Seasonal Changes in the Ratio of Microbial Biomass P to Total P in Soils of Grazed Pastures

Phosphorus (P) utilisation efficiency in pasture soils is higher than in arable soils. Because there is a considerable amount of microbial biomass in the root mat layer, which is peculiar to permanent pasture, the microbial biomass P (MBP) contribution may be important in supplying soil P to pasture plants (Chen et al., 2000; He et al., 1997). In the present study, we investigated seasonal changes in MBP and other forms of P relative to total soil P in two pastures in which P uptake was estimated to be different

Removal of forbidden states in a three-α\alpha system

The ground and excited 0$^+$ states of $^{12}$C are investigated in a 3$\alpha$ macroscopic model using the deep potential of Buck, Friedrich and Wheatley. The elimination of forbidden states is performed either by constructing the allowed state space explicitly or by using the orthogonalizing pseudopotential. The well-known enigmatic behavior of the latter approach is resolved. It is safe to define the forbidden states referring to the underlying microscopic model.Comment: 18pages, 2figure

Nitrogen Budgets on a Pasture under Combined Utilization of Grazing and Cutting

Nitrogen budgets on a pasture being utilized for both grazing and cutting were investigated. A pasture containing tallfescue, orchard grass and white clover was divided into two areas: initially grazed (IA, 0.41ha) and grazed after cutting for hay (BA, 0.49ha). A herd of 4-5 cattle (heifers or steers of Japanese Black or Holstein) grazed at IA from 22 Apr. to 2 Jul. and grazed at both IA and BA from 3 Jul. to 21 Oct. 1999. The amount of N grazed from IA was 3 times higher than the sum of N of grazed herbage and harvested hay from BA. The amount of N inflow to soil as fertilizer or animal excreta seemed to relate to the difference in herbage production between IA and BA. The value of N surplus for the whole pasture was very similar to the value of the difference between inflow to soil and the sum of grazed herbage and harvested hay. N surplus in the pasture seemed to relate closely to soil N balance

Fast algorithm for calculating two-photon absorption spectra

We report a numerical calculation of the two-photon absorption coefficient of electrons in a binding potential using the real-time real-space higher-order difference method. By introducing random vector averaging for the intermediate state, the task of evaluating the two-dimensional time integral is reduced to calculating two one-dimensional integrals. This allows the reduction of the computation load down to the same order as that for the linear response function. The relative advantage of the method compared to the straightforward multi-dimensional time integration is greater for the calculation of non-linear response functions of higher order at higher energy resolution.Comment: 4 pages, 2 figures. It will be published in Phys. Rev. E on 1, March, 199

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, faster search tools, such as BLAT, do not have sufficient search sensitivity for metagenomic analysis. Thus, a sensitive and efficient homology search tool is in high demand for this type of analysis.We developed a new, highly efficient homology search algorithm suitable for graphics processing unit (GPU) calculations that was implemented as a GPU system that we called GHOSTM. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated indexes and then calculates local alignments around the candidate positions before calculating alignment scores. We implemented both of these processes on GPUs. The system achieved calculation speeds that were 130 and 407 times faster than BLAST with 1 GPU and 4 GPUs, respectively. The system also showed higher search sensitivity and had a calculation speed that was 4 and 15 times faster than BLAT with 1 GPU and 4 GPUs.We developed a GPU-optimized algorithm to perform sensitive sequence homology searches and implemented the system as GHOSTM. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We developed GHOSTM, which is a cost-efficient tool, and offer this tool as a potential solution to this problem

Wnt5a induces ROR1 to complex with HS1 to enhance migration of chronic lymphocytic leukemia cells.

ROR1 (receptor tyrosine kinase-like orphan receptor 1) is a conserved, oncoembryonic surface antigen expressed in chronic lymphocytic leukemia (CLL). We found that ROR1 associates with hematopoietic-lineage-cell-specific protein 1 (HS1) in freshly isolated CLL cells or in CLL cells cultured with exogenous Wnt5a. Wnt5a also induced HS1 tyrosine phosphorylation, recruitment of ARHGEF1, activation of RhoA and enhanced chemokine-directed migration; such effects could be inhibited by cirmtuzumab, a humanized anti-ROR1 mAb. We generated truncated forms of ROR1 and found its extracellular cysteine-rich domain or kringle domain was necessary for Wnt5a-induced HS1 phosphorylation. Moreover, the cytoplamic, and more specifically the proline-rich domain (PRD), of ROR1 was required for it to associate with HS1 and allow for F-actin polymerization in response to Wnt5a. Accordingly, we introduced single amino acid substitutions of proline (P) to alanine (A) in the ROR1 PRD at positions 784, 808, 826, 841 or 850 in potential SH3-binding motifs. In contrast to wild-type ROR1, or other ROR1P→︀A mutants, ROR1P(841)A had impaired capacity to recruit HS1 and ARHGEF1 to ROR1 in response to Wnt5a. Moreover, Wnt5a could not induce cells expressing ROR1P(841)A to phosphorylate HS1 or activate ARHGEF1, and was unable to enhance CLL-cell motility. Collectively, these studies indicate HS1 plays an important role in ROR1-dependent Wnt5a-enhanced chemokine-directed leukemia-cell migration

The Nanos3-3′UTR Is Required for Germ Cell Specific NANOS3 Expression in Mouse Embryos

BACKGROUND: The regulation of gene expression via a 3' untranslated region (UTR) plays essential roles in the discrimination of the germ cell lineage from somatic cells during embryogenesis. This is fundamental to the continuation of a species. Mouse NANOS3 is an essential protein required for the germ cell maintenance and is specifically expressed in these cells. However, the regulatory mechanisms that restrict the expression of this gene in the germ cells is largely unknown at present. METHODOLOGY/PRINCIPAL FINDINGS: In our current study, we show that differences in the stability of Nanos3 mRNA between germ cells and somatic cells is brought about in a 3'UTR-dependent manner in mouse embryos. Although Nanos3 is transcribed in both cell lineages, it is efficiently translated only in the germ lineage. We also find that the translational suppression of NANOS3 in somatic cells is caused by a 3'UTR-mediated mRNA destabilizing mechanism. Surprisingly, even when under the control of the CAG promoter which induces strong ubiquitous transcription in both germ cells and somatic cells, the addition of the Nanos3-3'UTR sequence to the coding region of exogenous gene was effective in restricting protein expression in germ cells. CONCLUSIONS/SIGNIFICANCE: Our current study thus suggests that Nanos3-3'UTR has an essential role in translational control in the mouse embryo

Nuclear Alpha-Particle Condensates

The $\alpha$-particle condensate in nuclei is a novel state described by a product state of $\alpha$'s, all with their c.o.m. in the lowest 0S orbit. We demonstrate that a typical $\alpha$-particle condensate is the Hoyle state ($E_{x}=7.65$ MeV, $0^+_2$ state in $^{12}$C), which plays a crucial role for the synthesis of $^{12}$C in the universe. The influence of antisymmentrization in the Hoyle state on the bosonic character of the $\alpha$ particle is discussed in detail. It is shown to be weak. The bosonic aspects in the Hoyle state, therefore, are predominant. It is conjectured that $\alpha$-particle condensate states also exist in heavier $n\alpha$ nuclei, like $^{16}$O, $^{20}$Ne, etc. For instance the $0^+_6$ state of $^{16}$O at $E_{x}=15.1$ MeV is identified from a theoretical analysis as being a strong candidate of a $4\alpha$ condensate. The calculated small width (34 keV) of $0^+_6$, consistent with data, lends credit to the existence of heavier Hoyle-analogue states. In non-self-conjugated nuclei such as $^{11}$B and $^{13}$C, we discuss candidates for the product states of clusters, composed of $\alpha$'s, triton's, and neutrons etc. The relationship of $\alpha$-particle condensation in finite nuclei to quartetting in symmetric nuclear matter is investigated with the help of an in-medium modified four-nucleon equation. A nonlinear order parameter equation for quartet condensation is derived and solved for $\alpha$ particle condensation in infinite nuclear matter. The strong qualitative difference with the pairing case is pointed out.Comment: 71 pages, 41 figures, review article, to be published in "Cluster in Nuclei (Lecture Notes in Physics) - Vol.2 -", ed. by C. Beck, (Springer-Verlag, Berlin, 2011