Isolation, characterization and physiological properties of an autolytic-deficient mutant of Streptococcus pneumoniae

Summary A spontaneous mutation in the gene lyt encoding the pneumococcal autolysin has been characterized. This mutation, named lyt-32, which behaves as a high-efficiency marker in pneumococcal transformation, is a single base pair GC deletion causing the appearance of two consecutive termination codons in the amino terminal part of the sequence of the autolysin gene. The mutant lyt gene did not code for a polypeptide of relative molecular mass corresponding to the pneumococcal E form amidase in Escherichia coli maxicells. Pneumococcal cells containing the lyt-32 mutation (M32) were fully transformable, multiplied at a normal growth rate forming small chains and showed a tolerant response when treated with beta-lactam antibiotics. Strain M32 represents the first example of a mutant of Streptococcus pneumoniae completely lacking amidase as a consequence of an alteration in the structural gene coding for the pneumococcal autolysin.     

Molecular dynamics simulation of silicate glasses

Summary Although the structure of glasses is not really accessible by experimental methods, molecular dynamics is a very useful alternative, as we have tried to demonstrate in this chapter. The simulations reproduce the broad macroscopic features found in these glasses, both structural and transport-related, providing a basis for the more detailed atomic scale features found in the simulated structures. An understanding of important aspects of alkali ion transport, such as the mixed alkali effect and anomalous behaviour in some alumino-silicates, can thus be approached from the atomistic pictures of the glasses produced by the simulations. Although there is room for improvements to the potential models available, it should be clear that the further application of computer simulation methods, such as molecular dynamics, promises to provide much needed advances in glass science and engineering.     

人乳头瘤病毒16型E_7开放读码框编码免疫反应表位的定位

用核酸外切酶Ⅲ和s1核酸酶,逐步缺失能在原核细胞中有效表达人乳瘤病毒16型E_7开放读码框的质粒P16E_7TNP1,获得了一系列DNA逐渐缩短的质粒。它们能在大肠杆菌中表达产生一组从羧基端往氨基端逐步减少的融合蛋白,用Western blot方法检测相应融合蛋白与阳性血清的免疫反应。分析实验结果,编码免疫反应表位的核酸序列于619至644之间。     

The performances of the chi-square test and complexity measures for signal recognition in biological sequences

With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the Pearson's chi-square test method to determine which parts of the Open Reading Frame (ORF) have significant effect on discriminating genes form pseudogenes. Moreover, different complexity measures and Pearson's chi-square test applied on the genes with high value of Pearson's chi-square statistic. We also compute the measures on homologous of these genes. The results illustrate that there is a region near the start codon with high value of chi-square statistic and low complexity that is conserve between homologous genes.     

新型戊肝病毒ORF3和部分ORF1基因的序列分析

用RT－PCR方法对2例感染新型HEV的样品进行了检测,并对PCR产物进行了克隆及测序。检测结果显示用常规PCR检测易造成ORF3中GC丰富区的缺失,但不同于已报道的HEVⅠ型、Ⅱ型和Ⅲ型,为一新的基因型。T1和T11与Ⅰ型在该区的核苷酸同源性为79％－82％;与Ⅱ型的同源性为80％－81％;和Ⅲ型的同源性为83％－85％。     

Circular codes in archaeal genomes

A new statistical method associating each trinucleotide with a frame is developed for identifying circular codes. Its sensibility allows the detection of several circular codes in the (protein coding) genes of archaeal genomes. Several properties of these circular codes are described, in particular the lengths of the minimal windows to retrieve the construction frames, a new definition of a parameter for measuring some probabilities of words generated by the circular codes, and the types of nucleotides in the trinucleotide sites. Some biological consequences are presented in Discussion.     

Effect of erbium ion concentration on structural and luminescence properties of lead borosilicate glasses for fiber amplifiers

This investigation reports, the effect of the concentration of erbium and lead ions on the physical, structural and optical properties of lead borosilicate glasses. These glasses were synthesized by the melt quench method. In the synthesis, the concentration of the erbium (Er³⁺) ion was varied in the order of 0.0, 0.1, 0.5, 1.0 and 2.0 mol% and lead (Pb²⁺) ion was varied in the order of 30, 29.9, 29.5, 29 and 28 mol%. The glasses were analyzed using X‐ray diffraction (XRD), Fourier transform infrared (FT‐IR) and UV–vis–NIR spectroscopy. From XRD, the amorphous nature of lead borosilicate glasses was confirmed. The functional groups which were present in the glasses have been identified by analyzing the FT‐IR spectrum. From the absorption spectra, the oscillator strengths as well as the Judd–Ofelt (JO) intensity parameters were determined and compared with other hosts. The JO intensity parameters were further used to calculate certain radiative properties for the excited luminescent levels of Er³⁺ ion. From emission spectra, full width at half maxima (FWHM), stimulated emission cross‐sections (σ_e) and certain lasing parameters were evaluated and compared with reference host glasses. The lifetimes of ⁴I_13/2 excited level of Er³⁺ ion have also been recorded and analyzed. The calculated and experimental lifetimes were compared in terms of quantum efficiencies. From the photoluminescence analysis, the erbium doped lead borosilicate glasses well suited for optical fiber amplifiers are discussed.     

The manipulation of ethnicity: from ethnic cooperation to violence and war in Yugoslavia

The story of the failure of bargaining among ethnic élites and of international diplomacy is well known. What has not been well explained is the spread and support for xenophobic nationalism and ethnic violence among people who had lived cooperatively for thirty-five years. I draw on key ideas of four views on ethnicity and ethnic conflict, and add the concept of cognitive frame in ethnic relations. Yugoslavs possessed two ethnic frames in their minds, an ethnic cooperation and peace frame for normal times, and a crisis frame anchored in World War II memories. Élite contention and mass media propaganda awakened the dormant crisis frame, suppressed the normal frame, and spread insecurity and fear. I explain why ethnic manipulation succeeded, people believed falsehoods, voted for nationalists, how moderates were purged and why men in militias killed innocent civilians.     

Emission analysis of RE3+ (RE = Sm,Dy):B2O3‐TeO2‐Li2O‐AlF3 glasses

This article reports on the optical properties of 0.5% mol of Sm³⁺, Dy³⁺ ion‐doped B₂O₃‐TeO₂‐Li₂O‐AlF₃ (LiAlFBT) glasses. The glass samples were characterized by optical absorption and emission spectra. Judd‐Ofelt theory was applied to analyze the optical absorption spectra and calculate the intensity parameters and radiative properties of the emission transitions. The emission spectra of Sm³⁺ and Dy³⁺:LiAlFBT glasses showed a bright reddish‐orange emission at 598 nm (⁴G_5/2 → ⁶H_7/2) and an intense yellow emission at 574 nm (⁴F_9/2 → ⁶H_13/2), respectively. Full width at half maximum (FWHM), stimulated emission cross section, gain bandwidth and optical gain values were also calculated to extend the applications of the Sm³⁺ and Dy³⁺:LiAlFBT glasses. Copyright © 2012 John Wiley & Sons, Ltd.     

Numerical Study of the Structural and Thermal Properties of Vitreous Silica

Abstract

We use classical molecular dynamics simulations to study both the structural modifications through the glass transition and the thermal conductivity k of a model silica glass. The first part is based on the Voronoï tessellation and we show that the structural freezing following upon the glass transition is noticeable in all the geometric characteristics of the Voronoï cells and a possible interpretation in terms of geometrical frustration is proposed.

In the second part we calculate k directly in the simulation box by using the standard equations of heat transport. The calculations have been done between 10 and 1000 Kelvin and the results are in good agreement with the experimental data at temperatures above 20 K. The plateau observed around 10 K can be accounted for by correcting our results taking into account finite size effects in a phenomenological way.