Induction of the ferritin gene (ftnA) of Escherichia coli by Fe2+–Fur is mediated by reversal of H-NS silencing and is RyhB independent

FtnA is the major iron-storage protein of Escherichia coli accounting for < or = 50% of total cellular iron. The FtnA gene (ftnA) is induced by iron in an Fe(2+)-Fur-dependent fashion. This effect is reportedly mediated by RyhB, the Fe(2+)-Fur-repressed, small, regulatory RNA. However, results presented here show that ftnA iron induction is independent of RyhB and instead involves direct interaction of Fe(2+)-Fur with an 'extended' Fur binding site (containing five tandem Fur boxes) located upstream (-83) of the ftnA promoter. In addition, H-NS acts as a direct repressor of ftnA transcription by binding at multiple sites (I-VI) within, and upstream of, the ftnA promoter. Fur directly competes with H-NS binding at upstream sites (II-IV) and consequently displaces H-NS from the ftnA promoter (sites V-VI) which in turn leads to derepression of ftnA transcription. It is proposed that H-NS binding within the ftnA promoter is facilitated by H-NS occupation of the upstream sites through H-NS oligomerization-induced DNA looping. Consequently, Fur displacement of H-NS from the upstream sites prevents cooperative H-NS binding at the downstream sites within the promoter, thus allowing access to RNA polymerase. This direct activation of ftnA transcription by Fe(2+)-Fur through H-NS antisilencing represents a new mechanism for iron-induced gene expression.

Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development

Environmental cues influence the development of stomata on the leaf epidermis, and allow plants to exert plasticity in leaf stomatal abundance in response to the prevailing growing conditions. It is reported that Arabidopsis thaliana ‘Landsberg erecta’ plants grown under low relative humidity have a reduced stomatal index and that two genes in the stomatal development pathway, SPEECHLESS and FAMA, become de novo cytosine methylated and transcriptionally repressed. These environmentally-induced epigenetic responses were abolished in mutants lacking the capacity for de novo DNA methylation, for the maintenance of CG methylation, and in mutants for the production of short-interfering non-coding RNAs (siRNAs) in the RNA-directed DNA methylation pathway. Induction of methylation was quantitatively related to the induction of local siRNAs under low relative humidity. Our results indicate the involvement of both transcriptional and post-transcriptional gene suppression at these loci in response to environmental stress. Thus, in a physiologically important pathway, a targeted epigenetic response to a specific environmental stress is reported and several of its molecular, mechanistic components are described, providing a tractable platform for future epigenetics experiments. Our findings suggest epigenetic regulation of stomatal development that allows for anatomical and phenotypic plasticity, and may help to explain at least some of the plant’s resilience to fluctuating relative humidity.

The child and imperial return: the mystery of Edwin Drood

The Mystery of Edwin Drood has often been read as an Imperial text, just as Dickens's work has repeatedly been considered in relation to its construction of childhood. Despite this, 'the child' has either been avoided in criticism of Dickens's last novel, or has actively been read as absent. In this essay, I return the ‘repressed’ child to a reading of Drood, and through this disrupt appeals to a hard-impacted Imperial structure I understand to be made within criticism of it.

Comparative biology of mammalian telomeres: hypotheses on ancestral states and the roles of telomeres in longevity determination

Progressive telomere shortening from cell division (replicative aging) provides a barrier for human tumor progression. This program is not conserved in laboratory mice, which have longer telomeres and constitutive telomerase. Wild species that do ⁄ do not use replicative aging have been reported, but the evolution of different phenotypes and a conceptual framework for understanding their uses of telomeres is lacking. We examined telomeres ⁄ telomerase in cultured cells from > 60 mammalian species to place different uses of telomeres in a broad mammalian context. Phylogeny-based statistical analysis reconstructed ancestral states. Our analysis suggested that the ancestral mammalian phenotype included short telomeres (< 20 kb, as we now see in humans) and repressed telomerase. We argue that the repressed telomerase was a response to a higher mutation load brought on by the evolution of homeothermy. With telomerase repressed, we then see the evolution of replicative aging. Telomere length inversely correlated with lifespan, while telomerase expression co-evolved with body size. Multiple independent times smaller, shorter-lived species changed to having longer telomeres and expressing telomerase. Trade-offs involving reducing the energetic ⁄ cellular costs of specific oxidative protection mechanisms (needed to protect < 20 kb telomeres in the absence oftelomerase) could explain this abandonment of replicative aging. These observations provide a conceptual framework for understanding different uses of telomeres in mammals, support a role for human-like telomeres in allowing longer lifespans to evolve, demonstrate the need to include telomere length in the analysis of comparative studies of oxidative protection in the biology of aging, and identify which mammals can be used as appropriate model organisms for the study of the role of telomeres in human cancer and aging. Key words: evolution of telomeres; immortalization; telomerase; replicative aging; senescence.

Analysis of expression of flagella by Salmonella enterica serotype Typhimurium by monoclonal antibodies recognising both phase specific and common epitopes

Monoclonal antibodies specific for phase 1 ("i" antigen), phase 2 ("1,2" antigen) and common epitopes of the flagellins of Salmonella enterica serotype Typhimurium were raised. Having confirmed their specificity, the monoclonal antibodies were used to develop semi-quantitative ELISAs in order to assess the relative expression of the two phases by strains of Typhimurium. The majority of Typhimurium strains representative of a wide cross-section of definitive types from animal and environmental sources preferentially expressed phase 1 antigen in vitro. DT40 strains were unique in expressing phase 2 preferentially. The ratio of phase 1 to phase 2 expressed by strains tended to be constant for any one strain when strains were grown on a number of conventional laboratory media. However, the ratio of phases was shown to be modulated by incubation at 42 degreesC and buffering media at pH values, notably 4.5, other than neutral. Selenite broth and Rambach media repressed flagellation. Crown Copyright (C) 2001 Published by Elsevier Science B.V. All rights reserved.

Backtracks: a devised performance

Backtracks aimed to investigate critical relationships between audio-visual technologies and live performance, emphasising technologies producing sound, contrasted with non-amplified bodily sound. Drawing on methodologies for studying avant garde theatre, live performance and the performing body, it was informed by work in critical and cultural theory by, for example, Steven Connor and Jonathan Rée, on the body's experience and interpretation of sound. The performance explored how shifting national boundaries, mobile workforces, complex family relationships, cultural pluralities and possibilities for bodily transformation have compelled a re-evaluation of what it means to feel 'at home' in modernity. Using montages of live and mediated images, disrupted narratives and sound, it evoked destablised identities which characterise contemporary lived experience, and enacted the displacement of certainties provided by family and nation, community and locality, body and selfhood. Homer's Odyssey framed the performance: elements could be traced in the mise-en-scène; in the physical presence of Athene, the narrator and Penelope weaving mementoes from the past into her loom; and in voice-overs from Homer's work. The performance drew on personal experiences and improvisations, structured around notions of journey. It presented incomplete narratives, memories, repressed anxieties and dreams through different combinations of sounds, music, mediated images, movement, voice and bodily sound. The theme of travel was intensified by performers carrying suitcases and umbrellas, by soundtracks incorporating travel effects, and by the distorted video images of forms of transport playing across 'screens' which proliferated across the space (sails, umbrellas, the loom, actors' bodies). The performance experimented with giving sound and silence performative dimensions, including presenting sound in visual and imagistic ways, for example by using signs from deaf sign language. Through-composed soundtracks of live and recorded song, music, voice-over, and noise exploited the viscerality of sound and disrupted cognitive interpretation by phenomenological, somatic experience, thereby displacing the impulse for closure/destination/home.

(Re)enchanting geography? The nature of being critical and the character of critique in human geography

Enchantment is a term frequently used by human geographers to express delight, wonder or that which cannot be simply explained. However, it is a concept that has yet to be subject to sustained critique, specifically how it can be used to progress geographic thought and praxis. This paper makes sense of, and space for, the unintelligibility of enchantment in order to encourage a less repressed, more cheerful way of engaging with the geographies of the world. We track back through our disciplinary heritage to explore how geographers have employed enchantment as a force through which the world inspires affective attachment. We review the terrain of the debate surrounding recent geographical engagements with enchantment, focusing on the nature of being critical and the character of critique in human geography, offering a new ‘enchanted’ stance to our geographical endeavours. We argue that the moment of enchantment has not passed with the current challenging climate; if anything, it is more pressing.

An intronic G run within HIV-1 intron 2 is critical for splicing regulation of vif mRNA

Within target T lymphocytes, human immunodeficiency virus type I (HIV-1) encounters the retroviral restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), which is counteracted by the HIV-1 accessory protein Vif. Vif is encoded by intron-containing viral RNAs that are generated by splicing at 3' splice site (3'ss) A1 but lack splicing at 5'ss D2, which results in the retention of a large downstream intron. Hence, the extents of activation of 3'ss A1 and repression of D2, respectively, determine the levels of vif mRNA and thus the ability to evade A3G-mediated antiviral effects. The use of 3'ss A1 can be enhanced or repressed by splicing regulatory elements that control the recognition of downstream 5'ss D2. Here we show that an intronic G run (G(I2)-1) represses the use of a second 5'ss, termed D2b, that is embedded within intron 2 and, as determined by RNA deep-sequencing analysis, is normally inefficiently used. Mutations of G(I2)-1 and activation of D2b led to the generation of transcripts coding for Gp41 and Rev protein isoforms but primarily led to considerable upregulation of vif mRNA expression. We further demonstrate, however, that higher levels of Vif protein are actually detrimental to viral replication in A3G-expressing T cell lines but not in A3G-deficient cells. These observations suggest that an appropriate ratio of Vif-to-A3G protein levels is required for optimal virus replication and that part of Vif level regulation is effected by the novel G run identified here.

Terrestrial exposure of oilfield flowline additives diminish soil structural stability and remediative microbial function

Onshore oil production pipelines are major installations in the petroleum industry, stretching many thousands of kilometres worldwide which also contain flowline additives. The current study focuses on the effect of the flowline additives on soil physico-chemical and biological properties and quantified the impact using resilience and resistance indices. Our findings are the first to highlight deleterious effect of flowline additives by altering some fundamental soil properties, including a complete loss of structural integrity of the impacted soil and a reduced capacity to degrade hydrocarbons mainly due to: (i) phosphonate salts (in scale inhibitor) prevented accumulation of scale in pipelines but also disrupted soil physical structure; (ii) glutaraldehyde (in biocides) which repressed microbial activity in the pipeline and reduced hydrocarbon degradation in soil upon environmental exposure; (iii) the combinatory effects of these two chemicals synergistically caused severe soil structural collapse and disruption of microbial degradation of petroleum hydrocarbons.

Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics

Background The rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere. Results Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere. Conclusions Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants.

Elevated CO(2) increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane

Because of the economical relevance of sugarcane and its high potential as a source of biofuel, it is important to understand how this crop will respond to the foreseen increase in atmospheric [CO(2)]. The effects of increased [CO(2)] on photosynthesis, development and carbohydrate metabolism were studied in sugarcane (Saccharum ssp.). Plants were grown at ambient (similar to 370 ppm) and elevated (similar to 720 ppm) [CO(2)] during 50 weeks in open-top chambers. The plants grown under elevated CO(2) showed, at the end of such period, an increase of about 30% in photosynthesis and 17% in height, and accumulated 40% more biomass in comparison with the plants grown at ambient [CO(2)]. These plants also had lower stomatal conductance and transpiration rates (-37 and -32%, respectively), and higher water-use efficiency (c.a. 62%). cDNA microarray analyses revealed a differential expression of 35 genes on the leaves (14 repressed and 22 induced) by elevated CO(2). The latter are mainly related to photosynthesis and development. Industrial productivity analysis showed an increase of about 29% in sucrose content. These data suggest that sugarcane crops increase productivity in higher [CO(2)], and that this might be related, as previously observed for maize and sorghum, to transient drought stress.

Alkaline phosphatase as a reporter of sigma(S) levels and rpoS polymorphisms in different E-coli strains

sigma(S) is responsible for the transcriptional regulation of genes related to protection against stresses and bacterial survival and it accumulates in the cell under conditions of stress, such as nutrient limitation. An increase in the levels of sigma(S) causes a reduction in the expression of genes that are transcribed by RNA polymerase associated with the principal sigma factor, sigma(70). phoA, that encodes alkaline phosphatase (AP) is expressed under phosphate shortage conditions, and is also repressed by sigma(S). Here we show that in a Pi-limited chemostat, accumulation of rpoS mutations is proportional to the intrinsic level of sigma(S) in the cells. Acquisition of mutations in rpoS relieves repression of the PHO genes. We also devised a non-destructive method based on the rpoS effect on AP that differentiates between rpo(S+) and rpoS mutants, as well as between high and low-sigma(S) producers. Using this method, we provide evidence that sigma(S) contributes to the repression of AP under conditions of Pi excess and that AP variation among different strains is at least partly due to intrinsic variation in sigma(S) levels. Consequently, a simple and non-destructive AP assay can be employed to differentiate between strains expressing different levels of sigma(S) on agar plates.

Fur controls iron homeostasis and oxidative stress defense in the oligotrophic alpha-proteobacterium Caulobacter crescentus

In most bacteria, the ferric uptake regulator (Fur) is a global regulator that controls iron homeostasis and other cellular processes, such as oxidative stress defense. In this work, we apply a combination of bioinformatics, in vitro and in vivo assays to identify the Caulobacter crescentus Fur regulon. A C. crescentus fur deletion mutant showed a slow growth phenotype, and was hypersensitive to H(2)O(2) and organic peroxide. Using a position weight matrix approach, several predicted Fur-binding sites were detected in the genome of C. crescentus, located in regulatory regions of genes not only involved in iron uptake and usage but also in other functions. Selected Fur-binding sites were validated using electrophoretic mobility shift assay and DNAse I footprinting analysis. Gene expression assays revealed that genes involved in iron uptake were repressed by iron-Fur and induced under conditions of iron limitation, whereas genes encoding iron-using proteins were activated by Fur under conditions of iron sufficiency. Furthermore, several genes that are regulated via small RNAs in other bacteria were found to be directly regulated by Fur in C. crescentus. In conclusion, Fur functions as an activator and as a repressor, integrating iron metabolism and oxidative stress response in C. crescentus.

Experiências de interação do Instituto de Biotecnologia da Universidade de Caxias do Sul com a comunidade

Este estudo tem a finalidade de analisar experiências de interação Universidade – Empresa, em projetos do Instituto de Biotecnologia - ( IB ) da Universidade de Caxias do Sul – ( UCS ), a qual, como Instituição produtora e disseminadora de conhecimentos, busca atuar ativamente na transformação tecnológica da Região Nordeste do Estado do RS. Procura-se analisar as experiências de interação entre os pesquisadores da área de biotecnologia da UCS, as empresas do setor produtivo e a comunidade, identificando possíveis mecanismos e problemas. O IB foi criado para que, através dos resultados de suas pesquisas, possa contribuir efetivamente com os anseios da Comunidade a qual está inserida. Este estudo se constitui na análise de múltiplos casos de interação em oito projetos desenvolvidos no IB. Os dados foram coletados através de entrevistas com os coordenadores dos projetos no IB e com os responsáveis pela interação nas organizações parceiras, num total de 16 entrevistas.O estudo evidencia que as interações ocorrem a partir de contatos informais, baseadas na amizade entre os parceiros e oriundas, principalmente, do esforço do pesquisador. Os entrevistados acentuam a necessidade de uso de mecanismos formais de interação para agilizar e viabilizar projetos conjuntos do IB com empresas do setor produtivo e a comunidade, através de parcerias consolidadas. Finalmente, considera-se que, para assegurar o crescimento da interação com a comunidade, é urgente possibilitar, através de mecanismos formais, que a pesquisa científica desenvolvida no Instituto de biotecnologia da UCS volte-se prioritariamente para a identificação de problemas regionais, buscando as respectivas soluções, na perspectiva do desenvolvimento integrado da Região.

A correção de erros : inimiga ou aliada? : a reescrita como estratégia de correção e de conscientização na produção escrita de aprendizes de inglês como língua estrangeira

Este estudo preliminar descreve uma proposta de correção de erros nas produções escritas de doze (12) alunos de nível básico de língua inglesa da Universidade de Caxias do Sul (UCS). O objetivo é investigar a relevância da reescrita como estratégia de conscientização, de acordo com a Hipótese do Noticing de Schmidt (1990), buscando promover a correção gramatical e o aprimoramento da produção textual. Nesse contexto, a correção passa a ser uma aliada e não inimiga do aprendiz. O feedback corretivo fornecido através do uso de uma Tabela de Marcação, a conscientização dos erros através da reescrita e o envolvimento dos aprendizes no processo de auto-análise de seus textos revelaram-se condições facilitadoras na busca das formas corretas e na prevenção do erro. A análise dos dados demonstrou uma possível ruptura com a previsibilidade implícita na Hipótese do Noticing, que propõe que prestar atenção a determinados aspectos lingüísticos possibilita sua melhor assimilação e a não recorrência de erros. Os trabalhos evidenciaram uma melhoria progressiva na qualidade da produção escrita apesar do aumento do número de erros, possivelmente devido a uma desinibição por parte dos aprendizes em escrever e a sua opção em assumir riscos na produção de estruturas lingüísticas mais complexas, o que não inviabiliza a proposta da reescrita como estratégia de conscientização.