Inferring the fitness effects of DNA mutations from polymorphism and divergence data: statistical power to detect directional selection under stationarity and free recombination

The fitness effects of classes of DNA mutations can be inferred from patterns of nucleotide variation. A number of studies have attributed differences in levels of polymorphism and divergence between silent and replacement mutations to the action of natural selection. Here, I investigate the statistical power to detect directional selection through contrasts of DNA variation among functional categories of mutations. A variety of statistical approaches are applied to DNA data simulated under Sawyer and Hartl's Poisson random field model. Under assumptions of free recombination and stationarity, comparisons that include both the frequency distributions of mutations segregating within populations and the numbers of mutations fixed between populations have substantial power to detect even very weak selection. Frequency distribution and divergence tests are applied to silent and replacement mutations among five alleles of each of eight Drosophila simulans genes. Putatively "preferred" silent mutations segregate at higher frequencies and are more often fixed between species than "unpreferred" silent changes, suggesting fitness differences among synonymous codons. Amino acid changes tend to be either rare polymorphisms or fixed differences, consistent with a combination of deleterious and adaptive protein evolution. In these data, a substantial fraction of both silent and replacement DNA mutations appear to affect fitness.     

An Entropy Theoretic Inversion Formula for the Distribution of Proper Values of a Compact Positive Operator

A formula for estimating -entropy of a compact positive operator in terms of the distribution of proper values of such an operator was given by Prosser and Root. In this paper, an inversion formula for estimating the distribution of proper values of a compact positive operator in terms of -entropy of such an operator is given.     

Molecular and structural characterization of the spindle pole bodies in the fission yeast Schizosaccharomyces japonicus var japonicus

The structure and localization of the microtubule organization centres (MTOCs) of the fission yeast Schizosaccharomyces japonicus var. japonicus were examined by fluorescence microscopy and electron microscopy. Spindle pole bodies (SPBs), which are the fungal equivalent of centrosomes, of Sz. japonicus were visualized by immunofluorescent staining using a monoclonal anti-gamma-tubulin antibody. The behaviour of the SPBs during the cell cycle mostly coincided with previous reports on the most widely used fission yeast Schizosaccharomyces pombe. We cloned the gamma-tubulin gene from Sz. japonicus by PCR using redundant sets of primers corresponding to conserved regions of known gamma-tubulins. The predicted amino acid sequence of Sz. japonicus gamma-tubulin was most similar to the Sz. pombe gamma-tubulin. Under the electron microscope, the SPBs of Sz. japonicus were detected as electron-dense multilayered structures located just outside the nuclear envelope. The SPBs of Sz. japonicus were composed of three electron-dense layers and were surrounded by fuzzy material. Each layer showed structural changes according to the progression of the cell cycle. In mitotic cells, the SPBs were located on the fenestrae of the nuclear envelopes through which the mitotic spindle microtubules ran into the nucleoplasm. Our results show that Sz. japonicus is a very potent and attractive organism for the investigation of the microtubule nucleation system and morphogenesis in yeasts. The Accession No. for the nucleotide sequence of the Sz. japonicus gtb1(+) gene is AF159163.     

A pneumatic air table realized by micro-EDM

This paper presents a one-dimensional (1-D) pneumatic actuator fabricated by combining several micromachining technologies such as microelectrodischarge machining (micro-EDM) as well as isotropic and anisotropic wet etching. Unlike the existing pneumatic actuators, which usually convey the object by means of friction, this device employs the dynamic pressure of inclined driving jets in order to enhance the horizontal transportation performance. Typical slider speeds of up to 5 cm/s can be obtained. Comparisons between different types of sliders are presented. By an appropriate patterning of the slider bottom surface, the speed could be increased by 50%-60%. Similarly, a maximum tangential force of 20 μN (equivalent shear stress: 2.2 μN/mm²) was obtained using this dynamic pressure concept. The latter is about two times larger than that of a slider with a smooth surface     

The synthesis of ultrafine titanium nitride in an r.f. plasma

The ultrafine titanium nitride particles with a statistical median size of about 10 nm were prepared by passing pure titanium powder (<25 m) through a radio-frequency (r.f.) argon-nitrogen plasma. The effects of the [N₂]/[Ti] molar ratio of the reactant on the nature of the products were investigated by chemical analysis, X-ray diffraction and electron microscopy. The conversion efficiency was close to 100%. The colour of the product was black, which is attributed to the particle size ranging from 5 to 150 nm. Most of the crystallites were single crystal and showed clear-cut habits of cubic phase. The chemical composition and lattice parameter of the products changed with the [N₂]/[Ti] ratio. The thermodynamics of the process were also considered. These results provide evidence to suggest that new materials can be produced by an r.f. plasma process, in particular, the ultrafine refractory nitrides.     

Surface grafting of poly(vinylamine) onto poly(ethylene) film by corona discharge‐induced grafting

Poly(vinylamine) (PVAm) was grafted on a poly(ethylene) (PE) film surface via the surface graft polymerization of N‐vinylformamide (NVF) and N‐vinylacetamide (NVA) and the subsequent hydrolysis of those grafted polymers. The surface was characterized by X‐ray photoelectron spectroscopy (XPS), contact angle, moisture absorption, and the leakage of electrostatic charge from the films. PNVF and PNVA were introduced onto the surface of the PE film successfully, in spite of the fact that the initiator for polymerization was a peroxide group. The grafted amounts of PNVF and PNVA were dependent on the grafting time. A PVAm‐grafted surface was obtained via the hydrolysis of the grafted PNVF. The grafted‐PNVA was not hydrolyzed under mild hydrolysis. The obtained PVAm‐grafted surface appeared to be useful for various applications, such as protein immobilization or chemical modification. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 72: 1583–1587, 1999     

Poly(N‐isopropylacrylamide)‐grafted silica as a support of platinum colloids: Preparation method,characterization, and catalytic properties in hydrogenation

We investigated the composition, properties, and utility of a novel hybrid material of poly(N‐isopropylacrylamide)‐grafted silica. The modified silica was prepared in two steps: (1) grafting silane layers of active precursors, such as initiator, transfer agent or comonomer onto the silica surface by solution deposition and (2) radical polymerization of N‐isopropylacrylamide (NIPAAm) on the grafted silane layers. Thermogravimetric analysis (TGA), elemental analysis (EA), FTIR spectroscopy, and TEM were used to characterize the layer composition, structure, and chemistry, respectively. Well‐dispersed platinum colloids have been prepared on the PNIPAAm‐grafted silica via the reduction of PtCl by ethanol. The immobilized Pt colloids were found to be active and stable heterogeneous catalysts for the hydrogenation of ally alcohol in ethanol. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 2678–2684, 2000     

Preparation and swelling properties of glycoside-bearing hydrogels by gamma-ray radiation to glycoside-bearing polymer aqueous solutions

γ-Ray radiation on poly(glucosyloxyethyl methacrylate) [poly(GEMA)] and poly(glucosyloxyethyl acrylate) [poly(GEA)] aqueous solutions without any crosslinkers gives glycoside-bearing hydrogels in a high yield. The degree of the swelling ratios of each obtained hydrogel in water was decreased with an increase in the total radiation dose to each polymer solution. In order to clarify the formation mechanism of obtained poly(GEMA) hydrogel by γ-ray radiation, the swelling properties of each hydrogel were also compared with those of poly(GEA) under various conditions. Poly(GEMA) in an organic solvent, N,N-dimethylformamide and dimethylsulfoxide, was not gelled by γ-ray radiation, although poly(GEA) was gelled under these conditions. These results suggest that the radiation formation mechanism of the poly(GEMA) hydrogels is different from that of the poly(GEA) hydrogels. In addition, the radiolysis of water is necessary in order to form the hydrogels for poly(GEMA). Next, we predicted the radiation formation mechanism of the poly(GEMA) hydrogels by the crosslinking between the glucoside moieties in poly(GEMA). © 1998 John Wiley & Sons, Inc. J. Appl. Polym. Sci. 70: 965–972, 1998     

Development of a 1 MV field-emission transmission electron microscope

We developed a 1 MV field-emission transmission electron microscope. This paper reports details and specifications of the instrument. The microscope was designed to obtain a bright and coherent electron beam by using the field emission gun equipped with a pre-accelerating magnetic lens and the high-voltage power supply with high stability (0.5 ppm min(-1)). Using this microscope, the brightness of 1.8 x 10(10) A cm(-2) sr(-1) and the lattice resolution of 49.8 pm were attained.