Icosahedral multi-component model sets

A quasiperiodic packing Q of interpenetrating copies of C, most of them only partially occupied, can be defined in terms of the strip projection method for any icosahedral cluster C. We show that in the case when the coordinates of the vectors of C belong to the quadratic field Q[\sqrt{5}] the dimension of the superspace can be reduced, namely, Q can be re-defined as a multi-component model set by using a 6-dimensional superspace.Comment: 7 pages, LaTeX2e in IOP styl

A molecular overlayer with the Fibonacci square grid structure

Quasicrystals differ from conventional crystals and amorphous materials in that they possess long-range order without periodicity. They exhibit orders of rotational symmetry which are forbidden in periodic crystals, such as five-, ten-, and twelve-fold, and their structures can be described with complex aperiodic tilings such as Penrose tilings and Stampfli-Gaehler tilings. Previous theoretical work explored the structure and properties of a hypothetical four-fold symmetric quasicrystal-the so-called Fibonacci square grid. Here, we show an experimental realisation of the Fibonacci square grid structure in a molecular overlayer. Scanning tunnelling microscopy reveals that fullerenes (C ) deposited on the two-fold surface of an icosahedral Al-Pd-Mn quasicrystal selectively adsorb atop Mn atoms, forming a Fibonacci square grid. The site-specific adsorption behaviour offers the potential to generate relatively simple quasicrystalline overlayer structures with tunable physical properties and demonstrates the use of molecules as a surface chemical probe to identify atomic species on similar metallic alloy surfaces

Structure of the icosahedral Ti-Zr-Ni quasicrystal

The atomic structure of the icosahedral Ti-Zr-Ni quasicrystal is determined by invoking similarities to periodic crystalline phases, diffraction data and the results from ab initio calculations. The structure is modeled by decorations of the canonical cell tiling geometry. The initial decoration model is based on the structure of the Frank-Kasper phase W-TiZrNi, the 1/1 approximant structure of the quasicrystal. The decoration model is optimized using a new method of structural analysis combining a least-squares refinement of diffraction data with results from ab initio calculations. The resulting structural model of icosahedral Ti-Zr-Ni is interpreted as a simple decoration rule and structural details are discussed.Comment: 12 pages, 8 figure

DICER1 mutations in childhood cystic nephroma and its relationship to DICER1-renal sarcoma

The pathogenesis of cystic nephroma of the kidney has interested pathologists for over 50 years. Emerging from its initial designation as a type of unilateral multilocular cyst, cystic nephroma has been considered as either a developmental abnormality or a neoplasm or both. Many have viewed cystic nephroma as the benign end of the pathologic spectrum with cystic partially differentiated nephroblastoma and Wilms tumor, whereas others have considered it a mixed epithelial and stromal tumor. We hypothesize that cystic nephroma, like the pleuropulmonary blastoma in the lung, represents a spectrum of abnormal renal organogenesis with risk for malignant transformation. Here we studied DICER1 mutations in a cohort of 20 cystic nephromas and 6 cystic partially differentiated nephroblastomas, selected independently of a familial association with pleuropulmonary blastoma and describe four cases of sarcoma arising in cystic nephroma, which have a similarity to the solid areas of type II or III pleuropulmonary blastoma. The genetic analyses presented here confirm that DICER1 mutations are the major genetic event in the development of cystic nephroma. Further, cystic nephroma and pleuropulmonary blastoma have similar DICER1 loss of function and ‘hotspot' missense mutation rates, which involve specific amino acids in the RNase IIIb domain. We propose an alternative pathway with the genetic pathogenesis of cystic nephroma and DICER1-renal sarcoma paralleling that of type I to type II/III malignant progression of pleuropulmonary blastoma

Highly Precise and Developmentally Programmed Genome Assembly in Paramecium Requires Ligase IV–Dependent End Joining

During the sexual cycle of the ciliate Paramecium, assembly of the somatic genome includes the precise excision of tens of thousands of short, non-coding germline sequences (Internal Eliminated Sequences or IESs), each one flanked by two TA dinucleotides. It has been reported previously that these genome rearrangements are initiated by the introduction of developmentally programmed DNA double-strand breaks (DSBs), which depend on the domesticated transposase PiggyMac. These DSBs all exhibit a characteristic geometry, with 4-base 5′ overhangs centered on the conserved TA, and may readily align and undergo ligation with minimal processing. However, the molecular steps and actors involved in the final and precise assembly of somatic genes have remained unknown. We demonstrate here that Ligase IV and Xrcc4p, core components of the non-homologous end-joining pathway (NHEJ), are required both for the repair of IES excision sites and for the circularization of excised IESs. The transcription of LIG4 and XRCC4 is induced early during the sexual cycle and a Lig4p-GFP fusion protein accumulates in the developing somatic nucleus by the time IES excision takes place. RNAi–mediated silencing of either gene results in the persistence of free broken DNA ends, apparently protected against extensive resection. At the nucleotide level, controlled removal of the 5′-terminal nucleotide occurs normally in LIG4-silenced cells, while nucleotide addition to the 3′ ends of the breaks is blocked, together with the final joining step, indicative of a coupling between NHEJ polymerase and ligase activities. Taken together, our data indicate that IES excision is a “cut-and-close” mechanism, which involves the introduction of initiating double-strand cleavages at both ends of each IES, followed by DSB repair via highly precise end joining. This work broadens our current view on how the cellular NHEJ pathway has cooperated with domesticated transposases for the emergence of new mechanisms involved in genome dynamics

Characterization of a Human Cell Line Stably Over-Expressing the Candidate Oncogene, Dual Specificity Phosphatase 12

Analysis of chromosomal rearrangements within primary tumors has been influential in the identification of novel oncogenes. Identification of the "driver" gene(s) within cancer-derived amplicons is, however, hampered by the fact that most amplicons contain many gene products. Amplification of 1q21-1q23 is strongly associated with liposarcomas and microarray-based comparative genomic hybridization narrowed down the likely candidate oncogenes to two: the activating transcription factor 6 (atf6) and the dual specificity phosphatase 12 (dusp12). While atf6 is an established transcriptional regulator of the unfolded protein response, the potential role of dusp12 in cancer remains uncharacterized.To evaluate the oncogenic potential of dusp12, we established stable cell lines that ectopically over-express dusp12 in isolation and determined whether this cell line acquired properties frequently associated with transformed cells. Here, we demonstrate that cells over-expressing dusp12 display increased cell motility and resistance to apoptosis. Additionally, over-expression of dusp12 promoted increased expression of the c-met proto-oncogene and the collagen and laminin receptor intergrin alpha 1 (itga1) which is implicated in metastasis.Collectively, these results suggest that dusp12 is oncologically relevant and exposes a potential association between dusp12 and established oncogenes that could be therapeutically targeted

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia

International audienceBACKGROUND: The genome of Paramecium tetraurelia, a unicellular model that belongs to the ciliate phylum, has been shaped by at least 3 successive whole genome duplications (WGD). These dramatic events, which have also been documented in plants, animals and fungi, are resolved over evolutionary time by the loss of one duplicate for the majority of genes. Thanks to a low rate of large scale genome rearrangement in Paramecium, an unprecedented large number of gene duplicates of different ages have been identified, making this organism an outstanding model to investigate the evolutionary consequences of polyploidization. The most recent WGD, with 51% of pre-duplication genes still in 2 copies, provides a snapshot of a phase of rapid gene loss that is not accessible in more ancient polyploids such as yeast. RESULTS: We designed a custom oligonucleotide microarray platform for P. tetraurelia genome-wide expression profiling and used the platform to measure gene expression during 1) the sexual cycle of autogamy, 2) growth of new cilia in response to deciliation and 3) biogenesis of secretory granules after massive exocytosis. Genes that are differentially expressed during these time course experiments have expression patterns consistent with a very low rate of subfunctionalization (partition of ancestral functions between duplicated genes) in particular since the most recent polyploidization event. CONCLUSIONS: A public transcriptome resource is now available for Paramecium tetraurelia. The resource has been integrated into the ParameciumDB model organism database, providing searchable access to the data. The microarray platform, freely available through NimbleGen Systems, provides a robust, cost-effective approach for genome-wide expression profiling in P. tetraurelia. The expression data support previous studies showing that at short evolutionary times after a whole genome duplication, gene dosage balance constraints and not functional change are the major determinants of gene retention

Murine Models and Cell Lines for the Investigation of Pheochromocytoma: Applications for Future Therapies?

Pheochromocytomas (PCCs) are slow-growing neuroendocrine tumors arising from adrenal chromaffin cells. Tumors arising from extra-adrenal chromaffin cells are called paragangliomas. Metastases can occur up to approximately 60% or even more in specific subgroups of patients. There are still no well-established and clinically accepted “metastatic” markers available to determine whether a primary tumor is or will become malignant. Surgical resection is the most common treatment for non-metastatic PCCs, but no standard treatment/regimen is available for metastatic PCC. To investigate what kind of therapies are suitable for the treatment of metastatic PCC, animal models or cell lines are very useful. Over the last two decades, various mouse and rat models have been created presenting with PCC, which include models presenting tumors that are to a certain degree biochemically and/or molecularly similar to human PCC, and develop metastases. To be able to investigate which chemotherapeutic options could be useful for the treatment of metastatic PCC, cell lines such as mouse pheochromocytoma (MPC) and mouse tumor tissue (MTT) cells have been recently introduced and they both showed metastatic behavior. It appears these MPC and MTT cells are biochemically and molecularly similar to some human PCCs, are easily visualized by different imaging techniques, and respond to different therapies. These studies also indicate that some mouse models and both mouse PCC cell lines are suitable for testing new therapies for metastatic PCC

SYMMETRY AND PHASE TRANSFORMATION

The symmetry properties are among the simplest deterministic principles which allow us to recognize equivalencies between different crystalline morphologies. The basic idea is essentially that the total symmetry of the resulting morphology reflects the symmetry of the originating process : for example, the different types of variants induced by a phase transition are related to the coset decomposition of the space groups of the involved structures onto their intersection group. A scheme has been proposed for the numbering and labelling of the variants nucleated in an anisotropic medium. More recently the importance of the Intersection Group has been pointed out as one of the basic ingredients for the study of precipitate morphology. The symmetry considerations are not only an easy way of reducing the configurational space of a certain physical property to a non redundant subspace, but they also allow for the determination of the "symmetry dictated extrema" of the considered physical property. This promising way will certainly induce a new development in the understanding of martensite morphologies

GENERAL GEOMETRICAL MODELS OF GRAIN BOUNDARIES

A la suite des travaux de Bollmann, de nombreux modèles géométriques ont été proposés pour décrire les joints de grains. Ces modèles ne s'appliquent qu'aux structures symorphiques ne contenant qu'un atome par maille. Les restrictions peuvent être facilement évitées en introduisant quelques concepts élémentaires de cristallographie qui conduisent à une description unifiée des interfaces homophases. La notion d'extrema imposés par la symétrie est discutée pour la relaxation de la translation rigide en relation avec les travaux originaux de G. Kalonji et J.W. Cahn.Geometric models of grain boundaries have been extensively studied following Bollmann's original ideas. These models apply only for symmorphic structures with one atom per primitive unit cell. These restrictions may be easily avoided by introducing some elementary concepts of crystallography which lead to an unified description of homophase interfaces. The notion of symmetry dictated extrema is discussed for the relaxation of the rigid body translation in connection with Kalonji and Cahn's original works