) space is closely related to transcription regulation. As powerful tools to study such 3D chromatin conformation, the recently developed Hi-C technologies enable a genome-wide measurement of pair-wise chromatin interaction. However, methods for the detection of biologically meaningful chromatin interactions, i.e. peak calling, from Hi-C data, are still under development. In our previous work, we have developed a novel hidden Markov random field (HMRF) based Bayesian method, which through explicitly modeling the non-negligible spatial dependency among adjacent pairs of loci manifesting in high resolution Hi-C data, achieves substantially improved robustness and enhanced statistical power in peak calling. Superior to peak callers that ignore spatial dependency both methodologically and in performance, our previous Bayesian framework suffers from heavy computational costs due to intensive computation incurred by modeling the correlated peak status of neighboring loci pairs and the inference of hidden dependency structure. Results: In this work, we have developed FastHiC, a novel approach based on simulated field approximation, which approximates the joint distribution of the hidden peak status by a set of independent random variables, leading to more tractable computation. Performance comparisons in real data analysis showed that FastHiC not only speeds up our original Bayesian method by more than five times, bus also achieves higher peak calling accuracy. Availability and Implementation: FastHiC is freely accessible at: http://www.unc.edu/~yunmli/FastHiC/ Contacts : yunli@med.unc.edu or ming.hu@nyumc.org Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2015-06-07
    Beschreibung: We report superconductivity and magnetism in a new family of topological semimetals, the ternary half-Heusler compound R PdBi ( R : rare earth). In this series, tuning of the rare earth f -electron component allows for simultaneous control of both lattice density via lanthanide contraction and the strength of magnetic interaction via de Gennes scaling, allowing for a unique tuning of the normal-state band inversion strength, superconducting pairing, and magnetically ordered ground states. Antiferromagnetism with ordering vector (1/2,1/2,1/2) occurs below a Néel temperature that scales with de Gennes factor dG, whereas a superconducting transition is simultaneously supressed with increasing dG . With superconductivity appearing in a system with noncentrosymmetric crystallographic symmetry, the possibility of spin-triplet Cooper pairing with nontrivial topology analogous to that predicted for the normal-state electronic structure provides a unique and rich opportunity to realize both predicted and new exotic excitations in topological materials.
    Digitale ISSN: 2375-2548
    Thema: Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2015-01-13
    Beschreibung: Hypertension is a common disorder and the leading risk factor for cardiovascular disease and premature deaths worldwide. Genome-wide association studies (GWASs) in the European population have identified multiple chromosomal regions associated with blood pressure, and the identified loci altogether explain only a small fraction of the variance for blood pressure. The differences in environmental exposures and genetic background between Chinese and European populations might suggest potential different pathways of blood pressure regulation. To identify novel genetic variants affecting blood pressure variation, we conducted a meta-analysis of GWASs of blood pressure and hypertension in 11 816 subjects followed by replication studies including 69 146 additional individuals. We identified genome-wide significant ( P 〈 5.0 x 10 –8 ) associations with blood pressure, which included variants at three new loci ( CACNA1D , CYP21A2 , and MED13L ) and a newly discovered variant near SLC4A7 . We also replicated 14 previously reported loci, 8 ( CASZ1 , MOV10 , FGF5 , CYP17A1 , SOX6 , ATP2B1 , ALDH2 , and JAG1 ) at genome-wide significance, and 6 ( FIGN , ULK4 , GUCY1A3 , HFE , TBX3-TBX5 , and TBX3 ) at a suggestive level of P = 1.81 x 10 –3 to 5.16 x 10 –8 . These findings provide new mechanistic insights into the regulation of blood pressure and potential targets for treatments.
    Print ISSN: 0964-6906
    Digitale ISSN: 1460-2083
    Thema: Biologie , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2013-01-17
    Beschreibung: The antipredatory responses/attachment behaviour of the green-lipped mussel Perna viridi s were studied under combined stresses of hypoxia and low salinity in the presence/absence of its predator, the swimming crab Thalamita danae . There were two oxygen concentrations (1.5 mg l –1 O 2 = hypoxic and 6.0 mg l –1 O 2 = normoxic) and two salinity levels (15 = low, 30 = normal). Byssus production performances (including byssal-thread number, byssal-thread diameter, byssal-thread length, cumulative byssal-thread length and volume and frequency of stalk-shedding) were evaluated after 48 h. All variables were significantly affected by dissolved oxygen (DO), salinity and predator presence. Interactive effects of these three factors on byssus production were also observed. Byssus production and frequency of stalk-shedding were lowest in hypoxia x low salinity, followed by normoxia x low salinity, hypoxia x normal salinity, while normoxia x normal salinity exhibited the highest values in both predator-presence and non-predator-presence groups. At each treatment of DO and salinity, all parameters in predator-presence groups were significantly higher than in non-predator-presence groups. Our results indicate that the environmental hypoxia and low salinity impair anti-predatory/attachment behaviour and show some synergistic effects. Since reduced byssus production makes the mussels more vulnerable to crab predators, the co-occurrence of hypoxia and low salinity may increase the rates of crab predation on P. viridi s in the field.
    Print ISSN: 0260-1230
    Digitale ISSN: 1464-3766
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2013-02-02
    Beschreibung: Doubly hidden Markov models (DHMMs) have been widely used to analyze a type of time process whose driving factors are hierarchical and hierarchically correlated. A common issue of these models is that they implicitly assume that the dwell time of any system state is constant or exponentially distributed. This property comes from the standard hidden Markov models and causes the DHMM to limitations in some actual application environment, where an application has latent temporal structure and does not follow the exponential distribution but has the period-like or variable-period feature. Such problems are frequently encountered in practice, e.g. network traffic. In this paper, we remove this limitation by a new structural discrete approach named nested hidden semi-Markov model. The proposed model includes a nested latent semi-Markov chain and one observable discrete stochastic process. The bottom latent semi-Markov chain is the core layer and controls the second-layer semi-Markov chain that generates the observable process. The state duration of both the semi-Markov chains can be variable or explicit. The model makes no assumptions on the distribution of the state-duration and the observable processes. An efficient forward and backward recursion procedure is developed for estimating the generator of the proposed model and inferring the underlying state processes for a given observation sequence. To evaluate the performance of the proposed model, we apply the model to the arrival process of network traffic and compare its simulation traffic and the real traffic. The performance evaluation in the experiments includes time dynamic process, auto-correlation, cross-correlation, statistical distribution and self-similarity.
    Print ISSN: 0010-4620
    Digitale ISSN: 1460-2067
    Thema: Informatik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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