Alternate Conformations Regulate Ribosomal Recoding in a Positive-sense RNA Virus

Positive-sense RNA viruses are important animal, plant, insect and bacteria pathogens and constitute the largest group of RNA viruses. Due to the relatively small size of their genomes, these viruses have evolved a variety of non-canonical translation mechanisms to optimize coding capacity expanding their proteome diversity. One such strategy is codon redefinition or recoding. First described in viruses, recoding is a programmed translation event in which codon alterations are context dependent. Recoding takes place in a subset of messenger RNA (mRNAs) with some products reflecting new, and some reflecting standard, meanings. The ratio between the two is both critical and highly regulated. While a variety of recoding mechanisms have been documented, (ribosome shunting, stop-carry on, termination-reinitiation, and translational bypassing), the two most extensively employed by RNA viruses are Programmed Ribosomal Frameshifting (PRF) and Programmed Ribosomal Readthrough (PRT). While both PRT and PRF subvert normal decoding for expression of C-terminal extension products, the former involves an alteration of reading frame, and the latter requires decoding of a non-sense codon. Both processes occur at a low but defined frequency, and both require Recoding Stimulatory Elements (RSE) for regulation and optimum functionality. These stimulatory signals can be embedded in the RNA in the form of sequence or secondary structure, or trans-acting factors outside the mRNA such as proteins or micro RNAs (miRNA). Despite 40+ years of study, the precise mechanisms by which viral RSE mediate ribosome recoding for the synthesis of their proteins, or how the ratio of these products is maintained, is poorly defined. This study reveals that in addition to a long distance RNA:RNA interaction, three alternate conformations and a phylogenetically conserved pseudoknot regulate PRT in the carmovirus Turnip crinkle virus (TCV).

Asymmetrical processing of olfactory input in the piriform cortex mediates "activation" of the avian navigation circuitry

The role of odors in the long-distance navigation of birds has elicited intense debate for more than half a century. Failure to resolve many of the issues fueling this debate is due at least in part to the absence of controls for a variety of non-specific effects that odors have on the navigational process. The present experiments were carried out to investigate whether the olfactory inputs are involved only in “activation” of neuronal circuitry involved in navigation or are also playing a role in providing directional information. Experienced adult pigeons were exposed to controlled olfactory stimuli during different segments of the journey (release site vs. displacement + release site). Protein levels of IEGs (immediate early genes used to mark synaptic activity) were analyzed in areas within the olfactory/navigation avian circuitry. The results indicate that 1) exposure to natural odors at the release site (and not before) elicit greater activation across brain regions than exposure to filtered air, artificial odors, and natural odors along the entire outward journey (from home to the release site, inclusive); 2) activation of the piriform cortex in terms of odor discrimination is lateralized; 3) activation of the navigation circuitry is achieved by means of lateralized activation of piriform cortex neurons. Altogether, the findings provide the first direct evidence that activation of the avian navigation circuitry is mediated by asymmetrical processing of olfactory input occurring in the right piriform cortex.

Posibles funciones de la familia génica de la glutamato descarboxilasa en Populus

Aunque hace más de 50 años que se describió que la glutamato descarboxilasa (GAD) lleva a cabo la descarboxilación del glutamato para producir GABA, y en animales ha sido muy estudiada debido al papel del GABA como neurotransmisor, la información disponible sobre las GADs de plantas es aún limitada, conociéndose sólo algunos aspectos de la regulación por calcio de su actividad enzimática o de expresión de algunos de los genes de su familia génica. El GABA es un metabolito que tradicionalmente se ha asociado a estrés, pero su papel en plantas todavía no está claro. En las últimas dos décadas los resultados experimentales obtenidos sobre la GAD y el GABA, destacando las alteraciones fenotípicas mostradas por plantas tratadas con GABA y por plantas transgénicas para GAD, han generado preguntas interesantes sobre el posible papel de este metabolito y la enzima en señalización en plantas. En plantas, son varios los papeles que se han propuesto para el metabolismo del GABA tales como su participación como componente del metabolismo del carbono y del nitrógeno (Fait y col., 2008), protección frente especies reactivas de oxigeno (Liu y col., 2011), regulación de la expresión génica incluyendo la regulación de genes implicados en la síntesis de hormonas (Khatiresan y col., 1997; Shi y col., 2010; Lancien y Roberts, 2006) y señalización a larga distancia (Beuve y col., 2004) y en gradiente guiando el crecimiento del tubo polínico (Palanivelu y col., 2013). Nuestro grupo de investigación ha sugerido un papel novedoso para la producción de GABA durante la xilogénesis en pino (Molina-Rueda y col., 2010, 2015). En base a estos antecedentes, los objetivos planteados para este trabajo han sido: la asignación de posibles funciones a las GADs de Populus en condiciones normales de crecimiento y en estrés abióticos, estudiar la adquisición del dominio de unión a calmodulina (CaMBD) de las GADs de plantas vasculares y analizar el efecto del GABA y del glutamato en las raíces de Populus. Las conclusiones que se derivan de los resultados de este trabajo se detallan a continuación. El dominio de unión a calmodulina de la GAD de plantas esta conservado en GADs de plantas consideradas ancestros de plantas vasculares y ausente en plantas no vasculares, lo que sitúa juntos en la evolución los eventos de adquisición del dominio de unión a CaM y el desarrollo del tejido vascular de plantas. Los resultados similares de la localización de GABA en xilema y una expresión GAD asociada a la formación de madera de reacción tanto en pino como en chopo apuntan a un papel relevante de la producción de GABA durante la xilogénesis en leñosas. La familia génica GAD posee seis genes codificando todos ellos para proteínas aparentemente funcionales y susceptibles de ser reguladas por calcio. Esta familia génica ha sufrido duplicaciones y eventos de especialización durante la evolución de Populus. Este trabajo ha posibilitado la asociación entre papeles específicos y los diferentes genes de esta familia. Beuvé N, Rispail N, Laine P, Cliquet J-B, Ourry A, Deunff F (2004) Putative role of Υ-aminobutyric acid as a long-distance signal in up-regulation of nitrate uptake in Brassica napus L. Plant Cell Environ. 27: 1035-1046 Fait A, Fromm H, Walter D, Galili G, Fernie AR (2008) Highway or byway: the metabolic role of the GABA shunt in plants. Trends in plant science 13: 14-19 Kathiresan A, Tung P, Chinnappa CC, Reid DM (1997) gamma-Aminobutyric acid stimulates ethylene biosynthesis in sunflower. Plant Physiol. 115: 129-135 Lancien M, Roberts MR (2006) Regulation of Arabidopsis thaliana 14-3-3 gene expression by ϒ-aminobutyric acid. Plant Cell Environ. 29: 1430-1436 Liu C, Zhao L, Yu G (2011) The dominant glutamic acid metabolic flux to produce gamma-amino butyric acid over proline in Nicotiana tabacum leaves under water stress relates to its significant role in antioxidant activity. Journal of integrative plant biology 53: 608-618 Molina-Rueda JJ, Pascual MB, Canovas FM, Gallardo F (2010) Characterization and developmental expression of a glutamate decarboxylase from maritime pine. Planta 232: 1471-1483 Molina-Rueda, J.J. y col., 2015. A putative role for γ-aminobutyric acid (GABA) in vascular development in pine seedlings. Planta 241: 257-267 Palanivelu R, Brass L, Edlund AF, D P (2003) Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell 114: 47-59 Shi SQ, Shi Z, Jiang ZP, Qi LW, Sun XM, Li CX, Liu JF, Xiao WF, Zhang SG (2010) Effects of exogenous GABA on gene expression of Caragana intermedia roots under NaCl stress: regulatory roles for H2O2 and ethylene production. Plant, cell & environment 33: 149-162

Curso online para a parte pral do Celpe-Bras : contribuições da avaliação de proficiência para o ensino-aprendizagem de PLE

Dissertação (mestrado)—Universidade de Brasília, Departamento de Línguas Estrangeiras e Tradução, Programa de Pós-Graduação em Linguística Aplicada, 2016.

Recruitment patterns and processes of coastal fish species in a temperate rocky reef

Tese de Doutoramento, Ciências do Mar, da Terra e do Ambiente, Ramo: Ciências do Mar, Especialização em Ecologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Accessibility impact of proposed Australian high speed rail

High speed rail (also commonly known as HSR) is highly regarded as one of the most significant innovation for mass passenger transportation to travellers willing to pay for reduced travel impediments (shorter travel time, convenience, safety, security, comfort, reliability, flexibility, uniqueness and attractiveness). The transport policy in Australia has until now focused primarily on private passenger car transport and air transportation to the degree that State and Federal Governments’ commitments and actions of rail-oriented mass transportation system still remains sketchy in spite of occasional political and public attentions into it. This has resulted in a limited use of passenger rail as a regional transport system. Using one of the several alternative HSR alignments proposed for the South-Eastern Coast of Australia connecting Melbourne, Canberra, Sydney and Brisbane, this study assesses the regional accessibility impacts of Australian HSR system by means of four indicators: location accessibility, economic potential accessibility, daily accessibility and commuting accessibility. These indicators are commonly used in transport geography literature and they offer different concepts of changes in regional accessibility conditions due to a long distance transport system. The results provide an understanding of differential effects on regional accessibility based on the geographical location and size of urban areas along HSR corridor.

Energy-efficiency analysis of cluster-based routing protocols in wireless sensor network

This paper extends the conditions of the cluster-based routing protocols in terms of general algorithm complexity of data fusion, general compressing ratio of data fusion, and network area with long distance. Corresponding three general evaluation methods to evaluate the energy efficiency of the cluster-based routing protocols such as LEACH, PEGASIS, and BCDCP are provided. Moreover, three facts are found in them: (1) High-level software energy macro model is used to compute the energy dissipation of general data fusion software and make the constant value of energy dissipation of 1-bit data fusion an especial instance. (2) Multi-hop energy efficiency is related to the radio hardware parameters and the dynamic topology of network and the above protocols do not exploit the best use of the energy efficiency of multi-hop scheme. (3) High-energy dissipation non-cluster-head nodes, whose number changes with the density of the sensor nodes in clusters, worsen the death of nodes. The numerical results of experiments reprove these discoveries. Furthermore, they provide helpful guide for improving the above routing protocols to extent their application ranges.

Space-crossing : community-based data forwarding in mobile social networks under the hybrid communication architecture

In this paper, we study two tightly coupled issues, space-crossing community detection and its influence on data forwarding in mobile social networks (MSNs). We propose a communication framework containing the hybrid underlying network with access point (AP) support for data forwarding and the base stations for managing most of control traffic. The concept of physical proximity community can be extended to be one across the geographical space, because APs can facilitate the communication among long-distance nodes. Space-crossing communities are obtained by merging some pairs of physical proximity communities. Based on the space-crossing community, we define two cases of node local activity and use them as the input of inner product similarity measurement. We design a novel data forwarding algorithm Social Attraction and Infrastructure Support (SAIS), which applies similarity attraction to route to neighbor more similar to destination, and infrastructure support phase to route the message to other APs within common connected components. We evaluate our SAIS algorithm on real-life datasets from MIT Reality Mining and University of Illinois Movement (UIM). Results show that space-crossing community plays a positive role in data forwarding in MSNs. Based on this new type of community, SAIS achieves a better performance than existing popular social community-based data forwarding algorithms in practice, including Simbet, Bubble Rap and Nguyen's Routing algorithms.

High interannual variability in connectivity and genetic pool of a temperate clingfish matches oceanographic transport predictions

Adults of most marine benthic and demersal fish are site-attached, with the dispersal of their larval stages ensuring connectivity among populations. In this study we aimed to infer spatial and temporal variation in population connectivity and dispersal of a marine fish species, using genetic tools and comparing these with oceanographic transport. We focused on an intertidal rocky reef fish species, the shore clingfish Lepadogaster lepadogaster, along the southwest Iberian Peninsula, in 2011 and 2012. We predicted high levels of self-recruitment and distinct populations, due to short pelagic larval duration and because all its developmental stages have previously been found near adult habitats. Genetic analyses based on microsatellites countered our prediction and a biophysical dispersal model showed that oceanographic transport was a good explanation for the patterns observed. Adult sub-populations separated by up to 300 km of coastline displayed no genetic differentiation, revealing a single connected population with larvae potentially dispersing long distances over hundreds of km. Despite this, parentage analysis performed on recruits from one focal site within the Marine Park of Arrábida (Portugal), revealed self-recruitment levels of 2.5% and 7.7% in 2011 and 2012, respectively, suggesting that both long- and short-distance dispersal play an important role in the replenishment of these populations. Population differentiation and patterns of dispersal, which were highly variable between years, could be linked to the variability inherent in local oceanographic processes. Overall, our measures of connectivity based on genetic and oceanographic data highlight the relevance of long-distance dispersal in determining the degree of connectivity, even in species with short pelagic larval durations.

Biological Impacts and Uses of Black Bass Competitive Fishing Tournaments on Large Lake Systems

Thesis (Master, Biology) -- Queen's University, 2016-09-28 15:06:46.124

Seed dispersal potential by wild mallard duck as estimated from digestive tract analysis

Dispersal of plant seeds by ducks and other waterbirds is of great importance to the ecology of freshwater habitats. To unravel the mechanisms of waterbird-mediated seed dispersal, numerous laboratory experiments have been conducted, but effects of seed and waterbird traits on dispersal potential have rarely been investigated under field conditions. Through analysis of the digestive tracts of 100 wild mallards (Anas platyrhynchos) across a winter season in the Netherlands, we assessed (i) the inter-individual and seasonal variability of seeds in the digestive tract, (ii) the variability of digestive tract organ size and gizzard grit mass, and (iii) the potential effects of seed species traits and gut traits on the survival potential of ingested seeds. We found 4548 ingested seeds of at least 66 plant species from a wide range of habitats, most of which were retained in the gizzard. Nineteen species had not previously been reported from mallard diets. Individual tracts contained anywhere between 0 and 1048 seeds, of up to 14 species (median of three species). Diet composition and digestive tract size varied substantially between individuals and over the course of the winter season. As predicted from controlled feeding studies, we found that also in wild mallards, size-dependent gut passage survival favours the dispersal of small-seeded species. Despite the large variation in gizzard and small intestine size in this study, their effect on the dispersal potential of ingested seeds in the field remains unclear. We found no difference in dispersal potential between plants species growing in wet or dry habitats. This study demonstrates that wild mallards are opportunistic seed consumers with a very diverse diet as reflected by seed species composition in both the foregut and hindgut. However, we also show that serious limitations of field-based analyses compared to controlled experiments can impede drawing conclusions about gut passage survival of seeds. The large variability in diet composition among individuals and over time indicates high endozoochorous dispersal potential for a wide range of plant species by wild mallard in aquatic and wetland, as well as surrounding terrestrial habitats.

Spatio-temporal patterns of herbage availability and livestock movements: A cross-border analysis in the Chinese-Mongolian Altay

Due to increasing population and the recent implementation of policies to intensify the use of land and water resources, the transhumant pastoral systems in the Chinese-Mongolian Altay-Dzungarian region are rapidly changing, leading to modifications of herd size, herd composition and spatial distribution of livestock grazing. This may have major consequences for the supply and quality of rangeland biomass. Despite similar topographic settings, the socio-political framework for Chinese and Mongolian pastoralists differs significantly, leading to differences in rangeland utilization. To substantiate these claims, the long-distance transhumance routes, frequency of pasture changes, daily grazing itineraries and size of pastures were recorded by means of GPS tracking of cattle and goats on 1,535 (China) and 1,396 (Mongolia) observation days. The status quo of the main seasonal pastures was captured by measuring the herbage offer and its nutritive value in 869 sampling spots. In the Altay-Dzungarian region, small ruminant herds covered up to 412 km (Mongolia) and grazed on up to nine pastures per year (China). In Mongolia, the herds’ average duration of stay at an individual pasture was longer than in China, particularly in spring and autumn. Herbage allowance at the onset of a grazing period (kg dry matter per sheep unit and day) ranged from 34/17 to 91/95 (China/Mongolia). Comparing crude protein and phosphorous concentrations of herbage, in China, the highest concentrations were measured for spring and summer pastures, whereas in Mongolia, the highest concentrations were determined for autumn and winter pastures. Based on our data, we conclude that regulation of animal numbers and access to pastures seemingly maintained pasture productivity in China, especially at high altitudes. However, this policy may prohibit flexible adaptation to sudden environmental constraints. In contrast, high stocking densities and grazing of pastures before flowering of herbaceous plants negatively affected rangeland productivity in Mongolia, especially for spring and summer pastures.

Numerical simulation of fresh SCC flow in wall and beam elements using flow dynamics models

Abstract : Recently, there is a great interest to study the flow characteristics of suspensions in different environmental and industrial applications, such as snow avalanches, debris flows, hydrotransport systems, and material casting processes. Regarding rheological aspects, the majority of these suspensions, such as fresh concrete, behave mostly as non-Newtonian fluids. Concrete is the most widely used construction material in the world. Due to the limitations that exist in terms of workability and formwork filling abilities of normal concrete, a new class of concrete that is able to flow under its own weight, especially through narrow gaps in the congested areas of the formwork was developed. Accordingly, self-consolidating concrete (SCC) is a novel construction material that is gaining market acceptance in various applications. Higher fluidity characteristics of SCC enable it to be used in a number of special applications, such as densely reinforced sections. However, higher flowability of SCC makes it more sensitive to segregation of coarse particles during flow (i.e., dynamic segregation) and thereafter at rest (i.e., static segregation). Dynamic segregation can increase when SCC flows over a long distance or in the presence of obstacles. Therefore, there is always a need to establish a trade-off between the flowability, passing ability, and stability properties of SCC suspensions. This should be taken into consideration to design the casting process and the mixture proportioning of SCC. This is called “workability design” of SCC. An efficient and non-expensive workability design approach consists of the prediction and optimization of the workability of the concrete mixtures for the selected construction processes, such as transportation, pumping, casting, compaction, and finishing. Indeed, the mixture proportioning of SCC should ensure the construction quality demands, such as demanded levels of flowability, passing ability, filling ability, and stability (dynamic and static). This is necessary to develop some theoretical tools to assess under what conditions the construction quality demands are satisfied. Accordingly, this thesis is dedicated to carry out analytical and numerical simulations to predict flow performance of SCC under different casting processes, such as pumping and tremie applications, or casting using buckets. The L-Box and T-Box set-ups can evaluate flow performance properties of SCC (e.g., flowability, passing ability, filling ability, shear-induced and gravitational dynamic segregation) in casting process of wall and beam elements. The specific objective of the study consists of relating numerical results of flow simulation of SCC in L-Box and T-Box test set-ups, reported in this thesis, to the flow performance properties of SCC during casting. Accordingly, the SCC is modeled as a heterogeneous material. Furthermore, an analytical model is proposed to predict flow performance of SCC in L-Box set-up using the Dam Break Theory. On the other hand, results of the numerical simulation of SCC casting in a reinforced beam are verified by experimental free surface profiles. The results of numerical simulations of SCC casting (modeled as a single homogeneous fluid), are used to determine the critical zones corresponding to the higher risks of segregation and blocking. The effects of rheological parameters, density, particle contents, distribution of reinforcing bars, and particle-bar interactions on flow performance of SCC are evaluated using CFD simulations of SCC flow in L-Box and T-box test set-ups (modeled as a heterogeneous material). Two new approaches are proposed to classify the SCC mixtures based on filling ability and performability properties, as a contribution of flowability, passing ability, and dynamic stability of SCC.

Early Modern Trading Networks in Europe. Cooperation and the case of Simon Ruiz.

In the early modern period, trade became a truly global phenomenon. The logistics, financial and organizational complexity associated with it increased in order to connect distant geographies and merchants from different backgrounds. How did these merchants prevent their partners from dishonesty in a time where formal institutions and legislation did not traverse these different worlds? This book studies the mechanisms and criteria of cooperation in early modern trading networks. It uses an interdisciplinary approach, through the case study of a Castilian long-distance merchant of the sixteenth century, Simon Ruiz, who traded within the limits of the Portuguese and Spanish overseas empires. Early Modern Trading Networks in Europe discusses the importance of reciprocity mechanisms, trust and reputation in the context of early modern business relations, using network analysis methodology, combining quantitative data with qualitative information. It considers how cooperation and prevention could simultaneously create a business relationship, and describes the mechanisms of control, policing and punishment used to avoid opportunism and deception among a group of business partners. Using bills of exchange and correspondence from Simon Ruiz’s private archive, it charts the evolution of this business network through time, debating which criteria should be included or excluded from business networks, as well as the emergence of standards. This book intends to put forward a new approach to early modern trade which focuses on individuals interacting in self-organized structures, rather than on states or empires. It shows how indirect reciprocity was much more frequent than direct reciprocity among early modern merchants and how informal norms, like ostracism or signaling, helped to prevent defection and deception in an effective way.

Urbanizarse o migrar: ¿Cuáles opciones ante la crisis? El devenir de las comunidades cafetaleras en el centro de Veracruz, México

ResumenLa baja de precios del café desde 1989 sorprendió a los pequeños productores en un momento en que tienen que adaptarse a las nuevas reglas de producción y comercialización impuestas por las políticas de modernización del gobierno de Salinas de Gortari (1988-1994). Las migraciones son una respuesta, entre otras, a la(s) crisis, a primera vista individual pero que afecta el devenir social, político y cultural de las comunidades. En este estudio se analizan los procesos migratorios nacientes en el centro de Veracruz, y se plantea  que si bien algunas comunidades pueden lograr una cierta “reconversión” gracias a la cercanía de centros urbanos que ofrecen alternativas de trabajo, en otras se inician procesos de migración lejana y colectiva que amenazan la reproducción misma de la comunidad rural en cuanto tal.AbstractThe sharp drop in the price of coffee since 1989 took small farmers by surprise at the time when they must adapt to the new rules of productions and marketing under the modernizing polices of the Salinas de Gortari government (1988-1994). Migrations are one response to the crisis (or crises). While seemingly an individual one, they affect the social, political and cultural future of those communities. This study discusses the emerging migratory processes in central Veracruz, and suggests that while some communities may attain a degree of “retrofitting” thanks to nearby urban centers offering job opportunities, others are undergoing long-distance, collective migratory processes which threaten the very reproduction of the rural community per se.