Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.

The physical pendulum in an advanced undergraduate course in mechanics

The physical pendulum treated with a Hamiltonian formulation is a natural topic for study in a course in advanced classical mechanics. For the past three years, we have been offering a series of problem sets studying this system numerically in our third-year undergraduate courses in mechanics. The problem sets investigate the physics of the pendulum in ways not easily accessible without computer technology and explore various algorithms for solving mechanics problems. Our computational physics is based on Mathematica with some C communicating with Mathematica, although nothing in this paper is dependent on that choice. We have nonetheless found this system, and particularly its graphics, to be a good one for use with undergraduates.

Low-energy ion outflows from the ionosphere during a major polar cap expansion — evidence for equatorward motion of inverted-V structures

Data from the Dynamics Explorer 1 satellite and the EISCAT and Sondrestrom incoherent scatter radars, have allowed a study of low-energy ion outflows from the ionosphere into the magnetosphere during a rapid expansion of the polar cap. From the combined radar data, a 200kV increase in cross-cap potential is estimated. The upflowing ions show “X” signatures in the pitch angle-time spectrograms in the expanding midnight sector of the auroral oval. These signatures reveal low-energy (below about 60eV), light-ion beams sandwiched between two regions of ion conics and are associated with inverted-V electron precipitation. The lack of mass dispersion of the poleward edge of the event, despite great differences in the times of flight, reflects the equatorward expansion of the acceleration regions at velocities similar to those of the antisunward convection. In addition, a transient burst of upflow of 0+ is observed within the cap, possibly due to enhanced Joule heating during the event.

Homogeneous middles vs. heterogeneous tails, and the end of the ‘Inverted-U’: the share of the rich is what it’s all about

This paper examines the current global scene of distributional disparities within-nations. There are six main conclusions. First, about 80 per cent of the world’s population now live in regions whose median country has a Gini not far from 40. Second, as outliers are now only located among middle-income and rich countries, the ‘upwards’ side of the ‘Inverted-U’ between inequality and income per capita has evaporated (and with it the statistical support there was for the hypothesis that posits that, for whatever reason, ‘things have to get worse before they can get better’). Third, among middle-income countries Latin America and mineral-rich Southern Africa are uniquely unequal, while Eastern Europe follows a distributional path similar to the Nordic countries. Fourth, among rich countries there is a large (and growing) distributional diversity. Fifth, within a global trend of rising inequality, there are two opposite forces at work. One is ‘centrifugal’, and leads to an increased diversity in the shares appropriated by the top 10 and bottom 40 per cent. The other is ‘centripetal’, and leads to a growing uniformity in the income-share appropriated by deciles 5 to 9. Therefore, half of the world’s population (the middle and upper-middle classes) have acquired strong ‘property rights’ over half of their respective national incomes; the other half, however, is increasingly up for grabs between the very rich and the poor. And sixth, Globalisation is thus creating a distributional scenario in which what really matters is the income-share of the rich — because the rest ‘follows’ (middle classes able to defend their shares, and workers with ever more precarious jobs in ever more ‘flexible’ labour markets). Therefore, anybody attempting to understand the within-nations disparity of inequality should always be reminded of this basic distributional fact following the example of Clinton’s campaign strategist: by sticking a note on their notice-boards saying “It’s the share of the rich, stupid”.

Determination of the oxygen and nitrogen interstitial diffusion coeficient in niobium by mechanical spectroscopy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Study of interstitial oxygen mobility in RuSr2GdCu2O8 by internal friction

The discovery of the spatial uniform coexistence of superconductivity and ferromagnetism in ruthenocuprates, RuSr2GdCu2O8 (Ru-1212), has spurred an extraordinary development in the study of the competition between magnetism and superconductivity. However, several points of their preparation process and characterization that determine their superconductive behaviour are still obscure. The improvement of sample preparation conditions involves some thermal treatments in inert atmosphere. Anelastic spectroscopy measurements were made using an inverted torsion pendulum, operating with an oscillation frequency of 38 Hz, temperature in the 90 and 310 K range, heating rate of 1 K/min, and vacuum better than 10(-3) Pa. The results show anelastic relaxation peaks at 210 K related to the presence of interstitial oxygen atoms. The peaks decrease significantly with the oxygen loss caused by the heat treatments in vacuum, appearing again after the annealing of the sample in an oxygen atmosphere. These observed peaks are clearly related to the additional oxygen atoms, with activation energy 0.13 and 0.36 eV, and can be explained in terms by diffusional jumps of interstitial oxygen in the RuO2 planes. (C) 2009 Elsevier B.V. All rights reserved.

Dynamics of 5S rDNA in the tilapia (Oreochromis niloticus) genome: repeat units, inverted sequences, pseudogenes and chromosome loci

In higher eukaryotes, the 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units composed of a coding region and a non-transcribed spacer sequence (NTS). These tandem arrays can be found on either one or more chromosome pairs. 5S rDNA copies from the tilapia fish. Oreochromis niloticus, were cloned and the nucleotide sequences of the coding region and of the non-transcribed spacer were deter-mined. Moreover, the genomic organization of the 5S rDNA tandem repeats was investigated by fluorescence in situ hybridization (FISH) and Southern blot hybridization. Two 5S rDNA classes, one consisting of 1.4-kb repeats and another one with 0.5-kb repeats were identified and designated 5S rDNA type I and type II, respectively, An inverted 5S rRNA gene and a 5S rRNA putative pseudogene were also identified inside the tandem repeats of 5S rDNA type I. FISH permitted the visualization of the 5S rRNA genes at three chromosome loci, one of them consisting of arrays of the 5S rDNA type I, and the two others corresponding to arrays of the 5S rDNA type II. The two classes of the 5S rDNA. The presence of pseudogenes, and the inverted genes observed in the O. niloticus genome might be a consequence of the intense dynamics of the evolution of these tandem repeat elements. Copyright (C) 2002 S. Karger AG, Basel.

On chaotic behavior of a fixed offshore structure

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Stress induced ordering due interstitials in Nb-4.7 at.%Ta

The presence of interstitial elements in metals cause strong changes in their physical, chemical or mechanical properties. These interstitial impurities interact with the metallic matrix atoms by a relaxation process known as stress induced ordering. Relaxation processes give rise to a peak in the internal friction spectrum, known as Snock effect. The presence of substitutional solutes has a strong influence on Snoek effect, particularly if the substitutional solute element is the one, which interacts with the interstitial element. Anelastic spectroscopy measurements provide information of the behavior of these impurities in the metallic matrix. In this paper, polycrystalline samples of Nb-4.7 at.%Ta alloy have been analyzed in the as-received condition. Measurements of anelastic spectroscopy were carried out using an inverted torsion pendulum, operating with frequency of 2.0-30.0 Hz and in a temperature range between 300 and 700 K. It was observed the presence of a relaxation structure that have been attributed to stress induced ordering due to interstitial atoms around atoms of the metallic matrix. The relaxation structure have been decomposed in its constituent peaks, what it allowed to identify the following relaxation processes: Ta-O, Nb-O and Nb-N. (c) 2005 Elsevier B.V. All rights reserved.

Effect of interstitial impurities on internal friction measurements in niobium

Measurements of internal friction as a function of temperature were carried out in samples of mobium containing different amounts of interstitial solutes (oxygen and nitrogen) and one sample of mobium containing initially only nitrogen as interstitial solute. The experimental spectra of internal friction as a function of temperature were obtained with a torsion pendulum of the inverted Ke-type and resolved, using the method of successive subtraction, into a series of constituent Debye peaks corresponding to different interactions. For each relaxation process it was possible to obtain the height (Q(max)(-1)) and temperature (T-p) of the peak, the activation energy (E) and the relaxation time (t(o)). The height, shape and temperature of these peaks depend on the concentration of interstitial elements. The observed peaks were associated with matrix-interstitial (Nb-O, Nb-N) and interstitial-interstitial (O-N) interaction processes. (C) 2003 Elsevier B.V. All rights reserved.

Development of the inverted visceral yolk sac in three species of caviids (rodentia, caviomorpha, caviidae)

Guinea pig related rodents possess numerous derived placental characters. We attempt to identify diversity within the visceral yolk sac and its association with the chorioallantoic placenta in three species of caviids, two of them possessing a capsule formed by the decidua that covers the chorioallantoic placenta. The results verify that in early pregnancy all three species have in inverted yolk sac placenta. In advanced pregnancy the species differ: Galea spixii, as representative without a capsule, bear a yolk sac in apposition to the chorioallantoic placenta with signs of exchange activity until term. Galea is similar to other caviomorphs in this respect. In Dasyprocta leporina and Cuniculus paca, the representatives possessing a capsule, the yolk sac endoderm lacks signs of substance exchange. Evidently, the presence of a capsule prevents such ail interaction. The variations established here must be considered if animal models for human placentation are required which have restricted access to the chorioallantoic placenta from the outside. (C) 2008 Elsevier Ltd. All rights reserved.

A demonstration of dry and viscous damping of an oscillating pendulum

Damped oscillatory motion is one of the most widely studied movements in physics courses. Despite this fact, dry damped oscillatory motion is not commonly discussed in physics textbooks. In this work, we discuss the dry and viscous dampec pendulum, in a teaching experiment that can easily be performed by physics or engineering students.