Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria

BACKGROUND: The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera). RESULTS: A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor. CONCLUSION: Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis

Semiclassical approximation with zero velocity trajectories

We present a new semiclassical method that yields an approximation to the quantum mechanical wavefunction at a fixed, predetermined position. In the approach, a hierarchy of ODEs are solved along a trajectory with zero velocity. The new approximation is local, both literally and from a quantum mechanical point of view, in the sense that neighboring trajectories do not communicate with each other. The approach is readily extended to imaginary time propagation and is particularly useful for the calculation of quantities where only local information is required. We present two applications: the calculation of tunneling probabilities and the calculation of low energy eigenvalues. In both applications we obtain excellent agrement with the exact quantum mechanics, with a single trajectory propagation.Comment: 16 pages, 7 figure

Origin of magnetism in γ-fesi\u3csub\u3e 2 \u3c/sub\u3e/si(111) nanostructures

Magnetism has recently been observed in nominally nonmagnetic iron disilicide in the form of epitaxial γ-FeSi2 nanostructures on Si(111) substrate. To explore the origin of the magnetism in γ-FeSi2/Si(111) nanostructures, we performed a systematic first-principles study based on density functional theory. Several possible factors, such as epitaxial strain, free surface, interface, and edge, were examined. The calculations show that among these factors, only the edge can lead to the magnetism in γ-FeSi2/Si(111) nanostructures. It is shown that magnetism exhibits a strong dependency on the local atomic structure of the edge. Furthermore, magnetism can be enhanced by creating multiple-step edges. In addition, the results also reveal that edge orientation can have a significant effect on magnetism. These findings, thus, provide insights into a strategy to tune the magnetic properties of γ-FeSi2/Si(111) nanostructures through controlling the structure, population, and orientation of the edges

A meta-analysis of the investment-uncertainty relationship

In this article we use meta-analysis to investigate the investment-uncertainty relationship. We focus on the direction and statistical significance of empirical estimates. Specifically, we estimate an ordered probit model and transform the estimated coefficients into marginal effects to reflect the changes in the probability of finding a significantly negative estimate, an insignificant estimate, or a significantly positive estimate. Exploratory data analysis shows that there is little empirical evidence for a positive relationship. The regression results suggest that the source of uncertainty, the level of data aggregation, the underlying model specification, and differences between short- and long-run effects are important sources of variation in study outcomes. These findings are, by and large, robust to the introduction of a trend variable to capture publication trends in the literature. The probability of finding a significantly negative relationship is higher in more recently published studies. JEL Classification: D21, D80, E22 1

Lattice-Match Stabilization and Magnetic Properties of Metastable Epitaxial Permalloy-Disilicide Nanostructures on a Vicinal Si(111) Substrate

We report the epitaxial formation of metastable γ-(FexNi1−x)Si2 nanostructure arrays resulting from the reaction of Ni80Fe20 permalloy with vicinal Si(111) surface atoms. We then explore the effect of structure and composition on the nanostructure’s magnetic properties. The low-temperature annealing (T < 600 °C) of a pre-deposited permalloy film led to solid-phase epitaxial nucleation of compact disk-shaped island nanostructures decorating <110> ledges of the stepped surface, with either (2 × 2) or (3×3) R30° reconstructed flat top faces. High resolution scanning transmission electron microscopy analysis demonstrated fully coherent epitaxy of the islands with respect to the substrate, consistent with a well-matched CaF2-prototype structure associated with γ-FeSi2, along perfect atomically sharp interfaces. Energy dispersive spectroscopy detected ternary composition of the islands, with Fe and Ni atoms confined to the islands, and no trace of segregation. Our magnetometry measurements revealed the superparamagnetic behavior of the silicide islands, with a blocking temperature around 30 K, reflecting the size, shape, and dilute arrangement of the islands in the assembly

18S rDNA alignment

DNA sequence alignment of the 18S rRNA gene in Nexus forma

Tomographic layer-by-layer analysis of epitaxial iron-silicide nanostructures by DFT-assisted STS

Surface science techniques (STM, STS, and XPS) were combined with ab initio simulations to detect the local crystal structure and chemistry. Solid phase epitaxy of iron on vicinal Si(111) substrate resulted in the formation of (√3 x √3)R30° nanoislands and (2×2) films of γ-FeSi2(111). We identify these structures by comparing experimental normalized derivative conductance curves with tomographic simulated local density of states (LDOS). The thermodynamic tendency of γ-FeSi2(111) towards Si rich surfaces is manifested in Si rich termination layers and reconstructions. We show that a weighted average of the LDOS from the Fe layer and the reconstruction layer can explain the main states in the normalized derivative conductance curves, enabling in-situ identification of crystal structure and composition of epitaxial deposits

ALG11 DNA alignment

DNA sequence alignment of the ALG11 gene in Nexus forma

Combined_ALG11_COI_18SrRNA_Phylobayes

Phylogenetic tree presented in Figure 4: Bayesian consensus tree reconstructed using the CAT-GTR model for the concatenated DNA sequences of 18S rDNA, ALG11, and CO