Estimating translational selection in Eukaryotic Genomes

Natural selection on codon usage is a pervasive force that acts on a large variety of prokaryotic and eukaryotic genomes. Despite this, obtaining reliable estimates of selection on codon usage has proved complicated, perhaps due to the fact that the selection coefficients involved are very small. In this work, a population genetics model is used to measure the strength of selected codon usage bias, S, in 10 eukaryotic genomes. It is shown that the strength of selection is closely linked to expression and that reliable estimates of selection coefficients can only be obtained for genes with very similar expression levels. We compare the strength of selected codon usage for orthologous genes across all 10 genomes classified according to expression categories. Fungi genomes present the largest S values (2.24–2.56), whereas multicellular invertebrate and plant genomes present more moderate values (0.61–1.91). The large mammalian genomes (human and mouse) show low S values (0.22–0.51) for the most highly expressed genes. This might not be evidence for selection in these organisms as the technique used here to estimate S does not properly account for nucleotide composition heterogeneity along such genomes. The relationship between estimated S values and empirical estimates of population size is presented here for the first time. It is shown, as theoretically expected, that population size has an important role in the operativity of translational selection

Accretion onto the Companion of Eta Carinae During the Spectroscopic Event: II. X-Ray Emission Cycle

We calculate the X-ray luminosity and light curve for the stellar binary system Eta Carinae for the entire orbital period of 5.54 years. By using a new approach we find, as suggested before, that the collision of the winds blown by the two stars can explain the X-ray emission and temporal behavior. Most X-ray emission in the 2-10 \kev band results from the shocked secondary stellar wind. The observed rise in X-ray luminosity just before minimum is due to increase in density and subsequent decrease in radiative cooling time of the shocked fast secondary wind. Absorption, particularly of the soft X-rays from the primary wind, increases as the system approaches periastron and the shocks are produced deep inside the primary wind. However, absorption can not account for the drastic X-ray minimum. The 70 day minimum is assumed to result from the collapse of the collision region of the two winds onto the secondary star. This process is assumed to shut down the secondary wind, hence the main X-ray source. We show that this assumption provides a phenomenological description of the X-ray behavior around the minimum.Comment: The Astrophysical Journal, in pres

Structural and Functional Genomic Research in Model Legume Plants: The National BioResource Project (NBRP) in Japan

Lotus japonicus is a wild perennial plant with a small genome and a short life cycle. This plant is expected to play a role as the model organism of leguminous plants, which include important crop plants such as soybean (Glycine max). Legume Base, a resource centre for Lotus japonicus and Glycine max, was established in April 2004. The scope of Legume Base is the collection, development and conservation of the genetic resources of L. japonicus and G. max and the distribution of the material for utilization by the research community. DNA resources including genomic DNA clones will be also available through Legume Base web site

Application of thermoluminescence for detection of cascade shower 2: Detection of cosmic ray cascade shower at Mount Fuji

The results of a thermoluminescence (TL) chamber exposed at Mt. Fuji during Aug. '83 - Aug. '84 are reported. The TL signal induced by cosmic ray shower is detected and compared with the spot darkness of X-ray film exposed at the same time

Application of thermoluminescence for detection of cascade shower 1: Hardware and software of reader system

A reader system for the detection of cascade showers via luminescence induced by heating sensitive material (BaSO4:Eu) is developed. The reader system is composed of following six instruments: (1) heater, (2) light guide, (3) image intensifier, (4) CCD camera, (5) image processor, (6) microcomputer. The efficiency of these apparatuses and software application for image analysis is reported

Development and Verification for the Control Method Using Surplus Pressure of Primary Pumps in Chiller Plant Systems for Air Conditioning which Adopts Primary/Secondary Piping Systems PPT

The primary/secondary piping systems are often employed in large chiller plant Systems. Normally, the primary flow becomes more than secondary flow, and the flow difference returns to a chiller via decoupler, which is common to primary flow loop (chiller side) and secondary flow loop (load side). It is a huge energy loss, because the primary pumps use their head to lead much flow to the decoupler. Therefore, we have developed new control method using surplus pressure of the primary pump to reduce the primary and secondary pumps' energy. In this paper, we used this control method to the actual chiller plant buildings and verified its effectiveness. As a result, cold water conveyances, both primary loop and secondary loop, could be covered by only primary pumps during plant operating time, and the water conveyance power energy was reduced approximately 80%

High-temperature Superconductivity in Layered Nitrides \beta-Lix_xMNCl (M = Ti, Zr, Hf): Insights from Density-functional Theory for Superconductors

We present an ab initio analysis with density functional theory for superconductors (SCDFT) to understand the superconducting mechanism of doped layered nitrides \beta-Li$_x$MNCl (M=Ti, Zr, and Hf). The current version of SCDFT is based on the Migdal-Eliashberg theory and has been shown to reproduce accurately experimental superconducting-transition temperatures Tc of a wide range of phonon-mediated superconductors. In the present case, however, our calculated Tc$\leq$4.3 K (M=Zr) and $\leq$10.5 K (M=Hf) are found to be less than a half of the experimental Tc. In addition, Tc obtained in the present calculation increases with the doping concentration x, opposite to that observed in the experiment. Our results indicate that we need to consider some elements missing in the present SCDFT based on the Migdal-Eliashberg theory.Comment: 18 pages, 13 figures, submitted to Physical Review

Genetic Diversity in Zoysiagrass Ecotypes Based on Morphological Characteristics and SSR Markers

Zoysiagrass consists of a number of interfertile species, some of which are important grasses for turfgrass and grazing pasture in Japan. Recently, we developed simple sequence repeats (SSRs) markers from Zoysia japonica “Asagake” genomic DNA by enriched genomic library method (Yamamoto et al., 2002). Here we identify genetic diversity in 38 ecotypes of zoysiagrass (Z. matrella and Z. tenuifolia) from a group of southwest islands of Japan based on morphological characteristics and SSR markers

GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution

Integrating genome-scale sequence, expression, structural and protein interaction data from E. coli we establish an interaction between chaperone (GroEL) dependency and optimal codon usage.Highly expressed sporadic substrates of GroEL employ more optimal codons than expected, show enrichment for optimal codons at structurally sensitive sites and greater conservation of codon optimality under conditions of relaxed purifying selection.We suggest that highly expressed genes cannot routinely utilize GroEL for error control so that codon usage has evolved to provide complementary error limitation, whereas obligate GroEL substrates experience relaxed selection on codon usage.Our results support a critical role of misfolding prevention in gene evolution