Genomic organization and evolution of the 5S ribosomal DNA in Tilapiini fishes

5S rDNA sequences present an intense dynamism and have proved to be valuable as genetic markers to distinguish closed related species and also in the understanding of the evolutionary dynamic of repetitive sequences in the genomes. In order to identify patterns of 5S rDNA organization and their evolution in the genome of fish species, such genomic segment was investigated in the tilapias Oreochromis niloticus and Tilapia rendalli, and in the hybrid O. urolepis hornorum x O. mossambicus. A dual 5S rDNA system was identified in the three analyzed tilapia samples. Although each 5S rDNA class was conserved among the three samples, a distinct 5S rDNA genome organization pattern could be evidenced for each sample. The presence of a dual 5S rDNA system seems to be a general trait among non-related teleost fish orders, suggesting that evolutionary events of duplication have occurred before the divergence of the main groups of teleost fishes.

Molecular epidemiology and evolution of avian infectious bronchitis virus

Mutation and recombination processes are involved in the genetic and phenotypic variations of RNA viruses, leading to the emergence of new variant strains, and give rise to virus population diversity to be modeled by the host, particularly by the immune system, as occurred with infectious bronchitis virus (IBV) in chickens. The consequence is a continuous emergence of new IBV variants with regard to pathotypes, serotypes, and protectotypes. Nucleotide sequencing and subsequent genetic analysis of the S1 and N protein gene sequences provide a fast and accurate method to classify and predict IBV genotype, and a powerful instrument to monitor phylogenetic and epidemiological evolution of IBV variants. Despite the use of vaccination programmes, infectious bronchitis has become a serious problem in Brazil. Thus, a significant number of IBV field variants have been identified circulating in the Brazilian commercial poultries between 2000 to 2006 and more recently in Argentina. These viruses seem to be indigenous, because they demonstrated a low genetic relatedness with the majority of the reference strains from North America, Europe and Asia, but were moderately to highly related one to another. In summary, indigenous field IBV variants were evolving and circulating in the field in Brazil and Argentina, and should be considered as initial candidates for protection against current IBV infectious in chickens. However, in vitro and in vivo studies are needed to determine the pathogenicity and immunogenecity of these new isolates, before defining a new vaccine strain.

Aplicação do Índice Relaçáo Declividade-Extensão - RDE Na Bacia do Rio do Peixe (SP) para Detecção de Deformações Neotectô nicas

This paper presents the identification of tectonic deformation through the application of the stream-gradient index (slope x length) method in the Rio do Peixe hydrographic basin, located in western State of Sã o Paulo. The main principle used is that river valleys are the best tools for this type of analysis because of their fast adjustment to even the most gentle crustal deformations. This type of analysis for structural studies is extremely useful in the western region of the State of São Paulo, where deep chemical weathering results in a thick regolith and scarce outcrops. The stream length index is the ratio of the altimetric amplitude of each drainage and the natural logarithm of its length. The value obtained is plotted on maps at the median point of each drainage, allowing the drawings of lines with the same values (isodefs). Three anomalies (A, B and C) were identified along the Rio do Peixe valley representing uplift sectors indicated by the formation and distribution of Upper Quaternary deposits in terraces and modern fluvial plains and alluvial fans. In correlation with known tectonic data for this region it is possible to attribute the A and B anomalies to the Ribeirão Preto and Presidente Prudente crustal sutures, respectively. The smaller C anomaly needs further field investigation, but it could be associated with the Três Lagoas crustal suture. It must be emphasised that these sutures are inherited from the Precambrian Basement which had a strong influence on the Phanerozoic evolution in the whole sedimentary and volcanic stratigraphic pile of the Paraná Basin and on the dominant structural lineaments directions developed therein .The A, Band C anomalies are suggestive of renewed uplift as a result of neotectonic action in modern times.

Evolution of the South Atlantic passive continental margin in southern Brazil derived from zircon and apatite (U-Th-Sm)/He and fission-track data

The area between São Paulo and Porto Alegre in southeastern Brazil plays a key area to understand and quantify the evolution of the South Atlantic passive continental margin (SAPCM) in Brazil. In this contribution, we present new thermochronological data attained by fission-track and (U-Th-Sm)/He analysis on apatites and zircons from metamorphic, sedimentary and intrusive rocks. The zircon fission-track ages range between 108.4 (15.0) and 539.9 (68.4). Ma, the zircon (U-Th-Sm)/He ages between 72.9 (5.8) and 525.1(2.4). Ma, whereas the apatite fission-track ages range between 40.0 (5.3) and 134.7 (8.0). Ma, and the apatite (U-Th-Sm)/He ages between 32.1 (1.5) and 93.0 (2.5). Ma. The spatial distribution of these ages shows three distinct blocks with a different evolution cut by old fracture zones. While the central block exhibits an old stable block, the Northern and especially the Southern block underwent complex post-rift exhumation. The sample of the Northern block shows two distinct cooling phases in the Upper Cretaceous and the Paleogene to Neogene. After sedimentation of the Permian sandstones the samples of the Central block were never heated up over 100. °C with a following moderate to fast cooling phase in Cretaceous to Eocene time and a fast cooling between Oligocene to Miocene. The five thermal models obtained in the Southern block indicate a complex evolution with three cooling phases. The exhumation events of the three blocks correspond with the Paraná-Etendekka event, the alkaline intrusions due to the Trinidad hotspot, and the evolution of the continental rift basins in SE Brazil and are, therefore, most likely to be the major force for the post-rift evolution of the passive continental margin in SE Brazil, which therefore corresponds to the three main phases of the Andean orogeny. © 2013 Elsevier B.V.

Trichome structure and evolution in Neotropical lianas

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

Environment and dispersal paths override life strategies and residence time in determining regional patterns of invasion by alien plants

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Neoproterozoic to middle Palaeozoic evolution of the Central Asian Orogenic Belt in south-central Mongolia: chronological and geochemical perspectives

Mongolia occupies a central position within the eastern branch of the large accretionary Central Asian Orogenic Belt (CAOB) or Altaids. The present work aims to outline the geodynamic environment and possible evolution of this part of the eastern CAOB, predominantly from the Cambrian to the middle Palaeozoic. The investigation primarily focussed on zircon geochronology as well as whole-rock geochemical and Sm–Nd isotopic analyses for a variety of metaigneous rocks from the southern Hangay and Gobi-Altai regions in south-central Mongolia. The southern slope of the Hangay Mountains in central Mongolia exposes a large NWSE-trending middle Neoproterozoic ophiolitic complex (c. 650 Ma), which is tectonically integrated within an accretionary complex developed between the Precambrian Baydrag and Hangay crustal blocks. Formation of the entire accretionary system along the north-eastern margin of the Baydrag block mainly occurred during the early Cambrian, but convergence within this orogenic zone continued until the early Ordovician, because of on-going southward subduction-accretion of the Baydrag block. An important discovery is the identification of a late Mesoproterozoic to early Neoproterozoic belt within the northern Gobi-Altai that was reworked during the late Cambrian and throughout the late Ordovician/Devonian. Early Silurian low-grade mafic and felsic metavolcanic rocks from the northern Gobi-Altai display subduction-related geochemical features and highly heterogeneous Nd isotopic compositions, which suggest an origin at a mature active continental margin. Early Devonian protoliths of granodioritic and mafic gneisses from the southern Gobi-Altai display geochemical and Nd isotopic compositions compatible with derivation and evolution from predominantly juvenile crustal and mantel sources and these rocks may have been emplaced within the outboard portion of the late Ordovician/early Silurian active continental margin. Moreover, middle Devonian low-grade metavolcanic rocks from the southwestern Gobi-Altai yielded geochemical and Nd isotopic data consistent with emplacement in a transitional arc-backarc setting. The combined U–Pb zircon ages and geochemical data obtained from the Gobi-Altai region suggest that magmatism across an active continental margin migrated oceanwards through time by way of subduction zone retreat throughout the Devonian. Progressive extension of the continental margin was associated with the opening of a backarc basin and culminated in the late Devonian with the formation of a Japan-type arc front facing a southward open oceanic realm (present-day coordinates).

Land use management in mountainous areas: combining ground-based and EO (Earth Observation) data to investigate the shallow landsliding susceptibility in the Duron valley (Trento, Italy).

Throughout the alpine domain, shallow landslides represent a serious geologic hazard, often causing severe damages to infrastructures, private properties, natural resources and in the most catastrophic events, threatening human lives. Landslides are a major factor of landscape evolution in mountainous and hilly regions and represent a critical issue for mountainous land management, since they cause loss of pastoral lands. In several alpine contexts, shallow landsliding distribution is strictly connected to the presence and condition of vegetation on the slopes. With the aid of high-resolution satellite images, it's possible to divide automatically the mountainous territory in land cover classes, which contribute with different magnitude to the stability of the slopes. The aim of this research is to combine EO (Earth Observation) land cover maps with ground-based measurements of the land cover properties. In order to achieve this goal, a new procedure has been developed to automatically detect grass mantle degradation patterns from satellite images. Moreover, innovative surveying techniques and instruments are tested to measure in situ the shear strength of grass mantle and the geomechanical and geotechnical properties of these alpine soils. Shallow landsliding distribution is assessed with the aid of physically based models, which use the EO-based map to distribute the resistance parameters across the landscape.

Control over microstructure evolution and device performance in solution processable organic field-effect transistors

Die Arbeit beschäftigt sich mit der Kontrolle von Selbstorganisation und Mikrostruktur von organischen Halbleitern und deren Einsatz in OFETs. In Kapiteln 3, 4 und 5 eine neue Lösungsmittel-basierte Verabeitungsmethode, genannt als Lösungsmitteldampfdiffusion, ist konzipiert, um die Selbstorganisation von Halbleitermolekülen auf der Oberfläche zu steuern. Diese Methode als wirkungsvolles Werkzeug erlaubt eine genaue Kontrolle über die Mikrostruktur, wie in Kapitel 3 am Beispiel einer D-A Dyad bestehend aus Hexa-peri-hexabenzocoronene (HBC) als Donor und Perylene Diimide (PDI) als Akzeptor beweisen. Die Kombination aus Oberflächenmodifikation und Lösungsmitteldampf kann die Entnetzungseffekte ausgleichen, so dass die gewüschte Mikrostruktur und molekulare Organisation auf der Oberfläche erreicht werden kann. In Kapiteln 4 und 5 wurde diese Methode eingesetzt, um die Selbstorganisation von Dithieno[2, 3-d;2’, 3’-d’] benzo[1,2-b;4,5-b’]dithiophene (DTBDT) und Cyclopentadithiophene -benzothiadiazole copolymer (CDT-BTZ) Copolymer zu steuern. Die Ergebnisse könnten weitere Studien stimulieren und werfen Licht aus andere leistungsfaähige konjugierte Polymere. rnIn Kapiteln 6 und 7 Monolagen und deren anschlieβende Mikrostruktur von zwei konjugierten Polymeren, Poly (2,5-bis(3-alkylthiophen-2-yl)thieno[3,2-b]thiophene) PBTTT und Poly{[N,N ′-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis (dicarboximide)-2,6-diyl]-alt-5,5′- (2,2′-bithiophene)}, P(NDI2OD-T2)) wurden auf steife Oberflächen mittels Tauchbeschichtung aufgebracht. Da sist das erste Mal, dass es gelungen ist, Polymer Monolagen aus der Lösung aufzubringen. Dieser Ansatz kann weiter auf eine breite Reihe von anderen konjugierten Polymeren ausgeweitet werden.rnIn Kapitel 8 wurden PDI-CN2 Filme erfolgreich von Monolagen zu Bi- und Tri-Schichten auf Oberflächen aufgebracht, die unterschiedliche Rauigkeiten besitzen. Für das erste Mal, wurde der Einfluss der Rauigkeit auf Lösungsmittel-verarbeitete dünne Schichten klar beschrieben.rn

Landscape and forest structure at moose mortality sites on Isle Royale National Park. A LiDAR based assessment

Landscape structure and heterogeneity play a potentially important, but little understood role in predator-prey interactions and behaviourally-mediated habitat selection. For example, habitat complexity may either reduce or enhance the efficiency of a predator's efforts to search, track, capture, kill and consume prey. For prey, structural heterogeneity may affect predator detection, avoidance and defense, escape tactics, and the ability to exploit refuges. This study, investigates whether and how vegetation and topographic structure influence the spatial patterns and distribution of moose (Alces alces) mortality due to predation and malnutrition at the local and landscape levels on Isle Royale National Park. 230 locations where wolves (Canis lupus) killed moose during the winters between 2002 and 2010, and 182 moose starvation death sites for the period 1996-2010, were selected from the extensive Isle Royale Wolf-Moose Project carcass database. A variety of LiDAR-derived metrics were generated and used in an algorithm model (Random Forest) to identify, characterize, and classify three-dimensional variables significant to each of the mortality classes. Furthermore, spatial models to predict and assess the likelihood at the landscape scale of moose mortality were developed. This research found that the patterns of moose mortality by predation and malnutrition across the landscape are non-random, have a high degree of spatial variability, and that both mechanisms operate in contexts of comparable physiographic and vegetation structure. Wolf winter hunting locations on Isle Royale are more likely to be a result of its prey habitat selection, although they seem to prioritize the overall areas with higher moose density in the winter. Furthermore, the findings suggest that the distribution of moose mortality by predation is habitat-specific to moose, and not to wolves. In addition, moose sex, age, and health condition also affect mortality site selection, as revealed by subtle differences between sites in vegetation heights, vegetation density, and topography. Vegetation density in particular appears to differentiate mortality locations for distinct classes of moose. The results also emphasize the significance of fine-scale landscape and habitat features when addressing predator-prey interactions. These finer scale findings would be easily missed if analyses were limited to the broader landscape scale alone.

Molecular phylogenetic analyses identify Alpine differentiation and dysploid chromosome number changes as major forces for the evolution of the European endemic Phyteuma (Campanulaceae)

Phyteuma is a chromosomally and ecologically diverse vascular plant genus and constitutes an excellent system for studying both the role of chromosomal change for species diversification and the evolution of high-mountain biota. This kind of research is, however, hampered by the lack of a sound phylogenetic framework exacerbated by the notoriously low predictive power of traditional taxonomy with respect to phylogenetic relationships in Campanulaceae. Based on a comprehensive taxon sampling and analyses of nuclear and plastid sequence and AFLP fingerprint data, Phyteuma is confirmed as a monophyletic group sister to the monotypic Physoplexis, which is in line with their peculiar flower morphologies. Within Phyteuma two clades, largely corresponding to previously recognized sections, are consistently found. The traditional circumscription of taxonomic series is largely rejected. Whereas distinctness of the currently recognized species is mostly corroborated, some interspecific relationships remain ambiguous due to incongruences between nuclear and plastid data. Major forces for diversification and evolution of Phyteuma are descending dysploidy (i.e., a decrease in chromosome base number) as well as allopatric and ecological differentiation within the Alps, the genus' center of species diversity. (C) 2013 Elsevier Inc. All rights reserved.

Observations of the northern seasonal polar cap on Mars: I. Spring sublimation activity and processes

Spring sublimation of the seasonal CO2 northern polar cap is a dynamic process in the current Mars climate. Phenomena include dark fans of dune material propelled out onto the seasonal ice layer, polygonal cracks in the seasonal ice, sand flow down slipfaces, and outbreaks of gas and sand around the dune margins. These phenomena are concentrated on the north polar erg that encircles the northern residual polar cap. The Mars Reconnaissance Orbiter has been in orbit for three Mars years, allowing us to observe three northern spring seasons. Activity is consistent with and well described by the Kieffer model of basal sublimation of the seasonal layer of ice applied originally in the southern hemisphere. Three typical weak spots have been identified on the dunes for escape of gas sublimed from the bottom of the seasonal ice layer: the crest of the dune, the interface of the dune with the interdune substrate, and through polygonal cracks in the ice. Pressurized gas flows through these vents and carries out material entrained from the dune. Furrows in the dunes channel gas to outbreak points and may be the northern equivalent of southern radially-organized channels ("araneiform" terrain), albeit not permanent. Properties of the seasonal CO2 ice layer are derived from timing of seasonal events such as when final sublimation occurs. Modification of dune morphology shows that landscape evolution is occurring on Mars today, driven by seasonal activity associated with sublimation of the seasonal CO2 polar cap.

Potentials and constraints of modeling for transdisciplinary co-producing strategies for sustainable water governance

Both climate change and socio-economic development will significantly modify the supply and consumption of water in future. Consequently, regional development has to face aggravation of existing or emergence of new conflicts of interest. In this context, transdisciplinary co-production of knowledge is considered as an important means for coping with these challenges. Accordingly, the MontanAqua project aims at developing strategies for more sustainable water management in the study area Crans-Montana-Sierre (Switzerland) in a transdisciplinary way. It strives for co-producing system, target and transformation knowledge among researchers, policy makers, public administration and civil society organizations. The research process basically consisted of the following steps: First, the current water situation in the study region was investigated. How much water is available? How much water is being used? How are decisions on water distribution and use taken? Second, participatory scenario workshops were conducted in order to identify the stakeholders’ visions of regional development. Third, the water situation in 2050 was simulated by modeling the evolution of water resources and water use and by reflecting on the institutional aspects. These steps laid ground for jointly assessing the consequences of the stakeholders’ visions of development in view of scientific data regarding governance, availability and use of water in the region as well as developing necessary transformation knowledge. During all of these steps researchers have collaborated with stakeholders in the support group RegiEau. The RegiEau group consists of key representatives of owners, managers, users, and pressure groups related to water and landscape: representatives of the communes (mostly the presidents), the canton (administration and parliament), water management associations, agriculture, viticulture, hydropower, tourism, and landscape protection. The aim of the talk is to explore potentials and constraints of scientific modeling of water availability and use within the process of transdisciplinary co-producing strategies for more sustainable water governance.

Interdisciplinary assessment of complex regional water systems and their future evolution: how socioeconomic drivers can matter more than climate

Modeling of future water systems at the regional scale is a difficult task due to the complexity of current structures (multiple competing water uses, multiple actors, formal and informal rules) both temporally and spatially. Representing this complexity in the modeling process is a challenge that can be addressed by an interdisciplinary and holistic approach. The assessment of the water system of the Crans-Montana-Sierre area (Switzerland) and its evolution until 2050 were tackled by combining glaciological, hydrogeological, and hydrological measurements and modeling with the evaluation of water use through documentary, statistical and interview-based analyses. Four visions of future regional development were co-produced with a group of stakeholders and were then used as a basis for estimating future water demand. The comparison of the available water resource and the water demand at monthly time scale allowed us to conclude that for the four scenarios socioeconomic factors will impact on the future water systems more than climatic factors. An analysis of the sustainability of the current and future water systems based on four visions of regional development allowed us to identify those scenarios that will be more sustainable and that should be adopted by the decision-makers. The results were then presented to the stakeholders through five key messages. The challenges of communicating the results in such a way with stakeholders are discussed at the end of the article.

BCL2 mutation spectrum in B-cell non-Hodgkin lymphomas and patterns associated with evolution of follicular lymphoma

BCL2 is a target of somatic hypermutation in t(14;18) positive and also in a small fraction of t(14;18) negative diffuse large B-cell lymphoma (DLBCL), suggesting an aberrant role of somatic hypermutation (ASHM). To elucidate the prevalence of BCL2 mutations in lymphomas other than DLBCL, we Sanger-sequenced the hypermutable region of the BCL2 gene in a panel of 69 mature B-cell lymphomas, including Richter's syndrome DLBCL, marginal-zone lymphomas, post-transplant lymphoproliferative disorders, HIV-associated and common-variable immunodeficiency-associated DLBCL, all known to harbour ASHM-dependent mutations in other genes, as well as 16 t(14,18) negative and 21 t(14;18) positive follicular lymphomas (FLs). We also investigated the pattern of BCL2 mutations in longitudinal samples from 10 FL patients relapsing to FL or transforming to DLBCL (tFL). By direct sequencing, we found clonally represented BCL2 mutations in 2/16 (13%) of t(14;18) negative FLs, 2/16 (13%) HIV-DLBCLs, 1/9 (11%) of Richter's syndrome DLBCL, 1/17 (6%) of post-transplant lymphoproliferative disorders and 1/2 (50%) common-variable immunodeficiency-associated DLBCL. The proportion of mutated cases was significantly lower than in FLs carrying the t(14;18) translocation (15/21, 71%). However, the absence of t(14;18) by FISH or PCR and the molecular features of the mutations strongly suggest that BCL2 represents an additional target of ASHM in these entities. Analysis of the BCL2 mutation pattern in clonally related FL/FL and FL/tFL samples revealed two distinct scenarios of genomic evolution: (i) direct evolution from the antecedent FL clone, with few novel clonal mutations acquired by the tFL major clone, and (ii) evolution from a common mutated long-lived progenitor cell, which subsequently acquired distinct mutations in the FL and in the relapsed or transformed counterpart. Copyright © 2014 John Wiley & Sons, Ltd.