The Giant Impact Simulations with Density Independent Smoothed Particle Hydrodynamics

At present, the giant impact (GI) is the most widely accepted model for the origin of the Moon. Most of the numerical simulations of GI have been carried out with the smoothed particle hydrodynamics (SPH) method. Recently, however, it has been pointed out that standard formulation of SPH (SSPH) has difficulties in the treatment of a contact discontinuity such as a core-mantle boundary and a free surface such as a planetary surface. This difficulty comes from the assumption of differentiability of density in SSPH. We have developed an alternative formulation of SPH, density independent SPH (DISPH), which is based on differentiability of pressure instead of density to solve the problem of a contact discontinuity. In this paper, we report the results of the GI simulations with DISPH and compare them with those obtained with SSPH. We found that the disk properties, such as mass and angular momentum produced by DISPH is different from that of SSPH. In general, the disks formed by DISPH are more compact: while formation of a smaller mass moon for low-oblique impacts is expected with DISPH, inhibition of ejection would promote formation of a larger mass moon for high-oblique impacts. Since only the improvement of core-mantle boundary significantly affects the properties of circumplanetary disks generated by GI and DISPH has not been significantly improved from SSPH for a free surface, we should be very careful when some conclusions are drawn from the numerical simulations for GI. And it is necessary to develop the numerical hydrodynamical scheme for GI that can properly treat the free surface as well as the contact discontinuity.Comment: Accepted for publication in Icaru

Biochemical Characterization of Medaka (<i>Oryzias latipes</i>) Transglutaminases, OlTGK1 and OlTGK2, as Orthologues of Human Keratinocyte-Type Transglutaminase

<div><p>Calcium-dependent transglutaminases (TGs) are a family of enzymes that catalyze protein cross-linking and/or attachment of primary amines in a variety of organisms. Mammalian TGs are implicated in multiple biological events such as skin formation, blood coagulation, and extracellular matrix stabilization. Medaka (<i>Oryzias latipes</i>) has been used as a model fish to investigate the physiological functions of mammalian proteins. By analysis of the medaka genome, we found seven TGs orthologues, some of which apparently corresponded to the mammalian TG isozymes, TG1, TG2, and Factor XIII. All orthologues had preserved amino acid residues essential for enzymatic activity in their deduced primary structures. In this study, we analyzed biochemical properties of two orthologues (OlTGK1 and OlTGK2) of mammalian epithelium-specific TG (TG1) that are significantly expressed at the transcriptional level. Using purified recombinant proteins for OlTGK1 and OlTGK2, we characterized their catalytic reactions. Furthermore, immunohistochemical analyses of fish sections revealed higher expression in the pancreas (OTGK1), intervertebral disk (OlTGK2) and pharyngeal teeth (OlTGK2) as well as in the skin epidermis.</p></div

Immunohistochemical analysis of OlTGK1 using medaka sections.

<p>Whole body sections of medaka fixed with methanol and acetic acid following by paraffin were analyzed by immunostaining. The serial sections were stained with hematoxylin and eosin (HE) (A) and subjected to immunoreaction with an affinity-purified polyclonal antibody against OlTGK1 (B) as well as a rabbit immunoglobulin solution at a similar concentration (C). The whole body image (B) around the stained area was enlarged; pancreas (D), Brockmann body (E), and salivary gland (F). The scale bars indicate 2 mm (A) and 100 μm (D-F).</p

Immunostaining for OlTGK1 and OlTGK2 in the skin epidermis.

<p>Serial frozen tissue sections prepared and without fixation were subjected to immunohistochemical analysis using polyclonal antibodies as described in the legend to Figs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144194#pone.0144194.g004" target="_blank">4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144194#pone.0144194.g005" target="_blank">5</a>. The analysis focused on areas of the epidermis: OlTGK1 (A), OlTGK2 (B), and negative controls (C, D) are shown. Scale bar indicates 100 μm.</p

Purification of OlTGK1 and OlTGK2 recombinant proteins produced in bacteria.

<p>The soluble fraction containing recombinant OlTGK1 (A) and OlTGK2 (B) proteins were purified using metal ion affinity-gel and size exclusion chromatography. Each sample was subjected to 7.5% SDS-PAGE following Coomassie Brilliant Blue staining: lane 1; applied samples for affinity chromatography, lane 2; flow-through fractions, lane 3; washed fractions, lane 4; eluted fractions, lane 5; the peak fractions from the size separation performed using Superdex-200 increase. M: molecular mass marker.</p

Sequence alignment of human TGs and medaka orthologues and phylogenic tree based on primary structure.

<p>Sequence alignment around the catalytic triad including Cys (the active-site), His, and Asp was shown with respect to the major human TGs and the medaka orthologues: Human TG1 (NP_000350), TG2 (NP_004604), FXIII (NP_000120), as well as medaka orthologues. The catalytic triad, containing the active site Cys and the other two amino acid residues (Asp, His) is indicated by arrows. The possible residues coordinating calcium ion are indicated as circles. The numbers of the amino acid residues are described with the sequences. (A). The phylogenic tree was constructed (1000 boostrap trials, Neighbor-Joining Method plot) based on the deduced amino acid sequences for human FXIII, TG1, TG2, TG3 (NP_003236), TG4 (NP_003232), TG5 (NP_963925), TG6 (NP_945345), TG7 (NP_443187), and their medaka orthologues. Each cDNA sequence of medaka orthologues has been deposited to DDBJ (DNA Data Bank Japan) as following accession numbers: OlTGB (LC068825), OlTGT (LC068826), OlTGK1 (LC068829), OlTGK2 (LC068830), OlTGK3 (LC068831), OlTGF (LC068827), and OlTGO (LC068828) (B).</p