ALBERT

Description: Hornblende-bearing basanites and alkali basalts from the Rhön area of Germany (part of the Central European Volcanic Province; CEVP) have high TiO 2 (3–4 wt %), moderately high Mg# (mostly 〉0·50), variable Cr (400–30 ppm) and Ni (160–20 ppm) abundances, and are enriched in incompatible trace elements and rare earth elements (REE). In primitive mantle-normalized multi-element diagrams they show a strong depletion in Ba, Rb, and K relative to trace elements of similar incompatibility. Some alkali basalts and more differentiated rocks have lower Mg# and lower abundances of Ni and Cr, and have undergone fractionation of olivine, clinopyroxene, Fe–Ti oxides and amphibole. The trace element constraints (e.g. low Nb/U and Ce/Pb and the Nd–Sr–Pb isotope compositions of some basalts) indicate that assimilation of lower crustal material has modified the composition of the primary mantle-derived magmas. Most of the basanites and alkali basalts approach the Sr–Nd–Pb isotope compositions inferred for the EAR (European Asthenospheric Reservoir) component. Variations in REE abundances and correlations between REE ratios suggest partial melting of amphibole-bearing spinel peridotite containing a significant portion of non-peridotitic material (i.e. pyroxenite). The presence of residual amphibole, indicated by depletion of K and Rb relative to Ba and Nb, requires melting close to the asthenosphere–lithosphere boundary or within the lithospheric mantle, most probably of a veined mantle source. Temperature and pressure estimates indicate a depth of melting for the most primitive lavas at ~80 km at temperatures of ~1290°C. Based on Sr–Nd isotope and trace element constraints it is proposed that asthenospheric melts similar in composition to EAR melts observed elsewhere in the CEVP froze at the asthenosphere–lithosphere thermal boundary as veins in the lithospheric mantle. These veins were remelted after only short storage times by ascending asthenospheric melts, imposing the prominent amphibole signature upon the basalts. The fairly radiogenic Pb isotope signatures are expected to originate from melting of enriched, low melting temperature components incorporated in the depleted upper (asthenospheric) mantle and therefore do not require upwelling of deep-seated mantle sources for the Rhön or many other continental alkaline lavas with similar Pb isotope signatures.

Description: RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP–RNA interactions. Given a set of differentially regulated alternative exons obtained from RNA sequencing (RNA-seq) experiments, the rMAPS web server ( http://rmaps.cecsresearch.org ) performs motif analyses of RBPs in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. Similarly, rMAPS can also perform spatial analyses of RBP–RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq) experiments. We anticipate rMAPS will be a useful tool for elucidating RBP regulation of alternative exon splicing using high-throughput sequencing data.

Description: Basanites from the Tertiary Siebengebirge area of Germany (part of the Central European Volcanic Province; CEVP) have high Mg# (〉0·60), moderate to high Cr (〉300 ppm) and Ni (〉200 ppm) contents and strong light rare earth element enrichment, but systematic depletion in Rb and K relative to trace elements of similar compatibility in anhydrous mantle. Rare earth element melting models can explain the petrogenesis of these basanites in terms of partial melting of a spinel peridotite source containing residual amphibole. It is inferred that amphibole, indicated by the relative K and Rb depletion and the melting model, was precipitated in the spinel peridotite lithospheric mantle beneath the Siebengebirge, by metasomatic fluids or melts from a rising mantle diapir or plume. Alkali basalts and more differentiated rocks have lower Mg# and lower abundances of Ni and Cr, and have undergone fractionation of mainly olivine, clinopyroxene, Fe–Ti oxides, amphibole and plagioclase. Most of the basanites and alkali basalts approach the Sr–Nd–Pb isotope compositions inferred for the European Asthenospheric Reservoir component. Trace element constraints (i.e. low Nb/U and Ce/Pb ratios) and the Sr–Nd–Pb isotope composition of the differentiated rocks indicate that assimilation of lower crustal material has modified the composition of the primary mantle-derived magmas. High 207 Pb/ 204 Pb ratios in the differentiated lavas point to assimilation of ancient lower crustal components having high U/Pb and Th/Pb ratios. Relatively shallow melting of inferred amphibole-bearing spinel peridotite sources may suggest an origin from the metasomatized part of the thermal boundary layer. Application of new thermobarometric equations for the basaltic magmas indicates relatively normal mantle potential temperatures (1300–1400°C); thus the inferred mantle ‘baby plume’ or ‘hot finger’ is not thermally anomalous.

Description: Programmed genome rearrangements in the unicellular eukaryote Oxytricha trifallax produce a transcriptionally active somatic nucleus from a copy of its germline nucleus during development. This process eliminates noncoding sequences that interrupt coding regions in the germline genome, and joins over 225,000 remaining DNA segments, some of which require inversion or complex permutation to build functional genes. This dynamic genomic organization permits some single DNA segments in the germline to contribute to multiple, distinct somatic genes via alternative processing. Like alternative mRNA splicing, the combinatorial assembly of DNA segments contributes to genetic variation and facilitates the evolution of new genes. In this study, we use comparative genomic analysis to demonstrate that the emergence of alternative DNA splicing is associated with the origin of new genes. Short duplications give rise to alternative gene segments that are spliced to the shared gene segments. Alternative gene segments evolve faster than shared, constitutive segments. Genes with shared segments frequently have different expression profiles, permitting functional divergence. This study reports alternative DNA splicing as a mechanism of new gene origination, illustrating how the process of programmed genome rearrangement gives rise to evolutionary innovation.

Description: The fore-arc mantle above a subducting slab is a unique site where complex partial melting, melt/fluid–rock interaction, and deformation of mantle rocks occur. To constrain these geological and geodynamic processes we analyzed the deformation microstructures, crystal preferred orientations (CPOs or fabrics), and water content in natural harzburgites that occur as exhumed massifs in the North Qilian suture zone, NW China. These harzburgites are very fresh, and have mineral assemblages of olivine (~81–87 vol. %), orthopyroxene (~11–17 vol. %), clinopyroxene (~1–2 vol. %), and spinel (~1 vol. %). Detailed analyses of mineral textures, CPO patterns, and rotation axis distributions suggest that the plastic deformation of olivine and pyroxene was accommodated by activating a series of slip systems of dislocation. The olivine (A-/D-type fabric) shows dominant (010)[100] and/or (001)[100] slip systems, as well as other minor [100]-glide, {0 kl }[100], and [001]-glide slip systems. The orthopyroxene shows dominant (100)[001] and subordinate (010)[001] slip systems, with minor (100)[010] and (100)[0 vw ] slip systems. The water content is extremely low in the orthopyroxene (38–44 ppm by weight), equilibrated olivine (4–7 ppm), and bulk-rock samples (9–14 ppm). Previously published refractory mineral and whole-rock compositions, as well as estimated low-pressure (~1–2 GPa), high-temperature (~1100–1300°C), low-stress (~1–4 MPa) and water-poor conditions of deformation, suggest that these harzburgites represent a remnant of fossil fore-arc lithospheric mantle that was probably both formed (experienced partial melting and high-temperature melt/fluid–rock reaction) and deformed in a young and warm fore-arc mantle setting (i.e. juvenile subduction zone). Based on these results, a refined schematic model of olivine fabric distributions in subduction zones is proposed. In this model, the A-/D-type olivine fabrics are inferred to be prevalent in fore-arc lithospheric mantle. The opposing polarizing directions of A-/D-type olivine fabrics with other underlying anisotropic sources in the mantle wedge (e.g. B-type olivine fabrics and oriented serpentinite layers) may weaken the trench-parallel fast S-wave anisotropy contributed by the deformed fore-arc mantle, and thus provide an alternative explanation for the short or nearly null delay times of local shear-wave splitting (sourced from intra-slab earthquakes) that have been detected in some fore-arc regions. In addition, topotactic antigorite fabrics after the A-/D-type olivine fabric might play a minor role in contributing to the low P- and S-wave velocities, high V p / V s ratios, and large seismic anisotropies that are typically observed in fore-arc mantle.

Description: A general framework for a novel non-geodesic decomposition of high-dimensional spheres or high-dimensional shape spaces for planar landmarks is discussed. The decomposition, principal nested spheres, leads to a sequence of submanifolds with decreasing intrinsic dimensions, which can be interpreted as an analogue of principal component analysis. In a number of real datasets, an apparent one-dimensional mode of variation curving through more than one geodesic component is captured in the one-dimensional component of principal nested spheres. While analysis of principal nested spheres provides an intuitive and flexible decomposition of the high-dimensional sphere, an interesting special case of the analysis results in finding principal geodesics, similar to those from previous approaches to manifold principal component analysis. An adaptation of our method to Kendall’s shape space is discussed, and a computational algorithm for fitting principal nested spheres is proposed. The result provides a coordinate system to visualize the data structure and an intuitive summary of principal modes of variation, as exemplified by several datasets.

Description: Identifying differential features between conditions is a popular approach to understanding molecular features and their mechanisms underlying a biological process of particular interest. Although many tests for identifying differential expression of gene or gene sets have been proposed, there was limited success in developing methods for differential interactions of genes between conditions because of its computational complexity. We present a method for Evaluation of Dependency DifferentialitY (EDDY), which is a statistical test for differential dependencies of a set of genes between two conditions. Unlike previous methods focused on differential expression of individual genes or correlation changes of individual gene–gene interactions, EDDY compares two conditions by evaluating the probability distributions of dependency networks from genes. The method has been evaluated and compared with other methods through simulation studies, and application to glioblastoma multiforme data resulted in informative cancer and glioblastoma multiforme subtype-related findings. The comparison with Gene Set Enrichment Analysis, a differential expression-based method, revealed that EDDY identifies the gene sets that are complementary to those identified by Gene Set Enrichment Analysis. EDDY also showed much lower false positives than Gene Set Co-expression Analysis, a method based on correlation changes of individual gene–gene interactions, thus providing more informative results. The Java implementation of the algorithm is freely available to noncommercial users. Download from: http://biocomputing.tgen.org/software/EDDY .

Description: Acoustic target strength ( TS ) measurements were made of ex situ giant jellyfish Nemopilema nomurai Kishinouye at 38 and 120 kHz. These TS data may be useful for developing acoustic scattering models, and surveying giant jellyfish distributions and biomasses. Each jellyfish was tethered in seawater using a monofilament line that vertically penetrated its bell's centre. During the acoustic measurements, an underwater video camera was used to continuously monitor the jellyfish's behaviour. Acoustic measurements were made using split-beam transducers. TS measurements were made of 27 individual jellyfish, but data were analysed for 23 specimens (bell diameter in air, D air = 21–65 cm) at 38 kHz, and 19 specimens ( D air = 21–46 cm) at 120 kHz, respectively. Least-squares regression fits of TS vs. log( D air ) were TS 38kHz = 20•log 10 D air –82.7 ( r = 0.76) and TS 120kHz = 20•log 10 D air –86.7 ( r = 0.79). The mean TS values at 38 and 120 kHz, using the average D air = 40.3 cm and 35.5 cm, respectively, were –50.6 and –55.7 dB. The reduced TS , a function of the ratio of D air to wavelength (), was RTS ( D air /) = –6.1•log 10 ( D air /) –36.1 ( r = 0.51). These RTS values decreased with increasing D air /. Symbiotic medusa shrimp ( Latreutes anoplonyx Kemp) contributed negligible bias to our TS measurements of giant jellyfish. These ex situ TS measurements may be used in acoustic surveys to estimate the distributions and biomasses of N . nomurai .

Description: In this paper, we study operators for which T * T and T + T * commute. Let denote the class of such operators in L(H). We show that every operator in is subscalar of order 4. From this result, we give partial solutions to the invariant subspace problem. In addition, we examine some extensions of operators in . Finally, we prove that if T belongs to , then Weyl's theorem holds for T and the spectral mapping theorem corresponding to the Weyl spectrum is satisfied for T .

Description: The foot-and-mouth-disease virus (FMDV) utilizes non-canonical translation initiation for viral protein synthesis, by forming a specific RNA structure called internal ribosome entry site (IRES). Domain 3 in FMDV IRES is phylogenetically conserved and highly structured; it contains four-way junctions where intramolecular RNA–RNA interactions serve as a scaffold for the RNA to fold for efficient IRES activity. Although the 3D structure of domain 3 is crucial to exploring and deciphering the initiation mechanism of translation, little is known. Here, we employ a combination of various modeling approaches to propose candidate tertiary structures for the apical region of domain 3, thought to be crucial for IRES function. We begin by modeling junction topology candidates and build atomic 3D models consistent with available experimental data. We then investigate each of the four candidate 3D structures by molecular dynamics simulations to determine the most energetically favorable configurations and to analyze specific tertiary interactions. Only one model emerges as viable containing not only the specific binding site for the GNRA tetraloop but also helical arrangements which enhance the stability of domain 3. These collective findings, together with available experimental data, suggest a plausible theoretical tertiary structure of the apical region in FMDV IRES domain 3.