A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

BACKGROUND: Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. RESULTS: We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305) and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not involved in the integration or excision of island 4305. CONCLUSION: The "clone-and-transfer" approach of evolutionary study identifies genes whose expression patterns indicate the existence of genera-specific regulatory mechanisms that influence the expression of horizontally-transferred DNA sections. The results provide key information that can be used to facilitate the identification of these regulatory mechanisms

New Perspectives on Old Questions: Ella Hepworth Dixon’s One Doubtful Hour

Pour Ella Hepworth Dixon (1857–1932), comme pour beaucoup d'autres femmes écrivains et artistes de le fin du dix-neuvième siècle, des termes comme « féministe » ou « New Woman » (littéralement, « Nouvelle Femme ») n’étaient pas anodins : ils leur donnaient peut-être l’impression de limiter leur capacité à définir leur propre version de la féminité, particulièrement dans le contexte des débats populaires ou des satires sur le genre. Dans son recueil One Doubtful Hour and Other Side-Lights on the Feminine Temperament (1904), Dixon utilise son don pour l’écriture pour parler de l’identité féminine et dépeindre les combats qu’affrontent les femmes dans leur vie quotidienne à la fin du siècle. Elle aborde aussi des sujets tels que travailler et gagner de l’argent, rechercher un époux et se marier, et relever le défi que représente la vie dans une société de plus en plus ouverte sur le monde. Cet essai montre comment Dixon utilise le recueil de nouvelles pour atteindre des lectrices qui refusaient peut-être de se qualifier de féministes, mais qui étaient quand même sensibles à des modèles de féminité susceptibles de les aider à revoir leur conception personnelle du genre et du patriarcat. (Résumé traduit par Emilie Piarou

Good vibrations: Do electrical therapeutic massagers work?

Health, leisure and beauty activities are increasing in popularity, with a particular emphasis on self-help and alternative health practices. One product type that has increased sales with this expansion is the hand-held electric massager. These are products that use vibration as a means of alleviating muscular strains and pains, as well as promoting relaxation. Paradoxically, these products are extremely popular as gifts, but are soon discarded. A multi-disciplinary research team was commissioned by a British manufacturer of electrical consumer products to investigate user attitudes and perceptions of existing massagers, to identify areas of user dissatisfaction. The manufacturer was also concerned about a possible stigma attached to these products because of an association with sex aids. This paper provides an account of the perceptions of both consumers and therapists regarding the use of these products. Identifying the differences between the perceptions of consumers and therapists should help provide a basis for effective integration of user needs, manufacturer requirements, designers’ skills and sound therapeutic practice. The results provide insight to support the development of more effective hand-held massagers

Biogenesis of a Bacterial Organelle: The Carboxysome Assembly Pathway

SummaryThe carboxysome is a protein-based organelle for carbon fixation in cyanobacteria, keystone organisms in the global carbon cycle. It is composed of thousands of subunits including hexameric and pentameric proteins that form a shell to encapsulate the enzymes ribulose 1,5-bisphosphate carboxylase/oxygenase and carbonic anhydrase. Here, we describe the stages of carboxysome assembly and the requisite gene products necessary for progression through each. Our results demonstrate that, unlike membrane-bound organelles of eukaryotes, in carboxysomes the interior of the compartment forms first, at a distinct site within the cell. Subsequently, shell proteins encapsulate this procarboxysome, inducing budding and distribution of functional organelles within the cell. We propose that the principles of carboxysome assembly that we have uncovered extend to diverse bacterial microcompartments

The built environment predicts observed physical activity

Background: In order to improve our understanding of the relationship between the built environment and physical activity, it is important to identify associations between specific geographic characteristics and physical activity behaviors. Purpose: Examine relationships between observed physical activity behavior and measures of the built environment collected on 291 street segments in Indianapolis and St. Louis. Methods: Street segments were selected using a stratified geographic sampling design to ensure representation of neighborhoods with different land use and socioeconomic characteristics. Characteristics of the built environment on-street segments were audited using two methods: in-person field audits and audits based on interpretation of Google Street View imagery with each method blinded to results from the other. Segments were dichotomized as having a particular characteristic (e.g., sidewalk present or not) based on the two auditing methods separately. Counts of individuals engaged in different forms of physical activity on each segment were assessed using direct observation. Non-parametric statistics were used to compare counts of physically active individuals on each segment with built environment characteristic. Results: Counts of individuals engaged in physical activity were significantly higher on segments with mixed land use or all non-residential land use, and on segments with pedestrian infrastructure (e.g., crosswalks and sidewalks) and public transit. Conclusion: Several micro-level built environment characteristics were associated with physical activity. These data provide support for theories that suggest changing the built environment and related policies may encourage more physical activity

Methods and Compositions Based on Culturing Microorganisms in Low Sedimental Fluid Shear Conditions

The benefits of applying a low sedimental fluid shear environment to manipulate microorganisms were examined. Microorganisms obtained from a low sedimental fluid shear culture, which exhibit modified phenotypic and molecular genetic characteristics, are useful for the development of novel and improved diagnostics, therapeutics, vaccines, and bio-industrial products. Furthermore, application of low sedimental fluid conditions to microorganisms permits identification of molecules uniquely expressed under these conditions, providing a basis for the design of new therapeutic targets

Predictors of financial capacity performance in older adults using the Financial Competence Assessment Inventory

Background

Why pest plant control and native plant establishment failed : a restoration autopsy

Explaining restoration failure can be as important as touting success. We used a series of studies to understand the failure of techniques commonly used to restore wetland prairies in the Willamette Valley of western Oregon. Burning, fallowing, and solarization (covering tilled plots with plastic sheeting to heat the soil) had pronounced first-year effects on several individual species, but either did not reduce overall pest plant abundance or reduced the abundance of native species as well. The 34% overall plant cover in solarized plots was the only significant difference from the 60% cover present in control plots. All first-year responses essentially disappeared by the second year. These measures had little lasting effect on pest and other exotic plants because many survived treatment and resprouted. In addition, treatments had little effect on the number of seeds in the soil, leaving a pool of immediate and potential regeneration. Specific control measures of target plants, such as hand removal and repeat maintenance after initial treatments, should prove more successful. In a second study, three mixtures of native species sown into fallowing treatment plots had low emergence rates of 1% - 7%, despite high seed viability, and produced only 0% - 3% cover. Native species should be selected and sown at densities high enough to lead to significant numbers of surviving seedlings, especially in the face of competition from surviving pest plants

Esociformes: Esocidae, Pikes, and Umbridae (Mudminnows)

The order Esociformes (Pikes and Mudminnows) comprises two families, Esocidae (Pikes) and Umbridae (Mudminnows). The Pikes are a small Holarctic (Northern Hemisphere) family, that includes large, elongate predators with duckbill-like snouts full of sharp teeth. Popular with sport fishers, the largest Pikes fight fiercely on hook and line. As piscivorous, voracious, ambush predators, the Pikes play an important functional role in the trophic ecology and fish assemblage structure of many aquatic systems, especially in northern lakes. Other esocids, such as the Olympic Mudminnow, Novumbra hubbsi, and Blackfishes, genus Dallia, are interesting because of their tolerance of low dissolved oxygen and pH. The Alaska Blackfish, Dallia pectoralis, and the Northern Pike, Esox lucius, can also withstand the extremely cold conditions of the Arctic and subarctic waters of Canada, Alaska, and Siberia. The name Esocidae is derived from Linnaeus’s (1758) generic name for Pike, Esox, from the Latin word esox meaning Pike, which came originally from the Greek isox or possibly the Gaelic eog, ehawe (salmon) (Boschung & Mayden 2004)