Characterization of a Full-Length TTP Family Member Association with RNA Sequence Elements

Post-transcriptional regulation of cytoplasmic mRNAs is an efficient mechanism of regulating the amounts of active protein within a eukaryotic cell. RNA sequence elements located in the untranslated regions of mRNAs can influence transcript degradation or translation through associations with RNA-binding proteins. Tristetraprolin (TTP) is the best known member of a family of CCCH zinc finger proteins that targets adenosine-uridine rich element (ARE) binding sites in the 3’ untranslated regions (UTRs) of mRNAs, promoting transcript deadenylation through the recruitment of deadenylases. More specifically, TTP has been shown to bind AREs located in the 3’-UTRs of transcripts with known roles in the inflammatory response. The mRNA-binding region of the protein is the highly conserved CCCH tandem zinc finger (TZF) domain. The synthetic TTP TZF domain has been shown to bind with high affinity to the 13-mer sequence of UUUUAUUUAUUUU. However, the binding affinities of full-length TTP family members to the same sequence and its variants are unknown. Furthermore, the distance needed between two overlapping or neighboring UUAUUUAUU 9-mers for tandem binding events of a full-length TTP family member to a target transcript has not been explored. To address these questions, we recombinantly expressed and purified the full-length C. albicans TTP family member Zfs1. Using full-length Zfs1, tagged at the N-terminus with maltose binding protein (MBP), we determined the binding affinities of the protein to the optimal TTP binding sequence, UUAUUUAUU. Fluorescence anisotropy experiments determined that the binding affinities of MBP-Zfs1 to non-canonical AREs were influenced by ionic buffer strength, suggesting that transcript selectivity may be affected by intracellular conditions. Furthermore, electrophoretic mobility shift assays (EMSAs) revealed that separation of two core AUUUA sequences by two uridines is sufficient for tandem binding of MBP-Zfs1. Finally, we found evidence for tandem binding of MBP-Zfs1 to a 27-base RNA oligonucleotide containing only a single ARE-binding site, and showed that this was concentration and RNA length dependent; this phenomenon had not been seen previously. These data suggest that the association of the TTP TZF domain and the TZF domains of other species, to ARE-binding sites is highly conserved. Domains outside of the TZF domain may mediate transcript selectivity in changing cellular conditions, and promote protein-RNA interactions not associated with the ARE-binding TZF domain.

In summary, the evidence presented here suggests that Zfs1-mediated decay of mRNA targets may require additional interactions, in addition to ARE-TZF domain associations, to promote transcript destabilization and degradation. These studies further our understanding of post-transcriptional steps in gene regulation.

Weathering the crisis? Managing democracy at a national broadcaster

With post-2008 political and economic crises as its backdrop, this inquiry into the political roles and functions of public service broadcasting (PSB) in Ireland is principally concerned with examining the capacities for and actuality of critical and counter-hegemonic professional journalistic and institutional mediations of crisis. Recognising the diversity of influences on the normative identity of Irish PSB, the dissertation adopts a sociological approach that acknowledges the systemic embedding of media institutions in the broader field of power. An initial tracing of the formative impacts of endogenous and exogenous forces on the democratic horizons of PSB suggests that the present crisis conjuncture does not represent promising terrain for engendering critical crisis and recovery imaginaries. A methodologically diverse intra-institutional empirical research agenda aims to explore at close hand Irish PSB’s contingent navigation of crisis, encompassing ethnographic observation in the newsroom, practitioner interviews and textual analysis of broadcast output. These methods afford close analysis of practices of journalistic production and reflexivity, self-conceptions of the journalistic habitus, and ideological affinities of crisis framings in broadcast output. These analyses are supplemented by a participant observation study of the possibilities for public agenda-building in a key institutional venue of public participation in broadcasting governance. The findings offer an evidential basis for the arguments that the crisis has prompted only minimal changes to professional norms and practices of representation and inclusion; that journalistic crisis framings tend toward effecting hegemonic repair by lending support to neoliberal crisis and recovery imaginaries; and that the institutional openings for the building of public counterpower are highly constrained. The overall conclusion is made that the normative democratic orientation embedded in the professional and institutional projects of public service broadcasting help render it ill-equipped to act as a re-democratising countervailing power against the democratic regressions engendered by the present crisis of democratic capitalism.

Simply Genre Films: Extracting “King Lear” from “House of Strangers” and “Broken Lance"

The purpose of this thesis is to evaluate and refute Yvonne Griggs’ claims that the films “House of Strangers” (1949) and “Broken Lance” (1954) are as Griggs deems “genre-based adaptations” of William Shakespeare’s “King Lear.” I argue that the films, although they have some essential elements of “King Lear,” lack intentionality and reception, pivotal components in determining viability as a Shakespearean film adaptation. Using Griggs’ book as my critical background, I will show that these films are better classified under their respective genre categories, Western and film noir, not as “King Lear” genre adaptations. I will also suggest criteria for determining the level of canonicity of a “King Lear” film adaptation. Popularity of films does not determine validity, and a film does not need purported Shakespearean provenance to validate its ratings. Some films, like these, merely reference or pay homage to Shakespeare through use of essential elements of “King Lear”; here, I deem such affinities to be more unintentional than intentional.

Basalt analyses from different DSDP Holes in the Mozambique Basin and Ridge and from the Southwest Indian Ridge

Basalts from DSDP Sites 248, 249, 250 and 251 in the southwestern Indian Ocean formed in a complex tectonic region affected by the separation of Africa and South America. The different ages and variable geochemical features of these DSDP basalts probably reflect this tectonic complexity. For example, Site 251 on the flanks of the Southwest Indian Ridge is represented by normal MORB which probably originated at the Southwest Indian Ridge. Site 250 in the Mozambique Basin includes an older incompatible- element enriched unit which may represent basalt associated with the Prince Edward Fracture Zone; the upper unit is normal MORB. Basalts at Site 248 also in the Mozambique Basin are geochemically very unlike MORB and have strong continental affinities; they are also comparable in age to some of the continental Karroo basalts. They appear to be related to a subcontinental mantle source or to contamination by continental basement associated with the tectonic elevation of the Mozambique Ridge. Basalts from Site 249 on the Mozambique Ridge are relatively weathered but appear to be normal MORB. Their age, location, and composition are consistent with their origin at an early Cretaceous rift which has been postulated to have separated the Falkland Plateau from the Mozambique Ridge.

TABLE 2. - List of species of Garamaridea and Corophiidea collected in southern Tierra del Fuego

Species richness and faunistic affinities of gammaridean and corophiidean amphipods from southern Tierra del Fuego were studied. The material was collected with dredges and grabs at 7 locations (15 sampling stations) in a range of 5 to 35 m depth. A total of 61 species belonging to 20 families and 43 genera were identified. The genera Cephalophoxoides, Ceradocopsis and Photis are reported for the first time from the Magellan region and 3 species belonging to Atyhts, hchyrocerus and Photis appear to be new to science. Most of the species collected belong to Phoxocephalidae, whereas most individuals were contained in the Stenothoidae and Lysianassidae s.l. The analysis of the faunistic affinities showed that 16 species (39%) are endemic to the Magellan region, 9 species (22%) extend to the south, 5 species (12.2%) to the north and 5 other species (12.2%) to both the north and south. In addition, 6 species extend beyond the Magellan region as far as Oceania.

Dinoflagellate cysts in western equatorial Atlantic surface sediments

In contrast to the wide range of studies carried out in temperate and high-latitude oceanic regions, only a few studies have focused on recent and Holocene organic-walled dinoflagellate cyst assemblages from the tropics. This information is, however, essential for fully understanding the ability of species to adapt to different oceanographic regimes, and ultimately their potential application to local and regional palaeoenvironmental and palaeoceanographic reconstructions. Surface sediment samples of the western equatorial Atlantic Ocean north of Brazil, an area greatly influenced by Amazon River discharge waters, were therefore analysed in detail for their organic-walled dinoflagellate cyst content. A diverse association of 43 taxa was identified, and large differences in cyst distribution were observed. The cyst thanatocoenosis in bottom sediments reflects the seasonal advection of Amazon River discharge water through the Guyana Current and the North Equatorial Countercurrent well into the North Atlantic. To establish potential links between cyst distribution and the environmental conditions of the upper water column, distribution patterns were compared with mean temperature, salinity, density and stratification gradients within the upper water column (0-100 m) over different times of the year, using correspondence analysis and canonical correspondence analysis. The analyses show that differences in these parameters only play a subordinate role in determining species distribution. Instead, nutrient availability, or related factors, dominates the distribution pattern. The only possible indicators of slightly reduced salinities are Trinovantedinium applanatum and Lingulodinium machaerophorum. Four assemblage groups of cyst taxa with similar environmental affinities related to specific water masses/currents can be distinguished and have potential for palaeoenvironmental reconstruction.

TABLE 2. - Number of Asellota isopods collected in the Beagle Channel

The shallow-water Asellota from the Beagle Channel were investigated, based on material collected at four localities in 2001-2002. A total of 3,124 asellotes were sorted, and three new species and 12 new records of distribution were reported. The Paramunnidae showed the highest species diversity and abundance (11 species and 1,463 specimens). The present research raises the number of species known from the Beagle Channel to 23; of these, 16 were previously reported from the Magellan Straits, representing 69% of similarity. Based on the present results and published data, the faunistic affinities for the shallow-water Asellota was 30% between the Magellan region and the Scotia Arc, and 26% between the Magellan region and the Antarctic Peninsula.

Flux data of NU2_trap (Table A1)

Flux of bulk components, carbonate- and silicate-bearing skeleton organisms, and the d15N-isotopic signal were investigated on a 1-year time-series sediment trap deployed at the pelagic NU mooring site (Namibia Upwelling, ca. 29°S, 13°E) in the central Benguela System. The flux of bulk components mostly shows bimodal seasonality with major peaks in austral summer and winter, and moderate to low export in austral fall and spring. The calcium carbonate fraction dominates the export of particulates throughout the year, followed by lithogenic and biogenic opal. Planktonic foraminifera and coccolithophorids are major components of the carbonate fraction, while diatoms clearly dominate the biogenic opal fraction. Bulk d15N isotopic composition of particulate matter is positively correlated with the total mass flux during summer and fall, while negatively correlated during winter and spring. Seasonal changes in the intensity of the main oceanographic processes affecting the NU site are inferred from variations in bulk component flux, and in the flux and diversity patterns of individual species or group of species. Influence from the Namaqua (Hondeklip) upwelling cell through offshore migration of chlorophyll filaments is stronger in summer, while the winter flux maximum seems to reflect mainly in situ production, with less influence from the coastal and shelf upwelling areas. On a yearly basis, dominant microorganisms correspond well with the flora and fauna of tropical/subtropical waters, with minor contribution of near-shore organisms. The simultaneous occurrence of species with different ecological affinities mirrors the fact that the mooring site was located in a transitional region with large hydrographic variability over short-time intervals.

Ethnogenesis and Craniofacial Change in Japan from the Perspective of Nonmetric Traits

To examine population affinities in light of the ‘dual structure model’, frequencies of 21 nonmetric cranial traits were analyzed in 17 prehistoric to recent samples from Japan and five from continental northeast Asia. Eight bivariate plots, each representing a different bone or region of the skull, as well as cluster analysis of 21-trait mean measures of divergence using multidimensional scaling and additive tree techniques, revealed good discrimination between the Jomon-Ainu indigenous lineage and that of the immigrants who arrived from continental Asia after 300 BC. In Hokkaido, in agreement with historical records, Ainu villages of Hidaka province were least, and those close to the Japan Sea coast were most, hybridized with Wajin. In the central islands, clines were identified among Wajin skeletal samples whereby those from Kyushu most resembled continental northeast Asians, while those from the northernmost prefectures of Tohoku apparently retained the strongest indigenous heritage. In the more southerly prefectures of Tohoku, stronger traces of Jomon ancestry prevailed in the cohort born during the latest Edo period than in the one born after 1870. Thus, it seems that increased inter-regional mobility and gene flow following the Meiji Restoration initiated the most recent episode in the long process of demic diffusion that has helped to shape craniofacial change in Japan.

Nanotechnology in food industry II: risk assessment and legislation

Currently, there is increasing use of nanomaterials in the food industry thanks to the many advantages offered and make the products that contain them more competitive in the market. Their physicochemical properties often differ from those of bulk materials, which require specialized risk assessment. This should cover the risks to the health of workers and consumers as well as possible environmental risks. The risk assessment methods must go updating due to more widespread use of nanomaterials, especially now that are making their way down to consumer products. Today there is no specific legislation for nanomaterials, but there are several european dispositions and regulations that include them. This review gives an overview of the risk assessment and the existing current legislation regarding the use of nanotechnology in the food industry.

Resident perceptions of natural resources between cities and across scales in the Pacific Northwest

As the global population becomes increasingly urban, research is needed to explore how local culture, land use, and policy will influence urban natural resource management. We used a broad-scale comparative approach and survey of residents within the Portland (Oregon)-Vancouver (Washington) metropolitan areas, USA, two states with similar geographical and ecological characteristics, but different approaches to land-use planning, to explore resident perceptions about natural resources at three scales of analysis: property level (“at or near my house”), neighborhood (“within a 20-minute walk from my house”), and metro level (“across the metro area”). At the metro-level scale, nonmetric multidimensional scaling revealed that the two cities were quite similar. However, affinity for particular landscape characteristics existed within each city with the greatest difference generally at the property-level scale. Portland respondents expressed affinity for large mature trees, tree-lined streets, public transportation, and proximity to stores and services. Vancouver respondents expressed affinity for plentiful accessible parking. We suggest three explanations that likely are not mutually exclusive. First, respondents are segmented based on preferences for particular amenities, such as convenience versus commuter needs. Second, historical land-use and tax policy legacies may influence individual decisions. Third, more environmentally attuned worldviews may influence an individual’s desire to produce environmentally friendly outcomes. Our findings highlight the importance of acknowledging variations in residents’ affinities for landscape characteristics across different scales and locations because these differences may influence future land-use policies about urban natural resources.

Una planta sin clásicos. La berenjena en la farmacología medieval y renacentista

La berenjena (Solanum melongena L.) es una planta solanácea de múltiples variedades, cuyos ancestros salvajes se sitúan en Indochina y el este de África. Su cultivo fue muy temprano en zonas de China e India. Aun así, no se extendió al Occidente antiguo ni apenas se conoció, de ahí su ausencia en los textos clásicos de botánica y farmacología. Fueron los árabes quienes llevaron el cultivo de la planta por el Norte de África y Al-Andalus, de donde pasó ya a Europa. Los primeros testimonios occidentales de la berenjena aparecen en traducciones latinas de textos árabes, para incorporarse luego a la literatura farmacológica medieval y, más tarde ya, a la del Renacimiento, que empezó a tratar de ella por su posible parecido con una especie de mandrágora. Pese a que se le reconocían algunas virtudes medicinales, siempre se la tuvo bajo sospecha por ser de sabor poco agradable, indigesta y causante de algunas afecciones. Solo los botánicos de finales del Renacimiento describirían la planta y sus variedades con criterios más «científicos» y botánicos, ya sin apenas intereses farmacológicos.

Connections between Modern and Postmodern art and fashion.

This paper undertakes to construe the affinities and divergences in the genres of art and fashion throughout the 20th century through the use of particular visual and theoretical examples, examined at greater length in a more extensive study of ‘The relationship between the artist and the fashion designer in the twentieth century’ (Vettese, 2005). Examination of the 20th century has revealed two particular periods – ‘Modernism’ and ‘Postmodernism’ – that were evident and fitting to this analysis. The research is a summation of these findings, where the differences and affinities in the mechanisms of 20th century art and fashion, including imposing messages and innovation in Modernism and the mixed messages, recycling and commercial aspects of Postmodernism, are disseminated.

Towards balanced exploitation and management of the fishery resources of Uganda

A casual study of the hydrological map of Uganda would convince every serious fisherman and fisheater that he is most favoured to be in Uganda. The extent and distribution of the country's aquatic system plus the rich variety of fish species there is promises a fishery potential of considerable magnitude: The open waterways comprised by the Uganda portions of Lakes Victoria, Albert and Edward; and Lakes Kyoga, George plus minor lakes Wamala, Kijanebarora, mutanda, etc. occupy about 15% of the total surface area (91,000 m2; Depart. Land Survey, 1962). Most of the nation's fish supplies are currontly from this source. 1.2. A rich network of permanent and seasonal rivers and streams filling and/or emptying various water systems covers most of Uganda. This aquatic network is associated with a fish fauna whose immense significance as a source of protein is perhaps better appreciated by the local subsistance fisherman and consumer than by the fisheries scientist and manager in this country. Many species of this fish fauna have strong affinities with the open water systems while some are typically riverine. 1.3. Then there are wetlands composed mainly of expanses of swamp, but including some areas of bog. These cover about 2% of the country. While the variety of fish fauna found here is limited by the rather hostile nature of the environment (comparatively de-oxygenated under a canopy of dense stands of emergont vegetation) several specialised fishes e.g. Clarias spp. and Protpterus aethiopicus (Kamongo) occur here. Availability of permanent and seasonal sources of water, well distributed throughout most areas of Uganda, opens up immense potential for a variety of aquaculture practices. However, while active exploitation of much of these fishery resources is currently underway, important questions regarding the magnitudes of the various resource potentials and dynamics, and about suitable levels and modes of exploitation, are yet unanswered. These gaps in knowledge go about the fishery resources of Uganda would hinder formulation of adequate development and management schemes. This short paper examines some of the above problems and suggests some approaches towards balanced oxploitation and management of the fisheries of Uganda.

Caim, Gaspard, Melchior, Balthazar e demais cúmplices : jornada às avessas rumo à inefável transcendência

Tendo como ponto de partida a leitura intertextual das obras Caim, de José Saramago, e Gaspard, Melchior et Balthazar, de Michel Tournier, encaradas à luz da Teoria da Carnavalização do filósofo russo Mikhail Bakhtin, procura-se estabelecer afinidades e antinomias passíveis de constarem na temática da revisitação subversiva de mitos bíblicos. Assim sendo, pretende-se concluir, nomeadamente, acerca da relevância do diálogo efetuado pelos autores em torno da verdade oficial e sua reinterpretação, ainda que insolente; da validade da viagem de iniciação, enquanto lenitivo, “via-sacra” e demanda de absoluta Plenitude, empreendida pelos heróis e pelos anti-heróis; do grotesco na representação carnavalesca do corpo e da vida terrena; da presença de um discurso narrativo fazendo uso de uma linguagem subversiva, onde grotesco, ironia e/ou paródia são percetíveis; dos valores morais e ética social a preservar versus crítica acérrima ao poder instituído; da queda do Homem e do confronto com Deus e suas imperdoáveis limitações “humanas”; da presença do binómio entidade divina/entidade mefistofélica e o modo como as várias vozes narrativas surgem articuladas. Concomitantemente, pretende-se comprovar que os textos de José Saramago e Michel Tournier, embora mergulhando no desmascaramento, “profanação” e aparente niilismo do Texto Bíblico, na dessacralização de um cosmos oficial e na adoção do riso e impertinência enquanto catarse, longe de provocarem a aniquilação do mito, antes concorrem para uma releitura profícua, pois repleta de pluralidade de significados, onde o Transcendente, por oposição à desilusão prodigalizada pela vida terrena, é objeto de revitalização; pretendendo autores, narradores e leitores, postos em diálogo polifónico, a não reiteração de modos perniciosos de “estar” e “ser”, mas um olhar lúcido e puro sobre o futuro da Humanidade.