R-vine Models for Spatial Time Series with an Application to Daily Mean Temperature

We introduce an extension of R-vine copula models for the purpose of spatial dependency modeling and model based prediction at unobserved locations. The newly derived spatial R-vine model combines the flexibility of vine copulas with the classical geostatistical idea of modeling spatial dependencies by means of the distances between the variable locations. In particular the model is able to capture non-Gaussian spatial dependencies. For the purpose of model development and as an illustration we consider daily mean temperature data observed at 54 monitoring stations in Germany. We identify a relationship between the vine copula parameters and the station distances and exploit it in order to reduce the huge number of parameters needed to parametrize a 54-dimensional R-vine model needed to fit the data. The new distance based model parametrization results in a distinct reduction in the number of parameters and makes parameter estimation and prediction at unobserved locations feasible. The prediction capabilities are validated using adequate scoring techniques, showing a better performance of the spatial R-vine copula model compared to a Gaussian spatial model.Comment: 28 pages, 10 figure

A New Multielement Method for LA-ICP-MS Data Acquisition From Glacier Ice Cores

To answer pressing new research questions about the rate and timing of abrupt climate transitions, a robust system for ultrahigh-resolution sampling of glacier ice is needed. Here, we present a multielement method of LA-ICP-MS analysis wherein an array of chemical elements is simultaneously measured from the same ablation area. Although multielement techniques are commonplace for high-concentration materials, prior to the development of this method, all LA-ICP-MS analyses of glacier ice involved a single element per ablation pass or spot. This new method, developed using the LA-ICP-MS system at the W. M. Keck Laser Ice Facility at the University of Maine Climate Change Institute, has already been used to shed light on our flawed understanding of natural levels of Pb in Earth?s atmospherepublishersversionPeer reviewe

A New Multielement Method for LA-ICP-MS Data Acquisition from Glacier Ice Cores

To answer pressing new research questions about the rate and timing of abrupt climate transitions, a robust system for ultrahigh-resolution sampling of glacier ice is needed. Here, we present a multielement method of LA-ICP-MS analysis wherein an array of chemical elements is simultaneously measured from the same ablation area. Although multielement techniques are commonplace for high-concentration materials, prior to the development of this method, all LA-ICP-MS analyses of glacier ice involved a single element per ablation pass or spot. This new method, developed using the LA-ICP-MS system at the W. M. Keck Laser Ice Facility at the University of Maine Climate Change Institute, has already been used to shed light on our flawed understanding of natural levels of Pb in Earth?s atmospherepublishersversionPeer reviewe

New LA-ICP-MS cryocell and calibration technique for sub-millimeter analysis of ice cores

Ice cores provide a robust reconstruction of past climate. However, development of timescales by annual-layer counting, essential to detailed climate reconstruction and interpretation, on ice cores collected at low-accumulation sites or in regions of compressed ice, is problematic due to closely spaced layers. Ice-core analysis by laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) provides sub-millimeter-scale sampling resolution (on the order of 100μm in this study) and the low detection limits (ng L–1) necessary to measure the chemical constituents preserved in ice cores. We present a newly developed cryocell that can hold a 1m long section of ice core, and an alternative strategy for calibration. Using ice-core samples from central Greenland, we demonstrate the repeatability of multiple ablation passes, highlight the improved sampling resolution, verify the calibration technique and identify annual layers in the chemical profile in a deep section of an ice core where annual layers have not previously been identified using chemistry. In addition, using sections of cores from the Swiss/Italian Alps we illustrate the relationship between Ca, Na and Fe and particle concentration and conductivity, and validate the LA-ICP-MS Ca profile through a direct comparison with continuous flow analysis results

A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum.

Many bacteria move using a complex, self-assembling nanomachine, the bacterial flagellum. Biosynthesis of the flagellum depends on a flagellar-specific type III secretion system (T3SS), a protein export machine homologous to the export machinery of the virulence-associated injectisome. Six cytoplasmic (FliH/I/J/G/M/N) and seven integral-membrane proteins (FlhA/B FliF/O/P/Q/R) form the flagellar basal body and are involved in the transport of flagellar building blocks across the inner membrane in a proton motive force-dependent manner. However, how the large, multi-component transmembrane export gate complex assembles in a coordinated manner remains enigmatic. Specific for most flagellar T3SSs is the presence of FliO, a small bitopic membrane protein with a large cytoplasmic domain. The function of FliO is unknown, but homologs of FliO are found in >80% of all flagellated bacteria. Here, we demonstrate that FliO protects FliP from proteolytic degradation and promotes the formation of a stable FliP-FliR complex required for the assembly of a functional core export apparatus. We further reveal the subcellular localization of FliO by super-resolution microscopy and show that FliO is not part of the assembled flagellar basal body. In summary, our results suggest that FliO functions as a novel, flagellar T3SS-specific chaperone, which facilitates quality control and productive assembly of the core T3SS export machinery

FliP protein is unstable in the absence of FliO.

<p>(A) FliP protein stability in the presence and absence of FliO. Protein levels of chromosomally expressed FliP-3×FLAG were monitored at 0, 60, 120, and 180 min after arrest of de novo protein synthesis. Wild-type (WT) (EM2225), Δ<i>fliO</i> (EM3201). FliP protein levels were normalized to DnaK, and relative FliP levels report the mean ± SD, <i>n</i> = 6. (B) Stability of episomally expressed FliP-3×HA protein in Δ<i>fliP</i> and Δ<i>fliOP</i> mutants after arrest of de novo protein synthesis. Δ<i>fliP</i> + p<i>fliP</i> (TH17448), Δ<i>fliOP</i> + p<i>fliP</i> (EM1610). Relative FliP levels report the mean ± SD, <i>n</i> = 3. (C) Protein stability of chromosomally expressed FliP-3×HA in presence or absence of FliO in the WT (TH17323), Δ<i>fliO</i> (EM1274), Δ<i>clpXP</i> (EM4018), Δ<i>clpXP</i> Δ<i>fliO</i> (EM4019), Δ<i>lon</i> (EM4478), and Δ<i>lon</i> Δ<i>fliO</i> (EM4479) mutants.</p

Subcellular localization of FliO revealed by structured illumination microscopy.

<p>The subcellular localization of FliO-HaloTag (A) or FliN-HaloTag (B) fusions expressed from their native chromosomal locus was analyzed in the wild-type (WT) and mutant backgrounds defective in MS-ring assembly (Δ<i>fliF</i>) or flagellar-specific type III secretion system (fT3SS) function (Δ<i>flhBAE</i>). WT FliO-HaloTag (EM1077), WT FliN-HaloTag (EM1081), Δ<i>fliF</i> FliO-HaloTag (EM6254), Δ<i>fliF</i> FliN-HaloTag (EM2640), Δ<i>flhBAE</i> FliO-HaloTag (EM6256), and Δ<i>flhBAE</i> FliN-HaloTag (EM6258). Strains were treated with 20 nM HaloTag ligands (HTL tetramethylrhodamine [TMR]) and observed using structured illumination microscopy (SIM). The autofluorescence of bacteria upon excitation with a 488 nm laser is shown in the middle panels. Scale bar 2 μm.</p

Single-particle tracking of FliO and colocalization with the flagellar basal body.

<p>(A) Strains expressing chromosomal FliN-HaloTag (EM1081) or FliO-HaloTag (EM1077) fusions were treated with 20 nM HaloTag ligands (HTL tetramethylrhodamine [TMR]) and analyzed by total internal reflection fluorescence (TIRF) microscopy. As described before, 500 frames were acquired with 5 mW laser power at the focal plane. The autofluorescence of bacteria upon excitation with a 488 nm laser is shown in the upper left corner. Scale bar 1 μm. (B) Single-molecule tracking (SMT) of TMR-labeled FliN and FliO. Selected frames from a series of 500 frames are shown, and frame numbers are indicated. (C) Mean square displacement (MSD) plots of pooled trajectories of at least 25 bacteria recorded under the same conditions. The diffusion coefficient <i>D</i> was calculated using the Jaqaman algorithm. (D) Dual-color direct stochastic optical reconstruction microscopy (dSTORM) of fixed bacteria expressing chromosomal FlgE-3×HA and FliO-HaloTag fusions (EM1214). Scale bar 1 μm.</p

Assembly of FliP subassemblies in core export apparatus mutants and model of the coordinated assembly of the flagellar-specific type III secretion system (fT3SS).

<p>Left: The assembly of stable FliP subassemblies is dependent on FliO and FliR but not on FliQ or FliF. Anti-FLAG Western blot of blue native PAGE (BN-PAGE) of crude membrane extracts prepared from the wild-type (WT) harboring untagged FliP (LT2, TH437) and mutant strains encoding for chromosomal FliP-3×FLAG: WT (EM6221), Δ<i>fliO</i> (EM6222), Δ<i>fliQ</i> (EM6223), Δ<i>fliR</i> (EM6224), Δ<i>fliF</i> (EM4859). Strains EM6221, EM6222, EM6223, and EM6224 additionally harbored a deletion of the proximal rod components <i>flgBC</i> in order to arrest flagellar synthesis after assembly of the core export apparatus. Right: Model of the coordinated assembly of the core flagellar export apparatus. Upon initiation of flagellum assembly, the flagellar type III secretion system (T3SS)-specific chaperone FliO facilitates formation of an oligomeric complex containing FliP and FliR. FliO then presumably dissociates from the stable FliP–FliR core complex. The FliP–FliR core complex forms the nucleus for the assembly of FliQ, FlhB, and FlhA [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002267#pbio.2002267.ref011" target="_blank">11</a>], followed by MS-ring (FliF) polymerization and formation of the completed protein export-competent flagellar T3SS.</p