NMR investigation of ferricytochrome c unfolding: Detection of an equilibrium unfolding intermediate and residual structure in the denatured state

Horse ferricytochrome c (cyt c) undergoes exchange of one of its axial heme ligands (Met-80) for one or more non-native ligands under denaturing conditions. We have used 1H NMR spectroscopy to detect two conformations of paramagnetic cyt c with non-native heme ligation through a range of urea concentrations. One non-native form is an equilibrium unfolding intermediate observed under partially denaturing conditions and is attributed to replacement of Met-80 with one or more Lys side chains. The second non-native form, in which the native Met ligand is replaced by a His, is observed under strongly denaturing conditions. Thermodynamic analysis of these data indicates a relatively small ΔG (17 kJ/mol) for the transition from native to the Lys-ligated intermediate and a significantly larger ΔG (47 kJ/mol) for the transition from native to the His-ligated species. Although CD and fluorescence data indicate that the equilibrium unfolding of cyt c is a two-state process, these NMR results implicate an intermediate with His-Lys ligation.

Chaperone rings in protein folding and degradation

Chaperone rings play a vital role in the opposing ATP-mediated processes of folding and degradation of many cellular proteins, but the mechanisms by which they assist these life and death actions are only beginning to be understood. Ring structures present an advantage to both processes, providing for compartmentalization of the substrate protein inside a central cavity in which multivalent, potentially cooperative interactions can take place between the substrate and a high local concentration of binding sites, while access of other proteins to the cavity is restricted sterically. Such restriction prevents outside interference that could lead to nonproductive fates of the substrate protein while it is present in non-native form, such as aggregation. At the step of recognition, chaperone rings recognize different motifs in their substrates, exposed hydrophobicity in the case of protein-folding chaperonins, and specific “tag” sequences in at least some cases of the proteolytic chaperones. For both folding and proteolytic complexes, ATP directs conformational changes in the chaperone rings that govern release of the bound polypeptide. In the case of chaperonins, ATP enables a released protein to pursue the native state in a sequestered hydrophilic folding chamber, and, in the case of the proteases, the released polypeptide is translocated into a degradation chamber. These divergent fates are at least partly governed by very different cooperating components that associate with the chaperone rings: that is, cochaperonin rings on one hand and proteolytic ring assemblies on the other. Here we review the structures and mechanisms of the two types of chaperone ring system.

Invasion of minor veins of tobacco leaves inoculated with tobacco mosaic virus mutants defective in phloem-dependent movement.

To fully understand vascular transport of plant viruses, the viral and host proteins, their structures and functions, and the specific vascular cells in which these factors function must be determined. We report here on the ability of various cDNA-derived coat protein (CP) mutants of tobacco mosaic virus (TMV) to invade vascular cells in minor veins of Nicotiana tabacum L. cv. Xanthi nn. The mutant viruses we studied, TMV CP-O, U1mCP15-17, and SNC015, respectively, encode a CP from a different tobamovirus (i.e., from odontoglossum ringspot virus) resulting in the formation of non-native capsids, a mutant CP that accumulates in aggregates but does not encapsidate the viral RNA, or no CP. TMV CP-O is impaired in phloem-dependent movement, whereas U1mCP15-17 and SNC015 do not accumulate by phloem-dependent movement. In developmentally-defined studies using immunocytochemical analyses we determined that all of these mutants invaded vascular parenchyma cells within minor veins in inoculated leaves. In addition, we determined that the CPs of TMV CP-O and U1mCP15-17 were present in companion (C) cells of minor veins in inoculated leaves, although more rarely than CP of wild-type virus. These results indicate that the movement of TMV into minor veins does not require the CP, and an encapsidation-competent CP is not required for, but may increase the efficiency of, movement into the conducting complex of the phloem (i.e., the C cell/sieve element complex). Also, a host factor(s) functions at or beyond the C cell/sieve element interface with other cells to allow efficient phloem-dependent accumulation of TMV CP-O.

Sustainability in the Upper Colorado River Basin: A Struggle Between Water Resource Use and Remnants of the Natural Ecosystem

This study evaluated whether development of the Colorado River system has exceeded sustainability by comparing the trends in water use in the Colorado River. Two sustainable areas were identified in the upper basin and one in the lower-- the mainstream Colorado River, Green and Yampa rivers, and the Little Colorado River. These areas are also high priority recovery areas for four endangered fishes and protected by critical habitat provisions of the ESA. Unfortunately, the endangered fishes are declining because of habitat destruction and non-native species. If increasing water demand causes the fishes to go extinct the few sustainable areas will be lost. It will take careful management of the endangered fishes and water users to ensure these areas are maintained.

Some reflections on the impact of globalization in the teaching and learning of English in socalled “expanding circle” countries

This article deals with the ongoing debate on the complex role of English as an International Language, be it understood as a homogeneous entity (one language with an international role [EIL]) or a heterogeneous one (different varieties (WE or ELF) grouped under one label, «English») as well as on the implications of this «globalising» status for its teaching in non-native settings. Given the complexity of this phenomenon, whose study is still in its infancy, we attempt neither to provide definitive answers nor adopt a prescriptive attitude, but simply contribute to the discussion and clarification of this, to some extent, emergent, controversial situation.

Ecological restoration across the Mediterranean Basin as viewed by practitioners

Restoration efforts in the Mediterranean Basin have been changing from a silvicultural to an ecological restoration approach. Yet, to what extent the projects are guided by ecological restoration principles remains largely unknown. To analyse this issue, we built an on-line survey addressed to restoration practitioners. We analysed 36 restoration projects, mostly from drylands (86%). The projects used mainly soil from local sources. The need to comply with legislation was more important as a restoration motive for European Union (EU) than for non-EU countries, while public opinion and health had a greater importance in the latter. Non-EU countries relied more on non-native plant species than EU countries, thus deviating from ecological restoration guidelines. Nursery-grown plants used were mostly of local or regional provenance, whilst seeds were mostly of national provenance. Unexpected restoration results (e.g. inadequate biodiversity) were reported for 50% of the projects and restoration success was never evaluated in 22%. Long term evaluation (> 6 years) was only performed in 31% of cases, and based primarily on plant diversity and cover. The use of non-native species and species of exogenous provenances may: i) entail the loss of local genetic and functional trait diversity, critical to cope with drought, particularly under the predicted climate change scenarios, and ii) lead to unexpected competition with native species and/or negatively impact local biotic interactions. Absent or inappropriate monitoring may prevent the understanding of restoration trajectories, precluding adaptive management strategies, often crucial to create functional ecosystems able to provide ecosystem services. The overview of ecological restoration projects in the Mediterranean Basin revealed high variability among practices and highlighted the need for improved scientific assistance and information exchange, greater use of native species of local provenance, and more long-term monitoring and evaluation, including functional and ecosystem services' indicators, to improve and spread the practice of ecological restoration.

Embracing english as a lingua franca : learning from portuguese users of english in higher education

Tese de doutoramento, Linguística (Linguística Aplicada), Universidade de Lisboa, Faculdade de Letras, 2016

Body condition indices of Asian green mussels, Perna viridis, from Indonesia

While part of a single country, the Indonesian archipelago covers several biogeographic regions, and the high levels of national shipping likely facilitate transfer of non-native organisms between the different regions. Two vessels of a domestic shipping line appear to have served as a transport vector for the Asian green mussel Perna viridis (Linnaeus, 1758) between regions. This species is indigenous in the western but not in the eastern part of the archipelago, separated historically by the Sunda Shelf. The green mussels collected from the hulls of the ferries when in eastern Indonesia showed a significantly lower body condition index than similar-sized individuals from three different western-Indonesian mussel populations. This was presumably due to reduced food supply during the ships' voyages. Although this transportinduced food shortage may initially limit the invasive potential (through reduced reproductive rates) of the translocated individuals, the risk that the species will extend its distributional range further into eastern Indonesia is high. If the species becomes widely established in eastern Indonesia, there will then be an increased risk of incursions to Australia, where the mussel is listed as a high-priority pest species.

Out-of-School English and the possible effect it has on Second Language Acquisition : - a study on how students with different backgrounds acquire the English language outside of school

Second language acquisition is a field that has fascinated linguists for numerous years and is a topic that is very much connected to how English teachers in Sweden try to teach the English language to the students in their classrooms. In 2009 Sundqvist examined what possible effects extramural English could have on learners' oral proficiency and their vocabulary. In her study she found out that extramural English “is an independent variable and a possible path to progress in English” (Sundqvist, 2009, p. i).  In 2014, three Swedish secondary- and upper secondary school teachers started a project for the Erasmus+. These three teachers tried to create better teaching conditions and to come up with new methods for teaching English. During their investigation they noticed that students who had only been in Sweden for four years or less, seemed to get less exposed to English in their spare time than native Swedish students, which created a disadvantage for them. Since the time when these two studies were carried out, the number of immigrants has increased drastically, which creates the need for further investigation within this area of second language acquisition. In this study, I therefore investigate how much and in what way students come in contact with the English language outside of school. I also examine if there are any differences between native Swedish students versus non-native Swedish students and if so, how this might affect the students and their grades in English. The study was conducted through the use of questionnaires and through observations of different teaching situations, including the participating teachers' methods and the participating students' reactions. The results show that there are differences between native- and non-native students when it comes to extramural English activities. The results also show that these differences seem to affect the students' grades in English, in favour of the native Swedish students. The native students tend to spend more time on extramural English activities, especially in connection to the Internet and computer games, than the non-native students. These results indicate that something needs to be done in order to compensate for the non-native students' disadvantage.

‘All of this Belongs to Us’: Land, Horses, and Indigenous Resistance on the Yakama Indian Reservation, 1900-1950

In the early 1900s, the Yakima Indian Agency welcomed non-Native ranching operations onto Yakama tribal lands, taxing rangelands, and resulting in widespread overgrazing. By the 1920s, agency concern for the welfare of ranchers facilitated a need to gain access to tribal grazing lands sustaining Yakama horses. As a result, agency officials launched systematic assaults on Yakama horse herds, citing horses as culprits of overgrazing and land degradation. However, Yakamas showed little interest in removing their horses, and instead actively opposed settler encroachment on tribal grazing lands. Through analyzing archival sources, conducting interviews, and reviewing scholarly sources, I argue that Yakamas and settlers used horses as a terrain of struggle, whereby they asserted competing claims to Indigenous lands and resources. Examining horses as a tool of resistance provides a useful lens for understanding forms of Native opposition to colonial hegemony, while interrogating problematic tropes settlers utilized to justify divesting Native communities.

Increasing the efficacy of Judas goats by sterilisation and pregnancy termination

The use of Judas goats to locate remnant animals is a potentially powerful tool for enhancing goat-eradication efforts, which are especially important to island conservation. However, current Judas goat methodology falls short of its potential efficacy. Female Judas goats are often pregnant at the time of deployment or become impregnated in the field; pregnant females leave associated goats to give birth, causing downtime of Judas goat operations. Further, male Judas goats may inseminate remnant females. Sterilising Judas goats prior to deployment removes these inefficiencies. Here, we describe two methods (epididymectomy for males and tubal occlusion for females) that sterilise Judas goats while still maintaining sexual motivation and other behaviours associated with intact animals. These surgeries are straightforward, time efficient, and may be conducted in the field by staff with minimal training. Given the widespread and deleterious impacts of non-native herbivores to ecosystems and the importance of Judas operations in detecting animals at low densities, sterilisation and termination of pregnancy should be applied routinely in Judas goat (and possibly other species) programs to increase the efficacy of low-density control operations and eradication campaigns.

Ecology of Leptocoris Hahn (Hemiptera: Rhopalidae) Soapberry Bugs in Australia

Soapberry bugs are worldwide seed predators of plants in the family Sapindaceae. Australian sapinds are diverse and widespread, consisting of about 200 native trees and shrubs. This flora also includes two introduced environmental weeds, plus cultivated lychee (Litchi chinensis Sonn.), longan (Dimocarpus longan Lour.) and rambutan (Nephelium lappaceum L.). Accordingly, Australian soapberry bugs may be significant in ecology, conservation and agriculture. Here we provide the first account of their ecology. We find five species of Leptocoris Hahn in Australia, and list sapinds that do and do not serve as reproductive hosts. From museum and field records we map the continental distributions of the insects and primary hosts. Frequency of occupation varies among host species, and the number of hosts varies among the insects. In addition, differences in body size and beak length are related to host use. For example, the long-beaked Leptocoris tagalicus Burmeister is highly polyphagous in eastern rainforests, where it occurs on at least 10 native and non-native hosts. It aggregates on hosts with immature fruit and commences feeding before fruits dehisce. Most of its continental range, however, matches that of a single dryland tree, Atalaya hemiglauca F. Muell., which has comparatively unprotected seeds. The taxon includes a smaller and shorter-beaked form that is closely associated with Atalaya, and appears to be taxonomically distinct. The other widespread soapberry bug is the endemic Leptocoris mitellatus Bergroth. It too is short-beaked, and colonises hosts phenologically later than L. tagalicus, as seeds become more accessible in open capsules. Continentally its distribution is more southerly and corresponds mainly to that of Alectryon oleifolius Desf. Among all host species, the non-native environmental weeds Cardiospermum L. and Koelreuteria Laxm. are most consistently attacked, principally by L. tagalicus. These recent host shifts have biocontrol implications. In contrast, the sapinds planted as fruit crops appear to be less frequently used at present and mainly by the longer-beaked species.

A modelling approach to estimate the effect of exotic pollinators on exotic weed population dynamics: bumblebees and broom in Australia

The role of mutualisms in contributing to species invasions is rarely considered, inhibiting effective risk analysis and management options. Potential ecological consequences of invasion of non-native pollinators include increased pollination and seed set of invasive plants, with subsequent impacts on population growth rates and rates of spread. We outline a quantitative approach for evaluating the impact of a proposed introduction of an invasive pollinator on existing weed population dynamics and demonstrate the use of this approach on a relatively data-rich case study: the impacts on Cytisus scoparius (Scotch broom) from proposed introduction of Bombus terrestris. Three models have been used to assess population growth (matrix model), spread speed (integrodifference equation), and equilibrium occupancy (lattice model) for C. scoparius. We use available demographic data for an Australian population to parameterize two of these models. Increased seed set due to more efficient pollination resulted in a higher population growth rate in the density-independent matrix model, whereas simulations of enhanced pollination scenarios had a negligible effect on equilibrium weed occupancy in the lattice model. This is attributed to strong microsite limitation of recruitment in invasive C. scoparius populations observed in Australia and incorporated in the lattice model. A lack of information regarding secondary ant dispersal of C. scoparius prevents us from parameterizing the integrodifference equation model for Australia, but studies of invasive populations in California suggest that spread speed will also increase with higher seed set. For microsite-limited C. scoparius populations, increased seed set has minimal effects on equilibrium site occupancy. However, for density-independent rapidly invading populations, increased seed set is likely to lead to higher growth rates and spread speeds. The impacts of introduced pollinators on native flora and fauna and the potential for promoting range expansion in pollinator-limited 'sleeper weeds' also remain substantial risks.

Border Patrol in the Borderless World: Negotiating Intercultural Internet Discussion

Public Internet discussion forums appear to offer limitless opportunities for communication across linguistic, geographical and cultural borders. Closer inspection, however, reveals that cordial intercultural exchanges are far from widespread in this genre. And yet, such forums have a great deal to offer the independent language learner in terms of ease of access, potential for meaningful language practice and feedback, and exposure to different cultural conventions. This paper explores obstacles to the participation of advanced language learners in public forums of this kind through an examination of the speaking positions most readily available to the non-native speaker. A case study of sustained intercultural interaction on a public discussion thread suggests an alternative to these. Here a core of Francophone and Anglophone participants manage to negotiate an intercultural identity in order to pursue their communicative goals. The paper traces the way in which participants shift footing to regulate insider and outsider status on the forum and draws conclusions regarding the conditions for successful intercultural exchange in this genre

A corpus-based analysis of transfer effects and connected speech processes in Vietnamese English

This paper presents a corpus-based descriptive analysis of the most prevalent transfer effects and connected speech processes observed in a comparison of 11 Vietnamese English speakers (6 females, 5 males) and 12 Australian English speakers (6 males, 6 females) over 24 grammatical paraphrase items. The phonetic processes are segmentally labelled in terms of IPA diacritic features using the EMU speech database system with the aim of labelling departures from native-speaker pronunciation. An analysis of prosodic features was made using ToBI framework. The results show many phonetic and prosodic processes which make non-native speakers’ speech distinct from native ones. The corpusbased methodology of analysing foreign accent may have implications for the evaluation of non-native accent, accented speech recognition and computer assisted pronunciation- learning.