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.

Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots

Background: Seed storage proteins are a major source of dietary protein, and the content of such proteins determines both the quantity and quality of crop yield. Significantly, examination of the protein content in the seeds of crop plants shows a distinct difference between monocots and dicots. Thus, it is expected that there are different evolutionary patterns in the genes underlying protein synthesis in the seeds of these two groups of plants. Results: Gene duplication, evolutionary rate and positive selection of a major gene family of seed storage proteins (the 11S globulin genes), were compared in dicots and monocots. The results, obtained from five species in each group, show more gene duplications, a higher evolutionary rate and positive selections of this gene family in dicots, which are rich in 11S globulins, but not in the monocots. Conclusion: Our findings provide evidence to support the suggestion that gene duplication and an accelerated evolutionary rate may be associated with higher protein synthesis in dicots as compared to monocots.

Strong structural controllability and the multi-link inverted pendulum

This technical note investigates the controllability of the linearized dynamics of the multilink inverted pendulum as the number of links and the number and location of actuators changes. It is demonstrated that, in some instances, there exist sets of parameter values that render the system uncontrollable and so usual methods for assessing controllability are difficult to employ. To assess the controllability, a theorem on strong structural controllability for single-input systems is extended to the multiinput case.

Strong structural controllability and the multilink inverted pendulum

This technical note investigates the controllability of the linearized dynamics of the multilink inverted pendulum as the number of links and the number and location of actuators changes. It is demonstrated that, in some instances, there exist sets of parameter values that render the system uncontrollable and so usual methods for assessing controllability are difficult to employ. To assess the controllability, a theorem on strong structural controllability for single-input systems is extended to the multiinput case.

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.

Distinct clinical and neuropathological features of G51D SNCA mutation cases compared with SNCA duplication and H50Q mutation

Background: We and others have described the neurodegenerative disorder caused by G51D SNCA mutation which shares characteristics of Parkinson’s disease (PD) and multiple system atrophy (MSA). The objective of this investigation was to extend the description of the clinical and neuropathological hallmarks of G51D mutant SNCA-associated disease by the study of two additional cases from a further G51D SNCA kindred and to compare the features of this group with a SNCA duplication case and a H50Q SNCA mutation case. Results: All three G51D patients were clinically characterised by parkinsonism, dementia, visual hallucinations, autonomic dysfunction and pyramidal signs with variable age at disease onset and levodopa response. The H50Q SNCA mutation case had a clinical picture that mimicked late-onset idiopathic PD with a good and sustained levodopa response. The SNCA duplication case presented with a clinical phenotype of frontotemporal dementia with marked behavioural changes, pyramidal signs, postural hypotension and transiently levodopa responsive parkinsonism. Detailed post-mortem neuropathological analysis was performed in all cases. All three G51D cases had abundant α-synuclein pathology with characteristics of both PD and MSA. These included widespread cortical and subcortical neuronal α-synuclein inclusions together with small numbers of inclusions resembling glial cytoplasmic inclusions (GCIs) in oligodendrocytes. In contrast the H50Q and SNCA duplication cases, had α-synuclein pathology resembling idiopathic PD without GCIs. Phosphorylated α-synuclein was present in all inclusions types in G51D cases but was more restricted in SNCA duplication and H50Q mutation. Inclusions were also immunoreactive for the 5G4 antibody indicating their highly aggregated and likely fibrillar state. Conclusions: Our characterisation of the clinical and neuropathological features of the present small series of G51D SNCA mutation cases should aid the recognition of this clinico-pathological entity. The neuropathological features of these cases consistently share characteristics of PD and MSA and are distinct from PD patients carrying the H50Q or SNCA duplication.

Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching

Duplication at the Xq28 band including the MECP2 gene is one of the most common genomic rearrangements identified in neurodevelopmentally delayed males. Such duplications are non-recurrent and can be generated by a non-homologous end joining (NHEJ) mechanism. We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size from similar to 250 kb to similar to 2.6 Mb. Interestingly, in 77% of these non-recurrent duplications, the distal breakpoints grouped within a 215 kb genomic interval, located 47 kb telomeric to the MECP2 gene. The genomic architecture of this region contains both direct and inverted low-copy repeat (LCR) sequences; this same region undergoes polymorphic structural variation in the general population. Array CGH revealed complex rearrangements in eight patients; in six patients the duplication contained an embedded triplicated segment, and in the other two, stretches of non-duplicated sequences occurred within the duplicated region. Breakpoint junction sequencing was achieved in four duplications and identified an inversion in one patient, demonstrating further complexity. We propose that the presence of LCRs in the vicinity of the MECP2 gene may generate an unstable DNA structure that can induce DNA strand lesions, such as a collapsed fork, and facilitate a Fork Stalling and Template Switching event producing the complex rearrangements involving MECP2.

Duplication of R&D and industry concentration

The purpose of the literature on Research Joint Ventures (RJV), pioneered by DíAspremont and Jacquemin (1988) and Kamien, Muller, and Zang (1992), has been to combine the best of two worlds: to appropriately deal with R&D spillovers while preserving competition in the product market. Moreover, RJVs eliminate duplication of R&D. Thus, at least in theory, RJVs dominate other solutions such as subsidies. If, however, we are concerned about risks of cartelization, then Spenceís (1984) subsidy-based solution for independently acting firms, is a viable alternative that cannot be dismissed. Indeed, in contrast to the previous literature, we find that in the presence of R&D subsidies, market performance may unambiguously improve with the number of firms in the market.

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”.

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.

Non-linear dynamics of a tower orchard sprayer based on an inverted pendulum model

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

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.

Diagnostic agreement of conventional and inverted scanned panoramic radiographs in the detection of the mandibular canal and the mental foramen.

The aim of this study was to evaluate the diagnostic agreement of conventional panoramic radiographs and their inverted scanned images in the detection of the mandibular canal and mental foramen. A total of 77 panoramic radiographs obtained from the files of totally edentulous patients were used. Digitization was done by means of a scanner with brightness and contrast adjustment, as well as image inversion. The extension of mandibular canal was divided into anterior, middle, and posterior regions, and the presence of a radiopaque line that characterized the mandibular canal was classified according to a 5-point confidence scale. The mental foramen was classified in 4 types: continuous, separated, diffuse, and unidentified. Both conventional and inverted scanned panoramic radiographs were evaluated by 3 calibrated implantologists at 2 distinct moments with a minimum interval of 10 days between them. Intraexaminer agreement was evaluated by Kappa statistics by point and by 95% confidence interval. Because the intraexaminer level of agreement was low, interexaminer agreements could not be carried out. The results showed a substantial (in 2 situations), moderate (in 16 situations), and fair (in 18 situations) intraexaminer agreement for mandibular canal and a substantial (in 1 situation), fair (in 1 situation), and moderate (in 10 situations) intraeaminer agreement for mental foramen. There were no statistically significant differences in most instances. In conclusion, the diagnostic agreement of conventional and inverted scanned panoramic radiographs for detection of mandibular canal and mental foramen was low.